1
|
Kwak SH, Hernandez-Cancela RB, DiCorpo DA, Condon DE, Merino J, Wu P, Brody JA, Yao J, Guo X, Ahmadizar F, Meyer M, Sincan M, Mercader JM, Lee S, Haessler J, Vy HMT, Lin Z, Armstrong ND, Gu S, Tsao NL, Lange LA, Wang N, Wiggins KL, Trompet S, Liu S, Loos RJF, Judy R, Schroeder PH, Hasbani NR, Bos MM, Morrison AC, Jackson RD, Reiner AP, Manson JE, Chaudhary NS, Carmichael LK, Chen YDI, Taylor KD, Ghanbari M, van Meurs J, Pitsillides AN, Psaty BM, Noordam R, Do R, Park KS, Jukema JW, Kavousi M, Correa A, Rich SS, Damrauer SM, Hajek C, Cho NH, Irvin MR, Pankow JS, Nadkarni GN, Sladek R, Goodarzi MO, Florez JC, Chasman DI, Heckbert SR, Kooperberg C, Dupuis J, Malhotra R, de Vries PS, Liu CT, Rotter JI, Meigs JB. Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People With Type 2 Diabetes. Diabetes Care 2024:dc232274. [PMID: 38652672 DOI: 10.2337/dc23-2274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/14/2024] [Indexed: 04/25/2024]
Abstract
OBJECTIVE To identify genetic risk factors for incident cardiovascular disease (CVD) among people with type 2 diabetes (T2D). RESEARCH DESIGN AND METHODS We conducted a multiancestry time-to-event genome-wide association study for incident CVD among people with T2D. We also tested 204 known coronary artery disease (CAD) variants for association with incident CVD. RESULTS Among 49,230 participants with T2D, 8,956 had incident CVD events (event rate 18.2%). We identified three novel genetic loci for incident CVD: rs147138607 (near CACNA1E/ZNF648, hazard ratio [HR] 1.23, P = 3.6 × 10-9), rs11444867 (near HS3ST1, HR 1.89, P = 9.9 × 10-9), and rs335407 (near TFB1M/NOX3, HR 1.25, P = 1.5 × 10-8). Among 204 known CAD loci, 5 were associated with incident CVD in T2D (multiple comparison-adjusted P < 0.00024, 0.05/204). A standardized polygenic score of these 204 variants was associated with incident CVD with HR 1.14 (P = 1.0 × 10-16). CONCLUSIONS The data point to novel and known genomic regions associated with incident CVD among individuals with T2D.
Collapse
Affiliation(s)
- Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | | | - Daniel A DiCorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | | | - Jordi Merino
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Jie Yao
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - Fariba Ahmadizar
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Data Science and Biostatistics, Julius Global Health, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mariah Meyer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Murat Sincan
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Josep M Mercader
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Sujin Lee
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Ha My T Vy
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zhaotong Lin
- Department of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Nicole D Armstrong
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, AL
| | - Shaopeng Gu
- Department of Internal Medicine, Sanford Health, Sioux Falls, SD
| | - Noah L Tsao
- Corporal Michael J. Crescenz VA Medical Center and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ningyuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Stella Trompet
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Simin Liu
- Department of Epidemiology, Brown University, Providence, RI
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Renae Judy
- Corporal Michael J. Crescenz VA Medical Center and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
| | - Philip H Schroeder
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Natalie R Hasbani
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Maxime M Bos
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, Ohio State University, Columbus, OH
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ninad S Chaudhary
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, AL
| | | | - Yii-Der Ida Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Joyce van Meurs
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | | | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Ron Do
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Scott M Damrauer
- Corporal Michael J. Crescenz VA Medical Center and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, Perelman School of Medicine, Philadelphia, PA
| | - Catherine Hajek
- Department of Internal Medicine, Sanford Health, Sioux Falls, SD
| | - Nam H Cho
- Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Marguerite R Irvin
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, AL
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN
| | - Girish N Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Robert Sladek
- Department of Medicine and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Jose C Florez
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Daniel I Chasman
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA
| | - James B Meigs
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Department of General Internal Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, MA
| |
Collapse
|
2
|
Li Y, Chen GC, Moon JY, Arthur R, Sotres-Alvarez D, Daviglus ML, Pirzada A, Mattei J, Perreira KM, Rotter JI, Taylor KD, Chen YDI, Wassertheil-Smoller S, Wang T, Rohan TE, Kaufman JD, Kaplan R, Qi Q. Genetic subtypes of prediabetes, healthy lifestyle, and risk of type 2 diabetes. Diabetes 2024:db230699. [PMID: 38602922 DOI: 10.2337/db23-0699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024]
Abstract
Prediabetes is a heterogenous metabolic state with various risk for development of type 2 diabetes (T2D). In this study, we used genetic data on 7,227 US Hispanic/Latinos without diabetes from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) and 400,149 non-Hispanic whites without diabetes from the UK Biobank (UKBB) to calculate five partitioned polygenetic risk scores (pPRSs) representing various pathways related to T2D. Consensus clustering was performed in participants with prediabetes in HCHS/SOL (n=3,677) and UKBB (n=16,284) separately, based on these pPRSs. Six clusters of individuals with prediabetes with distinctive patterns of pPRSs and corresponding metabolic traits were identified in the HCHS/SOL, five of which were confirmed in the UKBB. Although baseline glycemic traits were similar across clusters, individuals in Cluster 5 and Cluster 6 showed elevated risk of T2D during follow-up compared to Cluster 1 (RR=1.29 [95% CI 1.08-1.53] and1.34 [1.13-1.60], respectively). Inverse associations between a healthy lifestyle score and risk of T2D were observed across different clusters, with a suggestively stronger association observed in Cluster 5 compared to Cluster 1. Among individuals with healthy lifestyle, those in Cluster 5 had a similar risk of T2D compared to those in Cluster 1 (RR=1.03 [0.91-1.18]). This study identified genetic subtypes of prediabetes which differed in risk of progression to T2D and in benefits from healthy lifestyle.
Collapse
Affiliation(s)
- Yang Li
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Guo-Chong Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Soochow University, Suzhou, China
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rhonda Arthur
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Daniela Sotres-Alvarez
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Amber Pirzada
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Josiemer Mattei
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Krista M Perreira
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Thomas E Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Joel D Kaufman
- Environmental & Occupational Health Sciences, Medicine, and Epidemiology, University of Washington, Seattle, WA 98105, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| |
Collapse
|
3
|
Kuiper LM, Shi W, Verlouw J, Hong YS, Arp P, Puiu D, Broer L, Xie J, Newcomb C, Rich SS, Taylor KD, Rotter JI, Bader JS, Guallar E, van Meurs JB, Arking DE. Longitudinal change in mitochondrial heteroplasmy exhibits positive selection for deleterious variants. medRxiv 2024:2024.03.27.24304930. [PMID: 38585741 PMCID: PMC10996716 DOI: 10.1101/2024.03.27.24304930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A common feature of human aging is the acquisition of somatic mutations, and mitochondria are particularly prone to mutation due to their inefficient DNA repair and close proximity to reactive oxygen species, leading to a state of mitochondrial DNA heteroplasmy1,2. Cross-sectional studies have demonstrated that detection of heteroplasmy increases with participant age3, a phenomenon that has been attributed to genetic drift4-7. In this first large-scale longitudinal study, we measured heteroplasmy in two prospective cohorts (combined n=1405) at two timepoints (mean time between visits, 8.6 years), demonstrating that deleterious heteroplasmies were more likely to increase in variant allele fraction (VAF). We further demonstrated that increase in VAF was associated with increased risk of overall mortality. These results challenge the claim that somatic mtDNA mutations arise mainly due to genetic drift, instead demonstrating positive selection for predicted deleterious mutations at the cellular level, despite an negative impact on overall mortality.
Collapse
Affiliation(s)
- Lieke M. Kuiper
- Genetic Laboratory, Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Wen Shi
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joost Verlouw
- Genetic Laboratory, Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Yun Soo Hong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pascal Arp
- Genetic Laboratory, Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Linda Broer
- Genetic Laboratory, Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Jiaqi Xie
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles Newcomb
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Eliseo Guallar
- Department of Epidemiology and Medicine, and Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health. Baltimore, MD, USA
| | - Joyce B.J. van Meurs
- Genetic Laboratory, Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Department of Orthopeadics & Sports Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Dan E. Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
4
|
Xiao S, Li VL, Lyu X, Chen X, Wei W, Abbasi F, Knowles JW, Tung ASH, Deng S, Tiwari G, Shi X, Zheng S, Farrell L, Chen ZZ, Taylor KD, Guo X, Goodarzi MO, Wood AC, Chen YDI, Lange LA, Rich SS, Rotter JI, Clish CB, Tahir UA, Gerszten RE, Benson MD, Long JZ. Lac-Phe mediates the effects of metformin on food intake and body weight. Nat Metab 2024:10.1038/s42255-024-00999-9. [PMID: 38499766 DOI: 10.1038/s42255-024-00999-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 01/30/2024] [Indexed: 03/20/2024]
Abstract
Metformin is a widely prescribed anti-diabetic medicine that also reduces body weight. There is ongoing debate about the mechanisms that mediate metformin's effects on energy balance. Here, we show that metformin is a powerful pharmacological inducer of the anorexigenic metabolite N-lactoyl-phenylalanine (Lac-Phe) in cells, in mice and two independent human cohorts. Metformin drives Lac-Phe biosynthesis through the inhibition of complex I, increased glycolytic flux and intracellular lactate mass action. Intestinal epithelial CNDP2+ cells, not macrophages, are the principal in vivo source of basal and metformin-inducible Lac-Phe. Genetic ablation of Lac-Phe biosynthesis in male mice renders animals resistant to the effects of metformin on food intake and body weight. Lastly, mediation analyses support a role for Lac-Phe as a downstream effector of metformin's effects on body mass index in participants of a large population-based observational cohort, the Multi-Ethnic Study of Atherosclerosis. Together, these data establish Lac-Phe as a critical mediator of the body weight-lowering effects of metformin.
Collapse
Affiliation(s)
- Shuke Xiao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Xudong Chen
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Fahim Abbasi
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joshua W Knowles
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Alan Sheng-Hwa Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Shuliang Deng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Gaurav Tiwari
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Shuning Zheng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Laurie Farrell
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Zsu-Zsu Chen
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Clary B Clish
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Usman A Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mark D Benson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA.
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
5
|
Wittich H, Ardlie K, Taylor KD, Durda P, Liu Y, Mikhaylova A, Gignoux CR, Cho MH, Rich SS, Rotter JI, Manichaikul A, Im HK, Wheeler HE. Transcriptome-wide association study of the plasma proteome reveals cis and trans regulatory mechanisms underlying complex traits. Am J Hum Genet 2024; 111:445-455. [PMID: 38320554 PMCID: PMC10940016 DOI: 10.1016/j.ajhg.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Regulation of transcription and translation are mechanisms through which genetic variants affect complex traits. Expression quantitative trait locus (eQTL) studies have been more successful at identifying cis-eQTL (within 1 Mb of the transcription start site) than trans-eQTL. Here, we tested the cis component of gene expression for association with observed plasma protein levels to identify cis- and trans-acting genes that regulate protein levels. We used transcriptome prediction models from 49 Genotype-Tissue Expression (GTEx) Project tissues to predict the cis component of gene expression and tested the predicted expression of every gene in every tissue for association with the observed abundance of 3,622 plasma proteins measured in 3,301 individuals from the INTERVAL study. We tested significant results for replication in 971 individuals from the Trans-omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA). We found 1,168 and 1,210 cis- and trans-acting associations that replicated in TOPMed (FDR < 0.05) with a median expected true positive rate (π1) across tissues of 0.806 and 0.390, respectively. The target proteins of trans-acting genes were enriched for transcription factor binding sites and autoimmune diseases in the GWAS catalog. Furthermore, we found a higher correlation between predicted expression and protein levels of the same underlying gene (R = 0.17) than observed expression (R = 0.10, p = 7.50 × 10-11). This indicates the cis-acting genetically regulated (heritable) component of gene expression is more consistent across tissues than total observed expression (genetics + environment) and is useful in uncovering the function of SNPs associated with complex traits.
Collapse
Affiliation(s)
- Henry Wittich
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - Kristin Ardlie
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Colchester, VT 05446, USA
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anna Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chris R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Heather E Wheeler
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA; Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
| |
Collapse
|
6
|
Suzuki K, Hatzikotoulas K, Southam L, Taylor HJ, Yin X, Lorenz KM, Mandla R, Huerta-Chagoya A, Melloni GEM, Kanoni S, Rayner NW, Bocher O, Arruda AL, Sonehara K, Namba S, Lee SSK, Preuss MH, Petty LE, Schroeder P, Vanderwerff B, Kals M, Bragg F, Lin K, Guo X, Zhang W, Yao J, Kim YJ, Graff M, Takeuchi F, Nano J, Lamri A, Nakatochi M, Moon S, Scott RA, Cook JP, Lee JJ, Pan I, Taliun D, Parra EJ, Chai JF, Bielak LF, Tabara Y, Hai Y, Thorleifsson G, Grarup N, Sofer T, Wuttke M, Sarnowski C, Gieger C, Nousome D, Trompet S, Kwak SH, Long J, Sun M, Tong L, Chen WM, Nongmaithem SS, Noordam R, Lim VJY, Tam CHT, Joo YY, Chen CH, Raffield LM, Prins BP, Nicolas A, Yanek LR, Chen G, Brody JA, Kabagambe E, An P, Xiang AH, Choi HS, Cade BE, Tan J, Broadaway KA, Williamson A, Kamali Z, Cui J, Thangam M, Adair LS, Adeyemo A, Aguilar-Salinas CA, Ahluwalia TS, Anand SS, Bertoni A, Bork-Jensen J, Brandslund I, Buchanan TA, Burant CF, Butterworth AS, Canouil M, Chan JCN, Chang LC, Chee ML, Chen J, Chen SH, Chen YT, Chen Z, Chuang LM, Cushman M, Danesh J, Das SK, de Silva HJ, Dedoussis G, Dimitrov L, Doumatey AP, Du S, Duan Q, Eckardt KU, Emery LS, Evans DS, Evans MK, Fischer K, Floyd JS, Ford I, Franco OH, Frayling TM, Freedman BI, Genter P, Gerstein HC, Giedraitis V, González-Villalpando C, González-Villalpando ME, Gordon-Larsen P, Gross M, Guare LA, Hackinger S, Hakaste L, Han S, Hattersley AT, Herder C, Horikoshi M, Howard AG, Hsueh W, Huang M, Huang W, Hung YJ, Hwang MY, Hwu CM, Ichihara S, Ikram MA, Ingelsson M, Islam MT, Isono M, Jang HM, Jasmine F, Jiang G, Jonas JB, Jørgensen T, Kamanu FK, Kandeel FR, Kasturiratne A, Katsuya T, Kaur V, Kawaguchi T, Keaton JM, Kho AN, Khor CC, Kibriya MG, Kim DH, Kronenberg F, Kuusisto J, Läll K, Lange LA, Lee KM, Lee MS, Lee NR, Leong A, Li L, Li Y, Li-Gao R, Ligthart S, Lindgren CM, Linneberg A, Liu CT, Liu J, Locke AE, Louie T, Luan J, Luk AO, Luo X, Lv J, Lynch JA, Lyssenko V, Maeda S, Mamakou V, Mansuri SR, Matsuda K, Meitinger T, Melander O, Metspalu A, Mo H, Morris AD, Moura FA, Nadler JL, Nalls MA, Nayak U, Ntalla I, Okada Y, Orozco L, Patel SR, Patil S, Pei P, Pereira MA, Peters A, Pirie FJ, Polikowsky HG, Porneala B, Prasad G, Rasmussen-Torvik LJ, Reiner AP, Roden M, Rohde R, Roll K, Sabanayagam C, Sandow K, Sankareswaran A, Sattar N, Schönherr S, Shahriar M, Shen B, Shi J, Shin DM, Shojima N, Smith JA, So WY, Stančáková A, Steinthorsdottir V, Stilp AM, Strauch K, Taylor KD, Thorand B, Thorsteinsdottir U, Tomlinson B, Tran TC, Tsai FJ, Tuomilehto J, Tusie-Luna T, Udler MS, Valladares-Salgado A, van Dam RM, van Klinken JB, Varma R, Wacher-Rodarte N, Wheeler E, Wickremasinghe AR, van Dijk KW, Witte DR, Yajnik CS, Yamamoto K, Yamamoto K, Yoon K, Yu C, Yuan JM, Yusuf S, Zawistowski M, Zhang L, Zheng W, Raffel LJ, Igase M, Ipp E, Redline S, Cho YS, Lind L, Province MA, Fornage M, Hanis CL, Ingelsson E, Zonderman AB, Psaty BM, Wang YX, Rotimi CN, Becker DM, Matsuda F, Liu Y, Yokota M, Kardia SLR, Peyser PA, Pankow JS, Engert JC, Bonnefond A, Froguel P, Wilson JG, Sheu WHH, Wu JY, Hayes MG, Ma RCW, Wong TY, Mook-Kanamori DO, Tuomi T, Chandak GR, Collins FS, Bharadwaj D, Paré G, Sale MM, Ahsan H, Motala AA, Shu XO, Park KS, Jukema JW, Cruz M, Chen YDI, Rich SS, McKean-Cowdin R, Grallert H, Cheng CY, Ghanbari M, Tai ES, Dupuis J, Kato N, Laakso M, Köttgen A, Koh WP, Bowden DW, Palmer CNA, Kooner JS, Kooperberg C, Liu S, North KE, Saleheen D, Hansen T, Pedersen O, Wareham NJ, Lee J, Kim BJ, Millwood IY, Walters RG, Stefansson K, Ahlqvist E, Goodarzi MO, Mohlke KL, Langenberg C, Haiman CA, Loos RJF, Florez JC, Rader DJ, Ritchie MD, Zöllner S, Mägi R, Marston NA, Ruff CT, van Heel DA, Finer S, Denny JC, Yamauchi T, Kadowaki T, Chambers JC, Ng MCY, Sim X, Below JE, Tsao PS, Chang KM, McCarthy MI, Meigs JB, Mahajan A, Spracklen CN, Mercader JM, Boehnke M, Rotter JI, Vujkovic M, Voight BF, Morris AP, Zeggini E. Genetic drivers of heterogeneity in type 2 diabetes pathophysiology. Nature 2024; 627:347-357. [PMID: 38374256 PMCID: PMC10937372 DOI: 10.1038/s41586-024-07019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024]
Abstract
Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes1,2 and molecular mechanisms that are often specific to cell type3,4. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P < 5 × 10-8) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores5 in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.
Collapse
Affiliation(s)
- Ken Suzuki
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, UK
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Konstantinos Hatzikotoulas
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Henry J Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Xianyong Yin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kim M Lorenz
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ravi Mandla
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alicia Huerta-Chagoya
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Giorgio E M Melloni
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nigel W Rayner
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ozvan Bocher
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ana Luiza Arruda
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Graduate School of Experimental Medicine, Technical University of Munich, Munich, Germany
- Munich School for Data Science, Helmholtz Munich, Neuherberg, Germany
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Simon S K Lee
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael H Preuss
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren E Petty
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip Schroeder
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brett Vanderwerff
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Mart Kals
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fiona Bragg
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London NorthWest Healthcare NHS Trust, London, UK
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jana Nano
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Amel Lamri
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sanghoon Moon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - James P Cook
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Jung-Jin Lee
- Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian Pan
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yang Hai
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tamar Sofer
- Department of Biostatistics, Harvard University, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard University, Boston, MA, USA
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Chloé Sarnowski
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Darryl Nousome
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Soo-Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Meng Sun
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Lin Tong
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Wei-Min Chen
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Suraj S Nongmaithem
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Victor J Y Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Claudia H T Tam
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Chinese University of Hong Kong, Hong Kong, China
| | - Yoonjung Yoonie Joo
- Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, South Korea
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bram Peter Prins
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Aude Nicolas
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Edmond Kabagambe
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Academics, Ochsner Health, New Orleans, LA, USA
| | - Ping An
- Division of Statistical Genomics, Washington University School of Medicine, St Louis, MO, USA
| | - Anny H Xiang
- Department of Research and Evaluation, Division of Biostatistics Research, Kaiser Permanente of Southern California, Pasadena, CA, USA
| | - Hyeok Sun Choi
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jingyi Tan
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - K Alaine Broadaway
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alice Williamson
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK
| | - Zoha Kamali
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jinrui Cui
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Manonanthini Thangam
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Linda S Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carlos A Aguilar-Salinas
- Unidad de Investigación en Enfermedades Metabólicas and Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sonia S Anand
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Alain Bertoni
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Brandslund
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Biochemistry, Vejle Hospital, Vejle, Denmark
| | - Thomas A Buchanan
- Department of Medicine, Division of Endocrinology and Diabetes, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus, University of Cambridge, Hinxton, UK
- National Institute for Health and Care Research (NIHR) Blood and Transplant Unit (BTRU) in Donor Health and Behaviour, Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Mickaël Canouil
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- University of Lille, Lille, France
| | - Juliana C N Chan
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, Chinese University of Hong Kong, Hong Kong, China
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Miao-Li Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Ji Chen
- Exeter Centre of Excellence in Diabetes (ExCEeD), Exeter Medical School, University of Exeter, Exeter, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shyh-Huei Chen
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Lee-Ming Chuang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Mary Cushman
- Department of Medicine, University of Vermont, Colchester, VT, USA
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus, University of Cambridge, Hinxton, UK
- National Institute for Health and Care Research (NIHR) Blood and Transplant Unit (BTRU) in Donor Health and Behaviour, Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Swapan K Das
- Section of Endocrinology and Metabolism, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Latchezar Dimitrov
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shufa Du
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qing Duan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Pauline Genter
- Department of Medicine, Division of Endocrinology and Metabolism, Lundquist Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hertzel C Gerstein
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Mexico City, Mexico
| | - Maria Elena González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Mexico City, Mexico
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Lindsay A Guare
- Genomics and Computational Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sophie Hackinger
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Liisa Hakaste
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
| | - Sohee Han
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | | | - Christian Herder
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Annie-Green Howard
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Willa Hsueh
- Department of Internal Medicine, Diabetes and Metabolism Research Center, Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Mengna Huang
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
- Center for Global Cardiometabolic Health, Brown University, Providence, RI, USA
| | - Wei Huang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Yi-Jen Hung
- Division of Endocrine and Metabolism, Tri-Service General Hospital Songshan Branch, Taipei, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - Mohammad Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | | | - Masato Isono
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hye-Mi Jang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Farzana Jasmine
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Chinese University of Hong Kong, Hong Kong, China
| | - Jost B Jonas
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Torben Jørgensen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Frederick K Kamanu
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fouad R Kandeel
- Department of Clinical Diabetes, Endocrinology and Metabolism, Department of Translational Research and Cellular Therapeutics, City of Hope, Duarte, CA, USA
| | | | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Geriatric and General Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Varinderpal Kaur
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jacob M Keaton
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Abel N Kho
- Division of General Internal Medicine and Geriatrics, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Health Information Partnerships, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Muhammad G Kibriya
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Kyung Min Lee
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Myung-Shik Lee
- Soochunhyang Institute of Medi-bio Science and Division of Endocrinology, Department of Internal Medicine, Soochunhyang University College of Medicine, Cheonan, South Korea
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nanette R Lee
- USC-Office of Population Studies Foundation, University of San Carlos, Cebu City, Philippines
| | - Aaron Leong
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Symen Ligthart
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Cecilia M Lindgren
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Adam E Locke
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, Division of Genomics and Bioinformatics, Washington University School of Medicine, St Louis, MO, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Andrea O Luk
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Chinese University of Hong Kong, Hong Kong, China
| | - Xi Luo
- Department of Biostatistics and Data Science, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Julie A Lynch
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Department of Clinical Science, Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Shiro Maeda
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, Japan
| | - Vasiliki Mamakou
- Dromokaiteio Psychiatric Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Sohail Rafik Mansuri
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Koichi Matsuda
- Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Olle Melander
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Huan Mo
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D Morris
- Usher Institute to the Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Filipe A Moura
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jerry L Nadler
- Department of Medicine and Pharmacology, New York Medical College, Valhalla, NY, USA
| | - Michael A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International, Glen Echo, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Uma Nayak
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Japan
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Sanjay R Patel
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Snehal Patil
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pei Pei
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Mark A Pereira
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fraser J Pirie
- Department of Diabetes and Endocrinology, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hannah G Polikowsky
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bianca Porneala
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gauri Prasad
- Academy of Scientific and Innovative Research, CSIR-Human Resource Development Campus, Ghaziabad, India
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Michael Roden
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebecca Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katheryn Roll
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Kevin Sandow
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alagu Sankareswaran
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Mohammad Shahriar
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Botong Shen
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jinxiu Shi
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Dong Mun Shin
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Nobuhiro Shojima
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Wing Yee So
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, Chinese University of Hong Kong, Hong Kong, China
| | - Alena Stančáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Biostatistics, Epidemiology, and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Chair of Genetic Epidemiology, Institute of Medical Information Processing, Biometry, and Epidemiology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Brian Tomlinson
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong, China
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Tam C Tran
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fuu-Jen Tsai
- Department of Medical Genetics and Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Jaakko Tuomilehto
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- National School of Public Health, Madrid, Spain
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Teresa Tusie-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Medicina Genómica y Toxiología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Miriam S Udler
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Adan Valladares-Salgado
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Jan B van Klinken
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Chemistry, Laboratory of Genetic Metabolic Disease, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Hospital, Los Angeles, CA, USA
| | - Niels Wacher-Rodarte
- Unidad de Investigación Médica en Epidemiologia Clinica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | | | - Ko Willems van Dijk
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Chittaranjan S Yajnik
- Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, India
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kyungheon Yoon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Salim Yusuf
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Liang Zhang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Leslie J Raffel
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UCI Irvine School of Medicine, Irvine, CA, USA
| | - Michiya Igase
- Department of Anti-Aging Medicine, Ehime University Graduate School of Medicine, Touon, Japan
| | - Eli Ipp
- Department of Medicine, Division of Endocrinology and Metabolism, Lundquist Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael A Province
- Division of Statistical Genomics, Washington University School of Medicine, St Louis, MO, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Craig L Hanis
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Erik Ingelsson
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Ya-Xing Wang
- Beijing Institute of Ophthalmology, Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - James C Engert
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Amélie Bonnefond
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Philippe Froguel
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Wayne H H Sheu
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Ronald C W Ma
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, Chinese University of Hong Kong, Hong Kong, China
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tiinamaija Tuomi
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
- Department of Endocrinology, Helsinki University Hospital, Helsinki, Finland
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
- Science and Engineering Research Board (SERB), Department of Science and Technology, Ministry of Science and Technology, Government of India, New Delhi, India
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dwaipayan Bharadwaj
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Guillaume Paré
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Michèle M Sale
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Habibul Ahsan
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Ayesha A Motala
- Department of Diabetes and Endocrinology, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kyong-Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Miguel Cruz
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Roberta McKean-Cowdin
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Harald Grallert
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Josee Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Woon-Puay Koh
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Donald W Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, University of Dundee, Dundee, UK
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London NorthWest Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Simin Liu
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
- Center for Global Cardiometabolic Health, Brown University, Providence, RI, USA
- Department of Medicine, Brown University Alpert School of Medicine, Providence, RI, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Danish Saleheen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Juyoung Lee
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Iona Y Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Kari Stefansson
- deCODE Genetics, Amgen, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Emma Ahlqvist
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Mark O Goodarzi
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Translational Medicine and Therapeutics, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Center for Precision Medicine, University of Pennsylvania - Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sebastian Zöllner
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Nicholas A Marston
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian T Ruff
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Sarah Finer
- Institute for Population Health Sciences, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Joshua C Denny
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Toranomon Hospital, Tokyo, Japan
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London NorthWest Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Jennifer E Below
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip S Tsao
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyong-Mi Chang
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - James B Meigs
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Cassandra N Spracklen
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Josep M Mercader
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marijana Vujkovic
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin F Voight
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, UK.
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
- TUM School of Medicine and Health, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany.
| |
Collapse
|
7
|
de Vries PS, Reventun P, Brown MR, Heath AS, Huffman JE, Le NQ, Bebo A, Brody JA, Temprano-Sagrera G, Raffield LM, Ozel AB, Thibord F, Jain D, Lewis JP, Rodriguez BAT, Pankratz N, Taylor KD, Polasek O, Chen MH, Yanek LR, Carrasquilla GD, Marioni R, Kleber ME, Trégouët DA, Yao J, Li-Gao R, Joshi PK, Trompet S, Martinez-Perez A, Ghanbari M, Howard TE, Reiner AP, Arvanitis M, Ryan KA, Bartz TM, Rudan I, Faraday N, Linneberg A, Ekunwe L, Davies G, Delgado GE, Suchon P, Guo X, Rosendaal FR, Klaric L, Noordam R, van Rooij F, Curran JE, Wheeler MM, Osburn WO, O'Connell JR, Boerwinkle E, Beswick A, Psaty BM, Kolcic I, Souto JC, Becker LC, Hansen T, Doyle MF, Harris SE, Moissl AP, Deleuze JF, Rich SS, van Hylckama Vlieg A, Campbell H, Stott DJ, Soria JM, de Maat MPM, Almasy L, Brody LC, Auer PL, Mitchell BD, Ben-Shlomo Y, Fornage M, Hayward C, Mathias RA, Kilpeläinen TO, Lange LA, Cox SR, März W, Morange PE, Rotter JI, Mook-Kanamori DO, Wilson JF, van der Harst P, Jukema JW, Ikram MA, Blangero J, Kooperberg C, Desch KC, Johnson AD, Sabater-Lleal M, Lowenstein CJ, Smith NL, Morrison AC. A genetic association study of circulating coagulation Factor VIII and von Willebrand Factor levels. Blood 2024:blood.2023021452. [PMID: 38320121 DOI: 10.1182/blood.2023021452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Coagulation Factor VIII (FVIII) and its carrier protein von Willebrand factor (VWF) are critical to coagulation and platelet aggregation. We leveraged whole genome sequence data from the Trans-Omics for Precision Medicine (TOPMed) program along with TOPMed-based imputation of genotypes in additional samples to identify genetic associations with circulating FVIII and VWF levels in a single variant meta-analysis including up to 45,289 participants. Gene-based aggregate tests were implemented in TOPMed. We identified three candidate causal genes and tested their functional effect on FVIII release from human liver endothelial cells (HLECs) and VWF release from human umbilical vein endothelial cells (HUVECs). Mendelian randomization was also performed to provide evidence for causal associations of FVIII and VWF with thrombotic outcomes. We identified associations (P<5×10-9) at seven new loci for FVIII (ST3GAL4, CLEC4M, B3GNT2, ASGR1, F12, KNG1, and TREM1/NCR2) and one for VWF (B3GNT2). VWF, ABO, and STAB2 were associated with FVIII and VWF in gene-based analyses. Multi-phenotype analysis of FVIII and VWF identified another three new loci, including PDIA3. Silencing of B3GNT2 and the previously reported CD36 gene decreased release of FVIII by HLECs, while silencing of B3GNT2, CD36, and PDIA3 decreased release of VWF by HVECs. Mendelian randomization supports causal association of higher FVIII and VWF with increased risk of thrombotic outcomes. Seven new loci were identified for FVIII and one for VWF, with evidence supporting causal associations of FVIII and VWF with thrombotic outcomes. B3GNT2, CD36, and PDIA3 modulate the release of FVIII and/or VWF in vitro.
Collapse
Affiliation(s)
- Paul S de Vries
- University of Texas Health Science Center at Houston, Houston, Texas, United States
| | - Paula Reventun
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Michael R Brown
- University of Texas Health Science Center at Houston, Houston, Texas, United States
| | - Adam S Heath
- University of Texas Health Science Center at Houston, Houston, Texas, United States
| | | | - Ngoc-Quynh Le
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Allison Bebo
- University of Texas Health Science Center at Houston, Houston, Texas, United States
| | | | | | - Laura M Raffield
- University of North Carolina at Chapel Hill, CHAPEL HILL, North Carolina, United States
| | | | - Florian Thibord
- National Heart, Lung, and Blood Institute, The Framingham Heart Study, Framingham, Massachusetts, United States
| | | | - Joshua P Lewis
- University of Maryland, Baltimore, Maryland, United States
| | | | - Nathan Pankratz
- University of Minnesota, Minneapolis, Minnesota, United States
| | - Kent D Taylor
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States
| | | | - Ming-Huei Chen
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham, Massachusetts, United States
| | - Lisa R Yanek
- Johns Hopkins Medical Institutions, Baltimore, Maryland, United States
| | | | | | | | | | - Jie Yao
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States
| | | | | | | | | | | | - Tom E Howard
- University of Texas Rio Grande Valley, Brownsville, Texas, United States
| | - Alex P Reiner
- Fred Hutchinson Cancer Center, Seattle, Washington, United States
| | - Marios Arvanitis
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States
| | - Kathleen A Ryan
- University of Maryland Baltimore, Baltimore, Maryland, United States
| | - Traci M Bartz
- University of Washington, Seattle, Washington, United States
| | - Igor Rudan
- University of Edinburgh, Edinburgh, United Kingdom
| | - Nauder Faraday
- Johns Hopkins University, Baltimore, Maryland, United States
| | | | - Lynette Ekunwe
- Jackson State University, Jackson, Mississippi, United States
| | - Gail Davies
- University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Xiuqing Guo
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States
| | | | | | | | | | - Joanne E Curran
- School of Medicine, University of Texas Rio Grande Valley, Brownsville, Texas, United States
| | | | - William O Osburn
- Johns Hopkins School of Medicine, Baltimore, Maryland, United States
| | - Jeffrey R O'Connell
- University of Maryland School of Medicine, Baltimore, Maryland, United States
| | | | | | - Bruce M Psaty
- Departments of Epidemiology and Health Systems and Population Health, University of Washington, United States
| | - Ivana Kolcic
- University of Split, Split, Croatia, Republic of
| | | | - Lewis C Becker
- Johns Hopkins University, Baltimore, Maryland, United States
| | | | - Margaret F Doyle
- Larner College of Medicine at the University of Vermont, Colchester, Vermont, United States
| | | | - Angela P Moissl
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Germany
| | | | - Stephen S Rich
- University of Virginia, Charlottesville, Virginia, United States
| | | | | | | | | | | | - Laura Almasy
- The Children's Hospital of Philadelphia, United States
| | | | - Paul L Auer
- MEDICAL COLLEGE OF WISCONSIN, Milwaukee, Wisconsin, United States
| | | | | | - Myriam Fornage
- School of Public Health, The University of Texas Health Science Center at Houston, United States
| | | | | | | | - Leslie A Lange
- University of Colorado, Anschutz Medical Campus, Aurora, Colorado, United States
| | - Simon R Cox
- University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Jerome I Rotter
- The Lundquist Institute at Harbor-UCLA, Torrance, California, United States
| | | | | | - Pim van der Harst
- Division of Heart and Lungs, Utrecht University, University Medical Center Utrecht, Utrecht, Netherlands
| | | | | | - John Blangero
- University of Texas Rio Grande Valley, Brownsville, United States
| | | | - Karl C Desch
- University of Michigan, Ann Arbor, Michigan, United States
| | - Andrew D Johnson
- National Heart, Lung, and Blood Institute, The Framingham Heart Study, Framingham, Massachusetts, United States
| | | | - Charles J Lowenstein
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | | | - Alanna C Morrison
- University of Texas at Houston Health Science Center, Houston, Texas, United States
| |
Collapse
|
8
|
Goodman MO, Faquih T, Paz V, Nagarajan P, Lane JM, Spitzer B, Maher M, Chung J, Cade BE, Purcell SM, Zhu X, Noordam R, Phillips AJK, Kyle SD, Spiegelhalder K, Weedon MN, Lawlor DA, Rotter JI, Taylor KD, Isasi CR, Sofer T, Dashti HS, Rutter MK, Redline S, Saxena R, Wang H. Genome-wide association analysis of composite sleep health scores in 413,904 individuals. medRxiv 2024:2024.02.02.24302211. [PMID: 38352337 PMCID: PMC10863010 DOI: 10.1101/2024.02.02.24302211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Recent genome-wide association studies (GWASs) of several individual sleep traits have identified hundreds of genetic loci, suggesting diverse mechanisms. Moreover, sleep traits are moderately correlated, and together may provide a more complete picture of sleep health, while also illuminating distinct domains. Here we construct novel sleep health scores (SHSs) incorporating five core self-report measures: sleep duration, insomnia symptoms, chronotype, snoring, and daytime sleepiness, using additive (SHS-ADD) and five principal components-based (SHS-PCs) approaches. GWASs of these six SHSs identify 28 significant novel loci adjusting for multiple testing on six traits (p<8.3e-9), along with 341 previously reported loci (p<5e-08). The heritability of the first three SHS-PCs equals or exceeds that of SHS-ADD (SNP-h2=0.094), while revealing sleep-domain-specific genetic discoveries. Significant loci enrich in multiple brain tissues and in metabolic and neuronal pathways. Post GWAS analyses uncover novel genetic mechanisms underlying sleep health and reveal connections to behavioral, psychological, and cardiometabolic traits.
Collapse
Affiliation(s)
- Matthew O Goodman
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Tariq Faquih
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Valentina Paz
- Instituto de Psicología Clínica, Facultad de Psicología, Universidad de la República, Montevideo, Uruguay
- MRC Unit for Lifelong Health & Ageing, Institute of Cardiovascular Science, University College London, London, United Kingdom
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Pavithra Nagarajan
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jacqueline M Lane
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Brian Spitzer
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Matthew Maher
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joon Chung
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Shaun M Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Psychiatry, Brigham and Women’s Hospital, Boston, MA, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew J. K. Phillips
- School of Psychological Sciences, Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC, Australia
| | - Simon D. Kyle
- Sir Jules Thorn Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Kai Spiegelhalder
- Department of Psychiatry and Psychotherapy, Medical Centre - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael N Weedon
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | - Deborah A. Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hassan S Dashti
- Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Martin K Rutter
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Diabetes, Endocrinology and Metabolism Centre, Manchester University NHS Foundation Trust, NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester, UK
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
| | - Richa Saxena
- Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| |
Collapse
|
9
|
Westerman KE, Kilpeläinen TO, Sevilla-Gonzalez M, Connelly MA, Wood AC, Tsai MY, Taylor KD, Rich SS, Rotter JI, Otvos JD, Bentley AR, Mora S, Aschard H, Rao DC, Gu C, Chasman DI, Manning AK. Refinement of a published gene-physical activity interaction impacting HDL-cholesterol: role of sex and lipoprotein subfractions. medRxiv 2024:2024.01.23.24301689. [PMID: 38313294 PMCID: PMC10836120 DOI: 10.1101/2024.01.23.24301689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Large-scale gene-environment interaction (GxE) discovery efforts often involve compromises in the definition of outcomes and choice of covariates for the sake of data harmonization and statistical power. Consequently, refinement of exposures, covariates, outcomes, and population subsets may be helpful to establish often-elusive replication and evaluate potential clinical utility. Here, we used additional datasets, an expanded set of statistical models, and interrogation of lipoprotein metabolism via nuclear magnetic resonance (NMR)-based lipoprotein subfractions to refine a previously discovered GxE modifying the relationship between physical activity (PA) and HDL-cholesterol (HDL-C). This GxE was originally identified by Kilpeläinen et al., with the strongest cohort-specific signal coming from the Women's Genome Health Study (WGHS). We thus explored this GxE further in the WGHS (N = 23,294), with follow-up in the UK Biobank (UKB; N = 281,380), and the Multi-Ethnic Study of Atherosclerosis (MESA; N = 4,587). Self-reported PA (MET-hrs/wk), genotypes at rs295849 (nearest gene: LHX1), and NMR metabolomics data were available in all three cohorts. As originally reported, minor allele carriers of rs295849 in WGHS had a stronger positive association between PA and HDL-C (pint = 0.002). When testing a range of NMR metabolites (primarily lipoprotein and lipid subfractions) to refine the HDL-C outcome, we found a stronger interaction effect on medium-sized HDL particle concentrations (M-HDL-P; pint = 1.0×10-4) than HDL-C. Meta-regression revealed a systematically larger interaction effect in cohorts from the original meta-analysis with a greater fraction of women (p = 0.018). In the UKB, GxE effects were stronger both in women and using M-HDL-P as the outcome. In MESA, the primary interaction for HDL-C showed nominal significance (pint = 0.013), but without clear differences by sex and with a greater magnitude using large, rather than medium, HDL-P as an outcome. Towards reconciling these observations, further exploration leveraging NMR platform-specific HDL subfraction diameter annotations revealed modest agreement across all cohorts in the interaction affecting medium-to-large particles. Taken together, our work provides additional insights into a specific known gene-PA interaction while illustrating the importance of phenotype and model refinement towards understanding and replicating GxEs.
Collapse
Affiliation(s)
- Kenneth E. Westerman
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tuomas O. Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Magdalena Sevilla-Gonzalez
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Alexis C. Wood
- USDA/ARS Children’s Nutrition Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael Y. Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Kent D. Taylor
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - James D. Otvos
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samia Mora
- Center for Lipid Metabolomics, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA, USA
| | - Hugues Aschard
- Department of Computational Biology, Institut Pasteur, Université de Paris, Paris, FR
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - DC Rao
- Division of Biostatistics, Washington University, St. Louis, MO, USA
| | - Charles Gu
- Division of Biostatistics, Washington University, St. Louis, MO, USA
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alisa K. Manning
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| |
Collapse
|
10
|
Verma SS, Gudiseva HV, Chavali VRM, Salowe RJ, Bradford Y, Guare L, Lucas A, Collins DW, Vrathasha V, Nair RM, Rathi S, Zhao B, He J, Lee R, Zenebe-Gete S, Bowman AS, McHugh CP, Zody MC, Pistilli M, Khachatryan N, Daniel E, Murphy W, Henderer J, Kinzy TG, Iyengar SK, Peachey NS, Taylor KD, Guo X, Chen YDI, Zangwill L, Girkin C, Ayyagari R, Liebmann J, Chuka-Okosa CM, Williams SE, Akafo S, Budenz DL, Olawoye OO, Ramsay M, Ashaye A, Akpa OM, Aung T, Wiggs JL, Ross AG, Cui QN, Addis V, Lehman A, Miller-Ellis E, Sankar PS, Williams SM, Ying GS, Cooke Bailey J, Rotter JI, Weinreb R, Khor CC, Hauser MA, Ritchie MD, O'Brien JM. A multi-cohort genome-wide association study in African ancestry individuals reveals risk loci for primary open-angle glaucoma. Cell 2024; 187:464-480.e10. [PMID: 38242088 DOI: 10.1016/j.cell.2023.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/24/2023] [Accepted: 12/04/2023] [Indexed: 01/21/2024]
Abstract
Primary open-angle glaucoma (POAG), the leading cause of irreversible blindness worldwide, disproportionately affects individuals of African ancestry. We conducted a genome-wide association study (GWAS) for POAG in 11,275 individuals of African ancestry (6,003 cases; 5,272 controls). We detected 46 risk loci associated with POAG at genome-wide significance. Replication and post-GWAS analyses, including functionally informed fine-mapping, multiple trait co-localization, and in silico validation, implicated two previously undescribed variants (rs1666698 mapping to DBF4P2; rs34957764 mapping to ROCK1P1) and one previously associated variant (rs11824032 mapping to ARHGEF12) as likely causal. For individuals of African ancestry, a polygenic risk score (PRS) for POAG from our mega-analysis (African ancestry individuals) outperformed a PRS from summary statistics of a much larger GWAS derived from European ancestry individuals. This study quantifies the genetic architecture similarities and differences between African and non-African ancestry populations for this blinding disease.
Collapse
Affiliation(s)
- Shefali S Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Harini V Gudiseva
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Venkata R M Chavali
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca J Salowe
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuki Bradford
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay Guare
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David W Collins
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vrathasha Vrathasha
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rohini M Nair
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sonika Rathi
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bingxin Zhao
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie He
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Roy Lee
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Selam Zenebe-Gete
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anita S Bowman
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Maxwell Pistilli
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Naira Khachatryan
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ebenezer Daniel
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jeffrey Henderer
- Department of Ophthalmology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Tyler G Kinzy
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA
| | - Sudha K Iyengar
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA
| | - Neal S Peachey
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA; Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Linda Zangwill
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA
| | - Christopher Girkin
- Department of Ophthalmology and Visual Sciences, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Radha Ayyagari
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA
| | - Jeffrey Liebmann
- Department of Ophthalmology, Columbia University Medical Center, Columbia University, New York, NY, USA
| | | | - Susan E Williams
- Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen Akafo
- Unit of Ophthalmology, Department of Surgery, University of Ghana Medical School, Accra, Ghana
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adeyinka Ashaye
- Department of Ophthalmology, University of Ibadan, Ibadan, Nigeria
| | - Onoja M Akpa
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tin Aung
- Singapore Eye Research Institute, Singapore, Singapore
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Ahmara G Ross
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qi N Cui
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Victoria Addis
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Lehman
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eydie Miller-Ellis
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Prithvi S Sankar
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Gui-Shuang Ying
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica Cooke Bailey
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA; Department of Pharmacology and Toxicology, Center for Health Disparities, Brody School of Medicine. East Carolina University, Greenville, NC, 27834, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Robert Weinreb
- Viterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joan M O'Brien
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. joan.o'
| |
Collapse
|
11
|
Scholz M, Horn K, Pott J, Wuttke M, Kühnapfel A, Nasr MK, Kirsten H, Li Y, Hoppmann A, Gorski M, Ghasemi S, Li M, Tin A, Chai JF, Cocca M, Wang J, Nutile T, Akiyama M, Åsvold BO, Bansal N, Biggs ML, Boutin T, Brenner H, Brumpton B, Burkhardt R, Cai J, Campbell A, Campbell H, Chalmers J, Chasman DI, Chee ML, Chee ML, Chen X, Cheng CY, Cifkova R, Daviglus M, Delgado G, Dittrich K, Edwards TL, Endlich K, Michael Gaziano J, Giri A, Giulianini F, Gordon SD, Gudbjartsson DF, Hallan S, Hamet P, Hartman CA, Hayward C, Heid IM, Hellwege JN, Holleczek B, Holm H, Hutri-Kähönen N, Hveem K, Isermann B, Jonas JB, Joshi PK, Kamatani Y, Kanai M, Kastarinen M, Khor CC, Kiess W, Kleber ME, Körner A, Kovacs P, Krajcoviechova A, Kramer H, Krämer BK, Kuokkanen M, Kähönen M, Lange LA, Lash JP, Lehtimäki T, Li H, Lin BM, Liu J, Loeffler M, Lyytikäinen LP, Magnusson PKE, Martin NG, Matsuda K, Milaneschi Y, Mishra PP, Mononen N, Montgomery GW, Mook-Kanamori DO, Mychaleckyj JC, März W, Nauck M, Nikus K, Nolte IM, Noordam R, Okada Y, Olafsson I, Oldehinkel AJ, Penninx BWJH, Perola M, Pirastu N, Polasek O, Porteous DJ, Poulain T, Psaty BM, Rabelink TJ, Raffield LM, Raitakari OT, Rasheed H, Reilly DF, Rice KM, Richmond A, Ridker PM, Rotter JI, Rudan I, Sabanayagam C, Salomaa V, Schneiderman N, Schöttker B, Sims M, Snieder H, Stark KJ, Stefansson K, Stocker H, Stumvoll M, Sulem P, Sveinbjornsson G, Svensson PO, Tai ES, Taylor KD, Tayo BO, Teren A, Tham YC, Thiery J, Thio CHL, Thomas LF, Tremblay J, Tönjes A, van der Most PJ, Vitart V, Völker U, Wang YX, Wang C, Wei WB, Whitfield JB, Wild SH, Wilson JF, Winkler TW, Wong TY, Woodward M, Sim X, Chu AY, Feitosa MF, Thorsteinsdottir U, Hung AM, Teumer A, Franceschini N, Parsa A, Köttgen A, Schlosser P, Pattaro C. X-chromosome and kidney function: evidence from a multi-trait genetic analysis of 908,697 individuals reveals sex-specific and sex-differential findings in genes regulated by androgen response elements. Nat Commun 2024; 15:586. [PMID: 38233393 PMCID: PMC10794254 DOI: 10.1038/s41467-024-44709-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/30/2023] [Indexed: 01/19/2024] Open
Abstract
X-chromosomal genetic variants are understudied but can yield valuable insights into sexually dimorphic human traits and diseases. We performed a sex-stratified cross-ancestry X-chromosome-wide association meta-analysis of seven kidney-related traits (n = 908,697), identifying 23 loci genome-wide significantly associated with two of the traits: 7 for uric acid and 16 for estimated glomerular filtration rate (eGFR), including four novel eGFR loci containing the functionally plausible prioritized genes ACSL4, CLDN2, TSPAN6 and the female-specific DRP2. Further, we identified five novel sex-interactions, comprising male-specific effects at FAM9B and AR/EDA2R, and three sex-differential findings with larger genetic effect sizes in males at DCAF12L1 and MST4 and larger effect sizes in females at HPRT1. All prioritized genes in loci showing significant sex-interactions were located next to androgen response elements (ARE). Five ARE genes showed sex-differential expressions. This study contributes new insights into sex-dimorphisms of kidney traits along with new prioritized gene targets for further molecular research.
Collapse
Affiliation(s)
- Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Janne Pott
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Department of Medicine IV - Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Andreas Kühnapfel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - M Kamal Nasr
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Sahar Ghasemi
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Man Li
- Division of Nephrology and Hypertension, Department of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Adrienne Tin
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS, USA
- Division of Nephrology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Massimiliano Cocca
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Judy Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Teresa Nutile
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso'-CNR, Naples, Italy
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Bjørn Olav Åsvold
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Endocrinology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, WA, USA
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - Mary L Biggs
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Thibaud Boutin
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Ben Brumpton
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Clinic of Thoracic and Occupational Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Ralph Burkhardt
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Jianwen Cai
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - John Chalmers
- The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Miao Ling Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Miao Li Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Renata Cifkova
- Center for Cardiovascular Prevention, Charles University in Prague, First Faculty of Medicine and Thomayer University Hospital, Prague, Czech Republic
- Department of Medicine II, Charles University in Prague, First Faculty of Medicine, Prague, Czech Republic
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Graciela Delgado
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Katalin Dittrich
- University Hospital for Children and Adolescents, Pediatric Research Unit, Medical Faculty, University Medical Center, University of Leipzig, Leipzig, Germany
| | - Todd L Edwards
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Karlhans Endlich
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center, VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
| | - Ayush Giri
- Division of Quantitative Sciences, Department of Obstetrics & Gynecology, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Iceland School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Stein Hallan
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Nephrology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Pavel Hamet
- Montreal University Hospital Research Center, CHUM, Montréal, QC, Canada
- Medpharmgene, Montreal, QC, Canada
| | - Catharina A Hartman
- Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Jacklyn N Hellwege
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bernd Holleczek
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
| | - Nina Hutri-Kähönen
- Tampere Centre for Skills Training and Simulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kristian Hveem
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Berend Isermann
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute for Laboratory Medicine, University of Leipzig, Leipzig, Germany
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany
- Beijing Institute of Ophthalmology, Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
- Privatpraxis Prof Jonas und Dr Panda-Jonas, Heidelberg, Germany
| | - Peter K Joshi
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Masahiro Kanai
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Wieland Kiess
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- University Hospital for Children and Adolescents, Pediatric Research Unit, Medical Faculty, University Medical Center, University of Leipzig, Leipzig, Germany
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Antje Körner
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- University Hospital for Children and Adolescents, Pediatric Research Unit, Medical Faculty, University Medical Center, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Alena Krajcoviechova
- Center for Cardiovascular Prevention, Charles University in Prague, First Faculty of Medicine and Thomayer University Hospital, Prague, Czech Republic
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
- Division of Nephrology and Hypertension, Loyola University Chicago, Chicago, IL, USA
| | - Bernhard K Krämer
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Mikko Kuokkanen
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, USA
| | - James P Lash
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and The Wellbeing Services County of Pirkanmaa, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Hengtong Li
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, and The Wellbeing Services County of Pirkanmaa, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | | | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC/Vrije Universiteit and GGZ inGeest, Amsterdam, the Netherlands
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, and The Wellbeing Services County of Pirkanmaa, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, and The Wellbeing Services County of Pirkanmaa, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Charlottesville, VA, USA
| | - Winfried März
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University Graz, Graz, Austria
- Synlab Academy, Synlab Holding Deutschland GmbH, Augsburg, Germany
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Yukinori Okada
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik, Iceland
| | - Albertine J Oldehinkel
- Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC/Vrije Universiteit and GGZ inGeest, Amsterdam, the Netherlands
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nicola Pirastu
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
- Biostatistics Unit - Population and Medical Genomics Programme, Genomics Research Centre, Human Technopole Palazzo Italia, Viale Rita Levi‑Montalcini, 1, 20157, Milan, Italy
| | | | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Tanja Poulain
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- University Hospital for Children and Adolescents, Pediatric Research Unit, Medical Faculty, University Medical Center, University of Leipzig, Leipzig, Germany
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Ton J Rabelink
- Department of Internal Medicine, Section of Nephrology, Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory of Experimental Vascular Research, Leiden University Medical Center, Leiden, the Netherlands
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Center of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Humaira Rasheed
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Medicine and Laboratory Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Anne Richmond
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Igor Rudan
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Neil Schneiderman
- Department of Psychology, University of Miami, Coral Gables, FL, USA
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Mario Sims
- Department of Social Medicine, Population and Public Health, University of California at Riverside School of Medicine, Riverside, CA, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Hannah Stocker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | | | | | | | - Per O Svensson
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Department of Cardiology, Södersjukhuset, Stockholm, Sweden
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
| | - Andrej Teren
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Cardiology and Intensive Care Medicine, University Hospital OWL of Bielefeld University, Campus Klinikum Bielefeld, Teutoburger Straße 50, 33604, Bielefeld, Germany
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Joachim Thiery
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute for Laboratory Medicine, University of Leipzig, Leipzig, Germany
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Laurent F Thomas
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Laboratory Medicine, St.Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Johanne Tremblay
- Montreal University Hospital Research Center, CHUM, Montréal, QC, Canada
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Chaolong Wang
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wen Bin Wei
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - John B Whitfield
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Sarah H Wild
- Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Tsinghua Medicine, Tsinghua University, Beijing, China
| | - Mark Woodward
- The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
- The George Institute for Global Health, School of Public Health, Imperial College London, London, UK
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | | | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Adriana M Hung
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Medical Center, Division of Nephrology & Hypertension, Nashville, TN, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Afshin Parsa
- Division of Kidney, Urologic and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
| |
Collapse
|
12
|
Li X, Owen LA, Taylor KD, Ostmo S, Chen YDI, Coyner AS, Sonmez K, Hartnett ME, Guo X, Ipp E, Roll K, Genter P, Chan RVP, DeAngelis MM, Chiang MF, Campbell JP, Rotter JI. Genome-wide association identifies novel ROP risk loci in a multiethnic cohort. Commun Biol 2024; 7:107. [PMID: 38233474 PMCID: PMC10794688 DOI: 10.1038/s42003-023-05743-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 12/26/2023] [Indexed: 01/19/2024] Open
Abstract
We conducted a genome-wide association study (GWAS) in a multiethnic cohort of 920 at-risk infants for retinopathy of prematurity (ROP), a major cause of childhood blindness, identifying 1 locus at genome-wide significance level (p < 5×10-8) and 9 with significance of p < 5×10-6 for ROP ≥ stage 3. The most significant locus, rs2058019, reached genome-wide significance within the full multiethnic cohort (p = 4.96×10-9); Hispanic and European Ancestry infants driving the association. The lead single nucleotide polymorphism (SNP) falls in an intronic region within the Glioma-associated oncogene family zinc finger 3 (GLI3) gene. Relevance for GLI3 and other top-associated genes to human ocular disease was substantiated through in-silico extension analyses, genetic risk score analysis and expression profiling in human donor eye tissues. Thus, we identify a novel locus at GLI3 with relevance to retinal biology, supporting genetic susceptibilities for ROP risk with possible variability by race and ethnicity.
Collapse
Affiliation(s)
- Xiaohui Li
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Leah A Owen
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT, USA.
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA.
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT, USA.
- Department of Ophthalmology, University at Buffalo the State University of New York, Buffalo, NY, USA.
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Susan Ostmo
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Aaron S Coyner
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Kemal Sonmez
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | | | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Eli Ipp
- Division of Endocrinology and Metabolism, Department of Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kathryn Roll
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Pauline Genter
- Division of Endocrinology and Metabolism, Department of Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - R V Paul Chan
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, IL, USA
| | - Margaret M DeAngelis
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, UT, USA
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
- Department of Ophthalmology, University at Buffalo the State University of New York, Buffalo, NY, USA
- Department of Biochemistry; Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York (SUNY), Buffalo, NY, USA
- Department of Neuroscience; Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York (SUNY), Buffalo, NY, USA
- Department of Genetics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo/State University of New York (SUNY), Buffalo, NY, USA
| | - Michael F Chiang
- National Eye Institute, National Institutes of Health, Bethesda, MD, USA
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - J Peter Campbell
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA.
| |
Collapse
|
13
|
Hughes O, Bentley AR, Breeze CE, Aguet F, Xu X, Nadkarni G, Sun Q, Lin BM, Gilliland T, Meyer MC, Du J, Raffield LM, Kramer H, Morton RW, Gouveia MH, Atkinson EG, Valladares-Salgado A, Wacher-Rodarte N, Dueker ND, Guo X, Hai Y, Adeyemo A, Best LG, Cai J, Chen G, Chong M, Doumatey A, Eales J, Goodarzi MO, Ipp E, Irvin MR, Jiang M, Jones AC, Kooperberg C, Krieger JE, Lange EM, Lanktree MB, Lash JP, Lotufo PA, Loos RJF, Ha My VT, Peralta-Romero J, Qi L, Raffel LJ, Rich SS, Rodriquez EJ, Tarazona-Santos E, Taylor KD, Umans JG, Wen J, Young BA, Yu Z, Zhang Y, Ida Chen YD, Rundek T, Rotter JI, Cruz M, Fornage M, Lima-Costa MF, Pereira AC, Paré G, Natarajan P, Cole SA, Carson AP, Lange LA, Li Y, Perez-Stable EJ, Do R, Charchar FJ, Tomaszewski M, Mychaleckyj JC, Rotimi C, Morris AP, Franceschini N. Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas. Cell Genom 2024; 4:100468. [PMID: 38190104 PMCID: PMC10794846 DOI: 10.1016/j.xgen.2023.100468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/31/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024]
Abstract
Chronic kidney disease is a leading cause of death and disability globally and impacts individuals of African ancestry (AFR) or with ancestry in the Americas (AMS) who are under-represented in genome-wide association studies (GWASs) of kidney function. To address this bias, we conducted a large meta-analysis of GWASs of estimated glomerular filtration rate (eGFR) in 145,732 AFR and AMS individuals. We identified 41 loci at genome-wide significance (p < 5 × 10-8), of which two have not been previously reported in any ancestry group. We integrated fine-mapped loci with epigenomic and transcriptomic resources to highlight potential effector genes relevant to kidney physiology and disease, and reveal key regulatory elements and pathways involved in renal function and development. We demonstrate the varying but increased predictive power offered by a multi-ancestry polygenic score for eGFR and highlight the importance of population diversity in GWASs and multi-omics resources to enhance opportunities for clinical translation for all.
Collapse
Affiliation(s)
- Odessica Hughes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA; UCL Cancer Institute, University College London, London, UK
| | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Girish Nadkarni
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas Gilliland
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mariah C Meyer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jiawen Du
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holly Kramer
- Division of Nephrology and Hypertension, Loyola University Chicago, Maywood, IL, USA
| | - Robert W Morton
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Adan Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Niels Wacher-Rodarte
- Unidad de Investigación Médica en Epidemiologia Clinica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Nicole D Dueker
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Yang Hai
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lyle G Best
- Missouri Breaks Industries Research Inc., Eagle Butte, SD, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Chong
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - James Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Eli Ipp
- Division of Endocrinology and Metabolism, Department of Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marguerite Ryan Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Minzhi Jiang
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alana C Jones
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jose E Krieger
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ethan M Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew B Lanktree
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - James P Lash
- Division of Nephrology, Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Paulo A Lotufo
- Center for Clinical and Epidemiological Research, Hospital Universitário, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vy Thi Ha My
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jesús Peralta-Romero
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Lihong Qi
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, USA
| | - Leslie J Raffel
- Department of Pediatrics, Genetic and Genomic Medicine, University of California, Irvine, Irvine, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Erik J Rodriquez
- Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Jason G Umans
- MedStar Health Research Institute, Hyattsville MD and Georgetown-Howard Universities Center for Clinical and Translational Science, Washington, DC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bessie A Young
- University of Washington School of Medicine, Seattle, WA, USA; Office of Healthcare Equity, UW Justice, Equity, Diversity, and Inclusion Center for Transformational Research (UW JEDI-CTR), University of Washington, Seattle, WA, USA; Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Zhi Yu
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | - Ying Zhang
- Center for American Indian Health Research, Department of Biostatistics and Epidemiology, Hudson College of Public Health, The University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Tanja Rundek
- Department of Neurology, Epidemiology and Public Health, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | | | - Alexandre C Pereira
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Aging Division, Brigham Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Guillaume Paré
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Shelley A Cole
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eliseo J Perez-Stable
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Ron Do
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fadi J Charchar
- School of Science, Psychology and Sport, Federation University, Ballarat, VIC, Australia; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Department of Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK; Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Josyf C Mychaleckyj
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, USA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK.
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
14
|
Kasela S, Aguet F, Kim-Hellmuth S, Brown BC, Nachun DC, Tracy RP, Durda P, Liu Y, Taylor KD, Johnson WC, Van Den Berg D, Gabriel S, Gupta N, Smith JD, Blackwell TW, Rotter JI, Ardlie KG, Manichaikul A, Rich SS, Barr RG, Lappalainen T. Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects. Am J Hum Genet 2024; 111:133-149. [PMID: 38181730 PMCID: PMC10806864 DOI: 10.1016/j.ajhg.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/07/2024] Open
Abstract
Bulk-tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, and context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs (iQTLs) for cell type, age, and other phenotypic variables in multi-omic, longitudinal data from the blood of individuals of diverse ancestries. By modeling the interaction between genotype and estimated cell-type proportions, we demonstrate that cell-type iQTLs could be considered as proxies for cell-type-specific QTL effects, particularly for the most abundant cell type in the tissue. The interpretation of age iQTLs, however, warrants caution because the moderation effect of age on the genotype and molecular phenotype association could be mediated by changes in cell-type composition. Finally, we show that cell-type iQTLs contribute to cell-type-specific enrichment of diseases that, in combination with additional functional data, could guide future functional studies. Overall, this study highlights the use of iQTLs to gain insights into the context specificity of regulatory effects.
Collapse
Affiliation(s)
- Silva Kasela
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA.
| | | | - Sarah Kim-Hellmuth
- New York Genome Center, New York, NY, USA; Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany; Computational Health Center, Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Brielin C Brown
- New York Genome Center, New York, NY, USA; Data Science Institute, Columbia University, New York, NY, USA
| | - Daniel C Nachun
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Russell P Tracy
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Peter Durda
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Yongmei Liu
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David Van Den Berg
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua D Smith
- Northwest Genomics Center, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
15
|
Giro P, Taylor KD, Shah SJ, Patel RB. The pK56M ICAM1 HFpEF risk variant and inflammatory biomarkers. Am Heart J Plus 2023; 36:100346. [PMID: 38074621 PMCID: PMC10704861 DOI: 10.1016/j.ahjo.2023.100346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 01/31/2024]
Abstract
Introduction The ICAM1 variant rs5491 (p.K56M) is common among Black individuals and has been associated with risk of heart failure with preserved ejection fraction (HFpEF). The pathways by which rs5491 leads to HFpEF are not known. Methods Among Black individuals within the Multi-Ethnic Study of Atherosclerosis, we evaluated associations of rs5491 with 3 inflammatory biomarkers (high-sensitivity C-reactive protein [hsCRP], interleukin-6 [IL-6], and tumor necrosis factor-α receptor 1 [TNFR-1]). Results Among 1558 Black participants (mean age 62 ± 10 y, 47 % female), each additional rs5491 allele was associated with higher hsCRP after covariate adjustment (β: 0.15, SE: 0.07, P = 0.02). Each additional rs5491 allele was associated with higher TNFR-1 (β: 0.06, SE: 0.02, P = 0.02), but not IL-6 (β: 0.04, SE: 0.04, P = 0.29). The association between rs5491 and HFpEF remained significant after adjustment for hsCRP. Conclusion In Black individuals, rs5491 (p.K56M) is associated with higher hsCRP and higher TNFR-1, but not IL-6.
Collapse
Affiliation(s)
- Pedro Giro
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Sanjiv J. Shah
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Ravi B. Patel
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| |
Collapse
|
16
|
Hasbani NR, Westerman KE, Kwak SH, Chen H, Li X, Di Corpo D, Wessel J, Bis JC, Sarnowski C, Wu P, Bielak LF, Guo X, Heard-Costa N, Kinney GL, Mahaney MC, Montasser ME, Palmer ND, Raffield LM, Terry JG, Yanek LR, Bon J, Bowden DW, Brody JA, Duggirala R, Jacobs DR, Kalyani RR, Lange LA, Mitchell BD, Smith JA, Taylor KD, Carson AP, Curran JE, Fornage M, Freedman BI, Gabriel S, Gibbs RA, Gupta N, Kardia SLR, Kral BG, Momin Z, Newman AB, Post WS, Viaud-Martinez KA, Young KA, Becker LC, Bertoni AG, Blangero J, Carr JJ, Pratte K, Psaty BM, Rich SS, Wu JC, Malhotra R, Peyser PA, Morrison AC, Vasan RS, Lin X, Rotter JI, Meigs JB, Manning AK, de Vries PS. Type 2 Diabetes Modifies the Association of CAD Genomic Risk Variants With Subclinical Atherosclerosis. Circ Genom Precis Med 2023; 16:e004176. [PMID: 38014529 PMCID: PMC10843644 DOI: 10.1161/circgen.123.004176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/29/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Individuals with type 2 diabetes (T2D) have an increased risk of coronary artery disease (CAD), but questions remain about the underlying pathology. Identifying which CAD loci are modified by T2D in the development of subclinical atherosclerosis (coronary artery calcification [CAC], carotid intima-media thickness, or carotid plaque) may improve our understanding of the mechanisms leading to the increased CAD in T2D. METHODS We compared the common and rare variant associations of known CAD loci from the literature on CAC, carotid intima-media thickness, and carotid plaque in up to 29 670 participants, including up to 24 157 normoglycemic controls and 5513 T2D cases leveraging whole-genome sequencing data from the Trans-Omics for Precision Medicine program. We included first-order T2D interaction terms in each model to determine whether CAD loci were modified by T2D. The genetic main and interaction effects were assessed using a joint test to determine whether a CAD variant, or gene-based rare variant set, was associated with the respective subclinical atherosclerosis measures and then further determined whether these loci had a significant interaction test. RESULTS Using a Bonferroni-corrected significance threshold of P<1.6×10-4, we identified 3 genes (ATP1B1, ARVCF, and LIPG) associated with CAC and 2 genes (ABCG8 and EIF2B2) associated with carotid intima-media thickness and carotid plaque, respectively, through gene-based rare variant set analysis. Both ATP1B1 and ARVCF also had significantly different associations for CAC in T2D cases versus controls. No significant interaction tests were identified through the candidate single-variant analysis. CONCLUSIONS These results highlight T2D as an important modifier of rare variant associations in CAD loci with CAC.
Collapse
Affiliation(s)
- Natalie R Hasbani
- Department of Epidemiology Human Genetics and Environmental Sciences, Human Genetics Center, The University of Texas Health Science Center at Houston School of Public Health (N.R.H., H.C., C.S., A.C.M., P.S.d.V.)
| | - Kenneth E Westerman
- Department of Medicine, Clinical and Translation Epidemiology Unit (K.E.W., A.K.M.), Massachusetts General Hospital, Boston
- Programs in Metabolism and Medical and Population Genetics (K.E.W., J.B.M., A.K.M.), Broad Institute, Cambridge
- Department of Medicine, Harvard Medical School, Boston, MA (K.E.W., J.B.M., A.K.M.)
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, South Korea (S.H.K.)
| | - Han Chen
- Department of Epidemiology Human Genetics and Environmental Sciences, Human Genetics Center, The University of Texas Health Science Center at Houston School of Public Health (N.R.H., H.C., C.S., A.C.M., P.S.d.V.)
- School of Biomedical Informatics, Center for Precision Health (H.C.), The University of Texas Health Science Center at Houston
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health (X. Li, X. Lin), Boston University School of Public Health, MA
| | - Daniel Di Corpo
- Department of Biostatistics (D.D., P.W.), Boston University School of Public Health, MA
| | - Jennifer Wessel
- Department of Epidemiology, Fairbanks School of Public Health, Indianapolis, IN (J.W.)
| | - Joshua C Bis
- Department of Medicine, Cardiovascular Health Research Unit (J.C.B., J.A.B., B.M.P.), University of Washington, Seattle
| | - Chloè Sarnowski
- Department of Epidemiology Human Genetics and Environmental Sciences, Human Genetics Center, The University of Texas Health Science Center at Houston School of Public Health (N.R.H., H.C., C.S., A.C.M., P.S.d.V.)
| | - Peitao Wu
- Department of Biostatistics (D.D., P.W.), Boston University School of Public Health, MA
| | - Lawrence F Bielak
- Department of Medicine, Harvard Medical School, Boston, MA (K.E.W., J.B.M., A.K.M.)
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-University of California Los Angeles Medical Center, Torrance (X.G., K.D.T.)
| | | | - Gregory L Kinney
- Department of Epidemiology, University of Colorado School of Public Health, Aurora (G.L.K., K.A.Y.)
| | - Michael C Mahaney
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville (M.C.M., J.E.C., J. Blangero)
| | - May E Montasser
- Department of Medicine, Division of Endocrinology Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore (M.E.M., B.D.M.)
| | - Nicholette D Palmer
- Department of Biochemistry (N.D.P., D.W.B.), Wake Forest School of Medicine, Winston-Salem, NC
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill (L.M.R.)
| | - James G Terry
- Department of Radiology, Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University Medical Center, Nashville, TN (J.G.T., J.J.C.)
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (L.R.Y., R.R.K., B.G.K., L.C.B.)
| | - Jessica Bon
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, PA (J. Bon)
| | - Donald W Bowden
- Department of Biochemistry (N.D.P., D.W.B.), Wake Forest School of Medicine, Winston-Salem, NC
| | - Jennifer A Brody
- Department of Medicine, Cardiovascular Health Research Unit (J.C.B., J.A.B., B.M.P.), University of Washington, Seattle
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen (R.D.)
| | | | - Rita R Kalyani
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (L.R.Y., R.R.K., B.G.K., L.C.B.)
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Aurora (L.A.L.)
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore (M.E.M., B.D.M.)
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, MD (B.D.M.)
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (L.F.B., J.A.S., S.L.R.K., P.A.P.)
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor (J.A.S.)
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-University of California Los Angeles Medical Center, Torrance (X.G., K.D.T.)
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson (A.P.C.)
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville (M.C.M., J.E.C., J. Blangero)
| | - Myriam Fornage
- Institute of Molecular Medicine (M.F.), The University of Texas Health Science Center at Houston
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology (B.I.F.), Wake Forest School of Medicine, Winston-Salem, NC
| | - Stacey Gabriel
- Genomics Platform (S.G., N.G.), Broad Institute, Cambridge
| | - Richard A Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX (R.A.G., Z.M.)
| | - Namrata Gupta
- Genomics Platform (S.G., N.G.), Broad Institute, Cambridge
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (L.F.B., J.A.S., S.L.R.K., P.A.P.)
| | - Brian G Kral
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (L.R.Y., R.R.K., B.G.K., L.C.B.)
| | - Zeineen Momin
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX (R.A.G., Z.M.)
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh School of Public Health, PA (A.B.N.)
| | - Wendy S Post
- Division of Cardiology, Johns Hopkins Medicine, Baltimore, MD (W.S.P.)
| | | | - Kendra A Young
- Department of Epidemiology, University of Colorado School of Public Health, Aurora (G.L.K., K.A.Y.)
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (L.R.Y., R.R.K., B.G.K., L.C.B.)
| | - Alain G Bertoni
- Epidemiology and Prevention, Wake Forest University School of Medicine, Winston-Salem, NC (A.G.B.)
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville (M.C.M., J.E.C., J. Blangero)
| | - John J Carr
- Department of Radiology, Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University Medical Center, Nashville, TN (J.G.T., J.J.C.)
| | - Katherine Pratte
- Department of Biostatistics, National Jewish Health, Denver, CO (K.P.)
| | - Bruce M Psaty
- Department of Medicine, Cardiovascular Health Research Unit (J.C.B., J.A.B., B.M.P.), University of Washington, Seattle
- Department of Epidemiology (B.M.P.), University of Washington, Seattle
- Department of Health Systems and Population Health (B.M.P.), University of Washington, Seattle
| | | | - Joseph C Wu
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville (J.C.W.)
- Department of Medicine, Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University School of Medicine (J.C.W.), Stanford University, CA
| | - Rajeev Malhotra
- Division of Cardiology (R.M.), Massachusetts General Hospital, Boston
- Department of Radiology Molecular Imaging Program at Stanford (R.M.), Stanford University, CA
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (L.F.B., J.A.S., S.L.R.K., P.A.P.)
| | - Alanna C Morrison
- Department of Epidemiology Human Genetics and Environmental Sciences, Human Genetics Center, The University of Texas Health Science Center at Houston School of Public Health (N.R.H., H.C., C.S., A.C.M., P.S.d.V.)
| | - Ramachandran S Vasan
- Framingham Heart Study, MA (N.H.-C., R.S.V.)
- Department of Quantitative and Qualitative Health Sciences, University of Texas Health San Antonio School of Public Health (R.S.V.)
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health (X. Li, X. Lin), Boston University School of Public Health, MA
| | | | - James B Meigs
- Division of General Internal Medicine (J.B.M.), Massachusetts General Hospital, Boston
- Programs in Metabolism and Medical and Population Genetics (K.E.W., J.B.M., A.K.M.), Broad Institute, Cambridge
- Department of Medicine, Harvard Medical School, Boston, MA (K.E.W., J.B.M., A.K.M.)
| | - Alisa K Manning
- Department of Medicine, Clinical and Translation Epidemiology Unit (K.E.W., A.K.M.), Massachusetts General Hospital, Boston
- Programs in Metabolism and Medical and Population Genetics (K.E.W., J.B.M., A.K.M.), Broad Institute, Cambridge
- Department of Medicine, Harvard Medical School, Boston, MA (K.E.W., J.B.M., A.K.M.)
| | - Paul S de Vries
- Department of Epidemiology Human Genetics and Environmental Sciences, Human Genetics Center, The University of Texas Health Science Center at Houston School of Public Health (N.R.H., H.C., C.S., A.C.M., P.S.d.V.)
| |
Collapse
|
17
|
Xiao S, Li VL, Lyu X, Chen X, Wei W, Abbasi F, Knowles JW, Deng S, Tiwari G, Shi X, Zheng S, Farrell L, Chen ZZ, Taylor KD, Guo X, Goodarzi MO, Wood AC, Ida Chen YD, Lange LA, Rich SS, Rotter JI, Clish CB, Tahir UA, Gerszten RE, Benson MD, Long JZ. Lac-Phe mediates the anti-obesity effect of metformin. bioRxiv 2023:2023.11.02.565321. [PMID: 37961394 PMCID: PMC10635077 DOI: 10.1101/2023.11.02.565321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Metformin is a widely prescribed anti-diabetic medicine that also reduces body weight. The mechanisms that mediate metformin's effects on energy balance remain incompletely defined. Here we show that metformin is a powerful pharmacological inducer of the anorexigenic metabolite Lac-Phe in mice as well as in two independent human cohorts. In cell culture, metformin drives Lac-Phe biosynthesis via inhibition of complex I, increased glycolytic flux, and intracellular lactate mass action. Other biguanides and structurally distinct inhibitors of oxidative phosphorylation also increase Lac-Phe levels in vitro. Genetic ablation of CNDP2, the principal biosynthetic enzyme for Lac-Phe, in mice renders animals resistant to metformin's anorexigenic and anti-obesity effects. Mediation analyses also support a role for Lac-Phe in metformin's effect on body mass index in humans. These data establish the CNDP2/Lac-Phe pathway as a critical mediator of the effects of metformin on energy balance.
Collapse
Affiliation(s)
- Shuke Xiao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Veronica L. Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Xudong Chen
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Fahim Abbasi
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Joshua W. Knowles
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Shuliang Deng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Gaurav Tiwari
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Shuning Zheng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Laurie Farrell
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Zsu-Zsu Chen
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Alexis C. Wood
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | | | - Usman A. Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Mark D. Benson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Jonathan Z. Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| |
Collapse
|
18
|
de Las Fuentes L, Schwander KL, Brown MR, Bentley AR, Winkler TW, Sung YJ, Munroe PB, Miller CL, Aschard H, Aslibekyan S, Bartz TM, Bielak LF, Chai JF, Cheng CY, Dorajoo R, Feitosa MF, Guo X, Hartwig FP, Horimoto A, Kolčić I, Lim E, Liu Y, Manning AK, Marten J, Musani SK, Noordam R, Padmanabhan S, Rankinen T, Richard MA, Ridker PM, Smith AV, Vojinovic D, Zonderman AB, Alver M, Boissel M, Christensen K, Freedman BI, Gao C, Giulianini F, Harris SE, He M, Hsu FC, Kühnel B, Laguzzi F, Li X, Lyytikäinen LP, Nolte IM, Poveda A, Rauramaa R, Riaz M, Robino A, Sofer T, Takeuchi F, Tayo BO, van der Most PJ, Verweij N, Ware EB, Weiss S, Wen W, Yanek LR, Zhan Y, Amin N, Arking DE, Ballantyne C, Boerwinkle E, Brody JA, Broeckel U, Campbell A, Canouil M, Chai X, Chen YDI, Chen X, Chitrala KN, Concas MP, de Faire U, de Mutsert R, de Silva HJ, de Vries PS, Do A, Faul JD, Fisher V, Floyd JS, Forrester T, Friedlander Y, Girotto G, Gu CC, Hallmans G, Heikkinen S, Heng CK, Homuth G, Hunt S, Ikram MA, Jacobs DR, Kavousi M, Khor CC, Kilpeläinen TO, Koh WP, Komulainen P, Langefeld CD, Liang J, Liu K, Liu J, Lohman K, Mägi R, Manichaikul AW, McKenzie CA, Meitinger T, Milaneschi Y, Nauck M, Nelson CP, O'Connell JR, Palmer ND, Pereira AC, Perls T, Peters A, Polašek O, Raitakari OT, Rice K, Rice TK, Rich SS, Sabanayagam C, Schreiner PJ, Shu XO, Sidney S, Sims M, Smith JA, Starr JM, Strauch K, Tai ES, Taylor KD, Tsai MY, Uitterlinden AG, van Heemst D, Waldenberger M, Wang YX, Wei WB, Wilson G, Xuan D, Yao J, Yu C, Yuan JM, Zhao W, Becker DM, Bonnefond A, Bowden DW, Cooper RS, Deary IJ, Divers J, Esko T, Franks PW, Froguel P, Gieger C, Jonas JB, Kato N, Lakka TA, Leander K, Lehtimäki T, Magnusson PKE, North KE, Ntalla I, Penninx B, Samani NJ, Snieder H, Spedicati B, van der Harst P, Völzke H, Wagenknecht LE, Weir DR, Wojczynski MK, Wu T, Zheng W, Zhu X, Bouchard C, Chasman DI, Evans MK, Fox ER, Gudnason V, Hayward C, Horta BL, Kardia SLR, Krieger JE, Mook-Kanamori DO, Peyser PA, Province MM, Psaty BM, Rudan I, Sim X, Smith BH, van Dam RM, van Duijn CM, Wong TY, Arnett DK, Rao DC, Gauderman J, Liu CT, Morrison AC, Rotter JI, Fornage M. Gene-educational attainment interactions in a multi-population genome-wide meta-analysis identify novel lipid loci. Front Genet 2023; 14:1235337. [PMID: 38028628 PMCID: PMC10651736 DOI: 10.3389/fgene.2023.1235337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Educational attainment, widely used in epidemiologic studies as a surrogate for socioeconomic status, is a predictor of cardiovascular health outcomes. Methods: A two-stage genome-wide meta-analysis of low-density lipoprotein cholesterol (LDL), high-density lipoprotein cholesterol (HDL), and triglyceride (TG) levels was performed while accounting for gene-educational attainment interactions in up to 226,315 individuals from five population groups. We considered two educational attainment variables: "Some College" (yes/no, for any education beyond high school) and "Graduated College" (yes/no, for completing a 4-year college degree). Genome-wide significant (p < 5 × 10-8) and suggestive (p < 1 × 10-6) variants were identified in Stage 1 (in up to 108,784 individuals) through genome-wide analysis, and those variants were followed up in Stage 2 studies (in up to 117,531 individuals). Results: In combined analysis of Stages 1 and 2, we identified 18 novel lipid loci (nine for LDL, seven for HDL, and two for TG) by two degree-of-freedom (2 DF) joint tests of main and interaction effects. Four loci showed significant interaction with educational attainment. Two loci were significant only in cross-population analyses. Several loci include genes with known or suggested roles in adipose (FOXP1, MBOAT4, SKP2, STIM1, STX4), brain (BRI3, FILIP1, FOXP1, LINC00290, LMTK2, MBOAT4, MYO6, SENP6, SRGAP3, STIM1, TMEM167A, TMEM30A), and liver (BRI3, FOXP1) biology, highlighting the potential importance of brain-adipose-liver communication in the regulation of lipid metabolism. An investigation of the potential druggability of genes in identified loci resulted in five gene targets shown to interact with drugs approved by the Food and Drug Administration, including genes with roles in adipose and brain tissue. Discussion: Genome-wide interaction analysis of educational attainment identified novel lipid loci not previously detected by analyses limited to main genetic effects.
Collapse
Affiliation(s)
- Lisa de Las Fuentes
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Karen L Schwander
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - Patricia B Munroe
- Clinical Pharmacology, Queen Mary University of London, London, United Kingdom
- National Institute for Health Research Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, United Kingdom
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
- Biochemistry and Molecular Genetics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Hugo Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States
- Département de Génomes et Génétique, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Stella Aslibekyan
- School of Public Health, Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Traci M Bartz
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Ching-Yu Cheng
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Medical School, Duke-National University of Singapore, Singapore, Singapore
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Fernando P Hartwig
- Postgraduate Programme in Epidemiology, Faculty of Medicine, Federal University of Pelotas, Pelotas, RS, Brazil
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Andrea Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School, Sao Paulo, SP, Brazil
| | - Ivana Kolčić
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Elise Lim
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States
| | - Alisa K Manning
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Solomon K Musani
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, United States
| | - Melissa A Richard
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Icelandic Heart Association, Kopavogur, Iceland
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
- National Institutes of Health, Baltimore, MD, United States
| | - Maris Alver
- Estonian Genome Center, Insititute of Genomics, University of Tartu, Tartu, Estonia
| | - Mathilde Boissel
- European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Barry I Freedman
- Nephrology Division, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States
| | - Sarah E Harris
- Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Meian He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang-Chi Hsu
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Federica Laguzzi
- Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Xiaoyin Li
- Department of Population and Quantitative Health Sciences, Cleveland, OH, United States
- Department of Mathematics and Statistics, St. Cloud State University, St. Cloud, MN, United States
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, University of Tampere, Tampere, Finland
- Finnish Cardiovascular Research Center, University of Tampere, Tampere, Finland
| | - Ilja M Nolte
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alaitz Poveda
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Muhammad Riaz
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Antonietta Robino
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Tamar Sofer
- Biostatistics, Department of Medicine, Brigham and Women's Hospital, Harvard University, Boston, MA, United States
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, United States
| | - Peter J van der Most
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Niek Verweij
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Erin B Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald and University of Greifswald, Greifswald, Germany
- German Center for Cardiovascular Research, Greifswald, Germany
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yiqiang Zhan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Dan E Arking
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Christie Ballantyne
- Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX, United States
- Houston Methodist Debakey Heart and Vascular Center, Houston, TX, United States
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States
| | - Ulrich Broeckel
- Section on Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Mickaël Canouil
- European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
| | - Xiaoran Chai
- Data Science Unit, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kumaraswamy Naidu Chitrala
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Maria Pina Concas
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Ulf de Faire
- Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Ahn Do
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States
| | - Virginia Fisher
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - James S Floyd
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States
| | - Terrence Forrester
- Tropical Medicine Research Institute, University of the West Indies, Mona, Jamaica
| | - Yechiel Friedlander
- Braun School of Public Health, Hadassah Medical Center, Hebrew University, Jerusalem, Israel
| | - Giorgia Girotto
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Göran Hallmans
- Section for Nutritional Research, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Sami Heikkinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald and University of Greifswald, Greifswald, Germany
| | - Steven Hunt
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States
- Department of Genetic Medicine, Weill Cornell Medicine in Qatar, Doha, Qatar
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Medicine and Public Health, The Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | | | - Carl D Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Jingjing Liang
- Department of Population and Quantitative Health Sciences, Cleveland, OH, United States
| | - Kiang Liu
- Epidemiology, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Kurt Lohman
- Division of Cardiology, Department of Medicine, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States
| | - Reedik Mägi
- Estonian Genome Center, Insititute of Genomics, University of Tartu, Tartu, Estonia
| | - Ani W Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Colin A McKenzie
- Tropical Medicine Research Institute, University of the West Indies, Mona, Jamaica
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | | | - Matthias Nauck
- German Center for Cardiovascular Research, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, United States
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School, Sao Paulo, SP, Brazil
| | - Thomas Perls
- Geriatrics Section, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Neuherberg, Germany
| | - Ozren Polašek
- University of Split School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Treva K Rice
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Charumathi Sabanayagam
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Medical School, Duke-National University of Singapore, Singapore, Singapore
| | - Pamela J Schreiner
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Stephen Sidney
- Division of Research, Kaiser Permanente of Northern California, Oakland, CA, United States
| | - Mario Sims
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh, United Kingdom
| | - Konstantin Strauch
- German Research Center for Environmental Health, Helmholtz Zentrum München, Institute of Genetic Epidemiology, Neuherberg, Germany
- Institute of Medical Informatics Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, Minneapolis, MN, United States
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Diana van Heemst
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Ya-Xing Wang
- Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
| | - Wen-Bin Wei
- Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
| | - Gregory Wilson
- Jackson Heart Study Graduate Training Center, School of Public, Jackson State University, Jackson, MS, United States
| | - Deng Xuan
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Jie Yao
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Caizheng Yu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Min Yuan
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Division of Cancer Control and Population Sciences, University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, PA, United States
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Diane M Becker
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Amélie Bonnefond
- European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Richard S Cooper
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, United States
| | - Ian J Deary
- Department of Psychology, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jasmin Divers
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Tõnu Esko
- Estonian Genome Center, Insititute of Genomics, University of Tartu, Tartu, Estonia
- Broad Institute, Massachusetts Institute of Technology and Harvard University, Boston, MA, United States
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Nutrition, Harvard Chan School of Public Health, Boston, MA, United States
| | - Philippe Froguel
- European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Jost B Jonas
- Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Timo A Lakka
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Karin Leander
- Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University of Tampere, Tampere, Finland
- Finnish Cardiovascular Research Center, University of Tampere, Tampere, Finland
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ioanna Ntalla
- Clinical Pharmacology, Queen Mary University of London, London, United Kingdom
- Celgene, Bristol Myers Squibb, Mississauga, ON, Canada
| | | | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Harold Snieder
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Pim van der Harst
- Division Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Henry Völzke
- German Center for Cardiovascular Research, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Lynne E Wagenknecht
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, United States
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Tangchun Wu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Cleveland, OH, United States
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, United States
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
- National Institute on Aging, National Institutes of Health, Bethesda, MD, United States
| | - Ervin R Fox
- Division of Cardiology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Bernardo L Horta
- Postgraduate Programme in Epidemiology, Faculty of Medicine, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Jose Eduardo Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo Medical School, Sao Paulo, SP, Brazil
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Michael M Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, United States
| | - Igor Rudan
- Centre for Global Health, The Usher Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Tien Yin Wong
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Medical School, Duke-National University of Singapore, Singapore, Singapore
| | - Donna K Arnett
- College of Public Health, Dean's Office, University of Kentucky, Lexington, KY, United States
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | - James Gauderman
- Division of Biostatistics, Population and Public Health Sciences, University of Southern California, Los Angeles, CA, United States
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Los Angeles, CA, United States
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, United States
| |
Collapse
|
19
|
Li X, Chen H, Selvaraj MS, Van Buren E, Zhou H, Wang Y, Sun R, McCaw ZR, Yu Z, Arnett DK, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Carson AP, Carlson JC, Chami N, Chen YDI, Curran JE, de Vries PS, Fornage M, Franceschini N, Freedman BI, Gu C, Heard-Costa NL, He J, Hou L, Hung YJ, Irvin MR, Kaplan RC, Kardia SL, Kelly T, Konigsberg I, Kooperberg C, Kral BG, Li C, Loos RJ, Mahaney MC, Martin LW, Mathias RA, Minster RL, Mitchell BD, Montasser ME, Morrison AC, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Rich SS, Sitlani CM, Smith JA, Taylor KD, Tiwari H, Vasan RS, Wang Z, Yanek LR, Yu B, Rice KM, Rotter JI, Peloso GM, Natarajan P, Li Z, Liu Z, Lin X. A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies. bioRxiv 2023:2023.10.30.564764. [PMID: 37961350 PMCID: PMC10634938 DOI: 10.1101/2023.10.30.564764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits (low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides) in 61,861 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered new associations with lipid traits missed by single-trait analysis, including rare variants within an enhancer of NIPSNAP3A and an intergenic region on chromosome 1.
Collapse
Affiliation(s)
- Xihao Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Margaret Sunitha Selvaraj
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Eric Van Buren
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zachary R. McCaw
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhi Yu
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Donna K. Arnett
- Provost Office, University of South Carolina, Columbia, SC, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jenna C. Carlson
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Charles Gu
- Division of Biology & Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Nancy L. Heard-Costa
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Yi-Jen Hung
- Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Marguerite R. Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tanika Kelly
- Department of Medicine, Division of Nephrology, University of Illinois Chicago, Chicago, IL, USA
| | - Iain Konigsberg
- Department of Biomedical Informatics, University of Colorado, Aurora, CO, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian G. Kral
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael C. Mahaney
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Lisa W. Martin
- George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan L. Minster
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - May E. Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Departments of Epidemiology, University of Washington, Seattle, WA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hemant Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ramachandran S. Vasan
- Framingham Heart Study, Framingham, MA, USA
- Department of Quantitative and Qualitative Health Sciences, UT Health San Antonio School of Public Health, San Antonia, TX, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Kenneth M. Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zhonghua Liu
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Xihong Lin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
| |
Collapse
|
20
|
Jakubek YA, Zhou Y, Stilp A, Bacon J, Wong JW, Ozcan Z, Arnett D, Barnes K, Bis JC, Boerwinkle E, Brody JA, Carson AP, Chasman DI, Chen J, Cho M, Conomos MP, Cox N, Doyle MF, Fornage M, Guo X, Kardia SLR, Lewis JP, Loos RJF, Ma X, Machiela MJ, Mack TM, Mathias RA, Mitchell BD, Mychaleckyj JC, North K, Pankratz N, Peyser PA, Preuss MH, Psaty B, Raffield LM, Vasan RS, Redline S, Rich SS, Rotter JI, Silverman EK, Smith JA, Smith AP, Taub M, Taylor KD, Yun J, Li Y, Desai P, Bick AG, Reiner AP, Scheet P, Auer PL. Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing. Nat Genet 2023; 55:1912-1919. [PMID: 37904051 PMCID: PMC10632132 DOI: 10.1038/s41588-023-01553-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 09/27/2023] [Indexed: 11/01/2023]
Abstract
Megabase-scale mosaic chromosomal alterations (mCAs) in blood are prognostic markers for a host of human diseases. Here, to gain a better understanding of mCA rates in genetically diverse populations, we analyzed whole-genome sequencing data from 67,390 individuals from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine program. We observed higher sensitivity with whole-genome sequencing data, compared with array-based data, in uncovering mCAs at low mutant cell fractions and found that individuals of European ancestry have the highest rates of autosomal mCAs and the lowest rates of chromosome X mCAs, compared with individuals of African or Hispanic ancestry. Although further studies in diverse populations will be needed to replicate our findings, we report three loci associated with loss of chromosome X, associations between autosomal mCAs and rare variants in DCPS, ADM17, PPP1R16B and TET2 and ancestry-specific variants in ATM and MPL with mCAs in cis.
Collapse
Affiliation(s)
- Yasminka A Jakubek
- Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Ying Zhou
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jason Bacon
- Department of Computer Science, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Justin W Wong
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Zuhal Ozcan
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Kathleen Barnes
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington Seattle, Seattle, WA, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nancy Cox
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret F Doyle
- Department of Pathology and Laboratory Medicine, The University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua P Lewis
- Department of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Xiaolong Ma
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Taralynn M Mack
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kari North
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Susan Redline
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Aaron P Smith
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY, USA
| | - Margaret Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeong Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yun Li
- Department of Biostatistics, Department of Genetics, Department of Computer Science, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Pinkal Desai
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Paul Scheet
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA.
| |
Collapse
|
21
|
Tobias DK, Manning AK, Wessel J, Raghavan S, Westerman KE, Bick AG, Dicorpo D, Whitsel EA, Collins J, Correa A, Cupples LA, Dupuis J, Goodarzi MO, Guo X, Howard B, Lange LA, Liu S, Raffield LM, Reiner AP, Rich SS, Taylor KD, Tinker L, Wilson JG, Wu P, Carson AP, Vasan RS, Fornage M, Psaty BM, Kooperberg C, Rotter JI, Meigs J, Manson JE. Clonal Hematopoiesis of Indeterminate Potential (CHIP) and Incident Type 2 Diabetes Risk. Diabetes Care 2023; 46:1978-1985. [PMID: 37756531 PMCID: PMC10620536 DOI: 10.2337/dc23-0805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/07/2023] [Indexed: 09/29/2023]
Abstract
OBJECTIVE Clonal hematopoiesis of indeterminate potential (CHIP) is an aging-related accumulation of somatic mutations in hematopoietic stem cells, leading to clonal expansion. CHIP presence has been implicated in atherosclerotic coronary heart disease (CHD) and all-cause mortality, but its association with incident type 2 diabetes (T2D) is unknown. We hypothesized that CHIP is associated with elevated risk of T2D. RESEARCH DESIGN AND METHODS CHIP was derived from whole-genome sequencing of blood DNA in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) prospective cohorts. We performed analysis for 17,637 participants from six cohorts, without prior T2D, cardiovascular disease, or cancer. We evaluated baseline CHIP versus no CHIP prevalence with incident T2D, including associations with DNMT3A, TET2, ASXL1, JAK2, and TP53 variants. We estimated multivariable-adjusted hazard ratios (HRs) and 95% CIs with adjustment for age, sex, BMI, smoking, alcohol, education, self-reported race/ethnicity, and combined cohorts' estimates via fixed-effects meta-analysis. RESULTS Mean (SD) age was 63.4 (11.5) years, 76% were female, and CHIP prevalence was 6.0% (n = 1,055) at baseline. T2D was diagnosed in n = 2,467 over mean follow-up of 9.8 years. Participants with CHIP had 23% (CI 1.04, 1.45) higher risk of T2D than those with no CHIP. Specifically, higher risk was for TET2 (HR 1.48; CI 1.05, 2.08) and ASXL1 (HR 1.76; CI 1.03, 2.99) mutations; DNMT3A was nonsignificant (HR 1.15; CI 0.93, 1.43). Statistical power was limited for JAK2 and TP53 analyses. CONCLUSIONS CHIP was associated with higher incidence of T2D. CHIP mutations located on genes implicated in CHD and mortality were also related to T2D, suggesting shared aging-related pathology.
Collapse
Affiliation(s)
- Deirdre K. Tobias
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Nutrition Department, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Alisa K. Manning
- Broad Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA
| | - Jennifer Wessel
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Department of Medicine, School of Medicine, and Diabetes Translational Research Center, Indiana University, Indianapolis, IN
| | - Sridharan Raghavan
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, and Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Kenneth E. Westerman
- Broad Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Daniel Dicorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Eric A. Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jason Collins
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | | | - Leslie A. Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, and Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Simin Liu
- Center for Global Cardiometabolic Health, Brown University, Providence, RI
| | - Laura M. Raffield
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Kent D. Taylor
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Lesley Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - James G. Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Ramachandran S. Vasan
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
- University of Texas School of Public Health, San Antonio, TX
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - James Meigs
- Department of Medicine, Harvard Medical School, and Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - JoAnn E. Manson
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Epidemiology Department, Harvard T.H. Chan School of Public Health, Boston, MA
| | | |
Collapse
|
22
|
Liu X, Sun X, Zhang Y, Jiang W, Lai M, Wiggins KL, Raffield LM, Bielak LF, Zhao W, Pitsillides A, Haessler J, Zheng Y, Blackwell TW, Yao J, Guo X, Qian Y, Thyagarajan B, Pankratz N, Rich SS, Taylor KD, Peyser PA, Heckbert SR, Seshadri S, Boerwinkle E, Grove ML, Larson NB, Smith JA, Vasan RS, Fitzpatrick AL, Fornage M, Ding J, Carson AP, Abecasis G, Dupuis J, Reiner A, Kooperberg C, Hou L, Psaty BM, Wilson JG, Levy D, Rotter JI, Bis JC, Satizabal CL, Arking DE, Liu C. Association Between Whole Blood-Derived Mitochondrial DNA Copy Number, Low-Density Lipoprotein Cholesterol, and Cardiovascular Disease Risk. J Am Heart Assoc 2023; 12:e029090. [PMID: 37804200 PMCID: PMC10757530 DOI: 10.1161/jaha.122.029090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023]
Abstract
Background The relationship between mitochondrial DNA copy number (mtDNA CN) and cardiovascular disease remains elusive. Methods and Results We performed cross-sectional and prospective association analyses of blood-derived mtDNA CN and cardiovascular disease outcomes in 27 316 participants in 8 cohorts of multiple racial and ethnic groups with whole-genome sequencing. We also performed Mendelian randomization to explore causal relationships of mtDNA CN with coronary heart disease (CHD) and cardiometabolic risk factors (obesity, diabetes, hypertension, and hyperlipidemia). P<0.01 was used for significance. We validated most of the previously reported associations between mtDNA CN and cardiovascular disease outcomes. For example, 1-SD unit lower level of mtDNA CN was associated with 1.08 (95% CI, 1.04-1.12; P<0.001) times the hazard for developing incident CHD, adjusting for covariates. Mendelian randomization analyses showed no causal effect from a lower level of mtDNA CN to a higher CHD risk (β=0.091; P=0.11) or in the reverse direction (β=-0.012; P=0.076). Additional bidirectional Mendelian randomization analyses revealed that low-density lipoprotein cholesterol had a causal effect on mtDNA CN (β=-0.084; P<0.001), but the reverse direction was not significant (P=0.059). No causal associations were observed between mtDNA CN and obesity, diabetes, and hypertension, in either direction. Multivariable Mendelian randomization analyses showed no causal effect of CHD on mtDNA CN, controlling for low-density lipoprotein cholesterol level (P=0.52), whereas there was a strong direct causal effect of higher low-density lipoprotein cholesterol on lower mtDNA CN, adjusting for CHD status (β=-0.092; P<0.001). Conclusions Our findings indicate that high low-density lipoprotein cholesterol may underlie the complex relationships between mtDNA CN and vascular atherosclerosis.
Collapse
Affiliation(s)
- Xue Liu
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
| | - Xianbang Sun
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
| | - Yuankai Zhang
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
| | - Wenqing Jiang
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
| | - Meng Lai
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of MedicineUniversity of WashingtonSeattleWAUSA
| | - Laura M. Raffield
- Department of GeneticsUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMIUSA
| | - Wei Zhao
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMIUSA
- Survey Research Center, Institute for Social ResearchUniversity of MichiganAnn ArborMIUSA
| | | | - Jeffrey Haessler
- Fred Hutchinson Cancer Center, Division of Public Health ScienceSeattleWAUSA
| | - Yinan Zheng
- Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | | | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor‐UCLA Medical CenterTorranceCAUSA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor‐UCLA Medical CenterTorranceCAUSA
| | - Yong Qian
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of HealthBaltimoreMDUSA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and PathologyUniversity of MinnesotaMinneapolisMNUSA
| | - Nathan Pankratz
- Department of Computational PathologyUniversity of MinnesotaMinneapolisMNUSA
| | - Stephen S. Rich
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVAUSA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor‐UCLA Medical CenterTorranceCAUSA
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMIUSA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit and Department of EpidemiologyUniversity of WashingtonSeattleWAUSA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative DiseasesUniversity of Texas Health Science Center at San AntonioSan AntonioTXUSA
- Framingham Heart Study, National Heart, Lung, and Blood InstituteFraminghamMAUSA
- Department of NeurologyBoston University School of MedicineBostonMAUSA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental SciencesThe University of Texas Health Science Center at HoustonHoustonTXUSA
- Human Genome Sequencing Center, Baylor College of MedicineHoustonTXUSA
| | - Megan L. Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental SciencesThe University of Texas Health Science Center at HoustonHoustonTXUSA
| | - Nicholas B. Larson
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine and ScienceRochesterMNUSA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMIUSA
- Survey Research Center, Institute for Social ResearchUniversity of MichiganAnn ArborMIUSA
| | - Ramachandran S. Vasan
- Framingham Heart Study, National Heart, Lung, and Blood InstituteFraminghamMAUSA
- Sections of Preventive Medicine and Epidemiology, and Cardiovascular MedicineBoston University School of MedicineBostonMAUSA
| | - Annette L. Fitzpatrick
- Departments of Family Medicine, Epidemiology, and Global HealthUniversity of WashingtonSeattleWAUSA
| | - Myriam Fornage
- Center for Human GeneticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Jun Ding
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of HealthBaltimoreMDUSA
| | - April P. Carson
- Department of MedicineUniversity of Mississippi Medical CenterJacksonMSUSA
| | - Goncalo Abecasis
- TOPMed Informatics Research CenterUniversity of MichiganAnn ArborMIUSA
| | - Josée Dupuis
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global HealthMcGill University Faculty of Medicine and Health SciencesMontréalQuebecCanada
| | - Alexander Reiner
- Fred Hutchinson Cancer Center, Division of Public Health ScienceSeattleWAUSA
| | - Charles Kooperberg
- Fred Hutchinson Cancer Center, Division of Public Health ScienceSeattleWAUSA
| | - Lifang Hou
- Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of MedicineUniversity of WashingtonSeattleWAUSA
- Departments of Epidemiology, and Health Systems and Population HealthUniversity of WashingtonSeattleWAUSA
| | - James G. Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical CenterBostonMAUSA
| | - Daniel Levy
- Framingham Heart Study, National Heart, Lung, and Blood InstituteFraminghamMAUSA
- Population Sciences BranchNational Heart, Lung, and Blood Institute, National Institutes of HealthMDBethesdaUSA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor‐UCLA Medical CenterTorranceCAUSA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of MedicineUniversity of WashingtonSeattleWAUSA
| | | | - Claudia L. Satizabal
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative DiseasesUniversity of Texas Health Science Center at San AntonioSan AntonioTXUSA
- Framingham Heart Study, National Heart, Lung, and Blood InstituteFraminghamMAUSA
- Department of NeurologyBoston University School of MedicineBostonMAUSA
| | - Dan E. Arking
- McKusick‐Nathans InstituteDepartment of Genetic MedicineJohns Hopkins University School of MedicineMDBaltimoreUSA
| | - Chunyu Liu
- Department of Biostatistics, School of Public HealthBoston UniversityBostonMAUSA
- Framingham Heart Study, National Heart, Lung, and Blood InstituteFraminghamMAUSA
| |
Collapse
|
23
|
Hu X, Logan JG, Kwon Y, Lima JAC, Jacobs DR, Duprez D, Brumback L, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Blackwell TW, Papanicolaou G, Mitchell GF, Rich SS, Rotter JI, Van Den Berg DJ, Chirinos JA, Hughes TM, Garrett-Bakelman FE, Manichaikul A. Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA. Sci Rep 2023; 13:17680. [PMID: 37848499 PMCID: PMC10582077 DOI: 10.1038/s41598-023-44806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
Despite the prognostic value of arterial stiffness (AS) and pulsatile hemodynamics (PH) for cardiovascular morbidity and mortality, epigenetic modifications that contribute to AS/PH remain unknown. To gain a better understanding of the link between epigenetics (DNA methylation) and AS/PH, we examined the relationship of eight measures of AS/PH with CpG sites and co-methylated regions using multi-ancestry participants from Trans-Omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA) with sample sizes ranging from 438 to 874. Epigenome-wide association analysis identified one genome-wide significant CpG (cg20711926-CYP1B1) associated with aortic augmentation index (AIx). Follow-up analyses, including gene set enrichment analysis, expression quantitative trait methylation analysis, and functional enrichment analysis on differentially methylated positions and regions, further prioritized three CpGs and their annotated genes (cg23800023-ETS1, cg08426368-TGFB3, and cg17350632-HLA-DPB1) for AIx. Among these, ETS1 and TGFB3 have been previously prioritized as candidate genes. Furthermore, both ETS1 and HLA-DPB1 have significant tissue correlations between Whole Blood and Aorta in GTEx, which suggests ETS1 and HLA-DPB1 could be potential biomarkers in understanding pathophysiology of AS/PH. Overall, our findings support the possible role of epigenetic regulation via DNA methylation of specific genes associated with AIx as well as identifying potential targets for regulation of AS/PH.
Collapse
Affiliation(s)
- Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jeongok G Logan
- School of Nursing, University of Virginia, Charlottesville, VA, USA
| | - Younghoon Kwon
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joao A C Lima
- Department of Internal Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David R Jacobs
- Division of Epidemiology, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Daniel Duprez
- Cardiovascular Division, University of Minnesota, Minneapolis, MN, USA
| | - Lyndia Brumback
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Elaine Cornell
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke University, Durham, NC, USA
| | - Russell P Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - Thomas W Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - George Papanicolaou
- Epidemiology Branch, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David J Van Den Berg
- Department of Preventive Medicine and Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Julio A Chirinos
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy M Hughes
- Department of Internal Medicine - Section of Gerontology and Geriatric Medicine, and Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, Department of Medicine, University of Virginia, 1340 Jefferson Park Ave., Pinn hall 6054, Charlottesville, VA, 22908, USA.
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
| |
Collapse
|
24
|
Araujo DS, Nguyen C, Hu X, Mikhaylova AV, Gignoux C, Ardlie K, Taylor KD, Durda P, Liu Y, Papanicolaou G, Cho MH, Rich SS, Rotter JI, Im HK, Manichaikul A, Wheeler HE. Multivariate adaptive shrinkage improves cross-population transcriptome prediction and association studies in underrepresented populations. HGG Adv 2023; 4:100216. [PMID: 37869564 PMCID: PMC10589725 DOI: 10.1016/j.xhgg.2023.100216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 10/24/2023] Open
Abstract
Transcriptome prediction models built with data from European-descent individuals are less accurate when applied to different populations because of differences in linkage disequilibrium patterns and allele frequencies. We hypothesized that methods that leverage shared regulatory effects across different conditions, in this case, across different populations, may improve cross-population transcriptome prediction. To test this hypothesis, we made transcriptome prediction models for use in transcriptome-wide association studies (TWASs) using different methods (elastic net, joint-tissue imputation [JTI], matrix expression quantitative trait loci [Matrix eQTL], multivariate adaptive shrinkage in R [MASHR], and transcriptome-integrated genetic association resource [TIGAR]) and tested their out-of-sample transcriptome prediction accuracy in population-matched and cross-population scenarios. Additionally, to evaluate model applicability in TWASs, we integrated publicly available multiethnic genome-wide association study (GWAS) summary statistics from the Population Architecture using Genomics and Epidemiology (PAGE) study and Pan-ancestry genetic analysis of the UK Biobank (PanUKBB) with our developed transcriptome prediction models. In regard to transcriptome prediction accuracy, MASHR models performed better or the same as other methods in both population-matched and cross-population transcriptome predictions. Furthermore, in multiethnic TWASs, MASHR models yielded more discoveries that replicate in both PAGE and PanUKBB across all methods analyzed, including loci previously mapped in GWASs and loci previously not found in GWASs. Overall, our study demonstrates the importance of using methods that benefit from different populations' effect size estimates in order to improve TWASs for multiethnic or underrepresented populations.
Collapse
Affiliation(s)
- Daniel S. Araujo
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - Chris Nguyen
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Xiaowei Hu
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Anna V. Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chris Gignoux
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, UC Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Ardlie
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, the Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Colchester, VT 05446, USA
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - George Papanicolaou
- Epidemiology Branch, Division of Cardiovascular Sciences, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, the Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - NHLBI TOPMed Consortium
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, UC Denver Anschutz Medical Campus, Aurora, CO 80045, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, the Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Laboratory for Clinical Biochemistry Research, University of Vermont, Colchester, VT 05446, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Epidemiology Branch, Division of Cardiovascular Sciences, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Section of Genetic Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Heather E. Wheeler
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| |
Collapse
|
25
|
Li T, Ferraro N, Strober BJ, Aguet F, Kasela S, Arvanitis M, Ni B, Wiel L, Hershberg E, Ardlie K, Arking DE, Beer RL, Brody J, Blackwell TW, Clish C, Gabriel S, Gerszten R, Guo X, Gupta N, Johnson WC, Lappalainen T, Lin HJ, Liu Y, Nickerson DA, Papanicolaou G, Pritchard JK, Qasba P, Shojaie A, Smith J, Sotoodehnia N, Taylor KD, Tracy RP, Van Den Berg D, Wheeler MT, Rich SS, Rotter JI, Battle A, Montgomery SB. The functional impact of rare variation across the regulatory cascade. Cell Genom 2023; 3:100401. [PMID: 37868038 PMCID: PMC10589633 DOI: 10.1016/j.xgen.2023.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/08/2023] [Accepted: 08/10/2023] [Indexed: 10/24/2023]
Abstract
Each human genome has tens of thousands of rare genetic variants; however, identifying impactful rare variants remains a major challenge. We demonstrate how use of personal multi-omics can enable identification of impactful rare variants by using the Multi-Ethnic Study of Atherosclerosis, which included several hundred individuals, with whole-genome sequencing, transcriptomes, methylomes, and proteomes collected across two time points, 10 years apart. We evaluated each multi-omics phenotype's ability to separately and jointly inform functional rare variation. By combining expression and protein data, we observed rare stop variants 62 times and rare frameshift variants 216 times as frequently as controls, compared to 13-27 times as frequently for expression or protein effects alone. We extended a Bayesian hierarchical model, "Watershed," to prioritize specific rare variants underlying multi-omics signals across the regulatory cascade. With this approach, we identified rare variants that exhibited large effect sizes on multiple complex traits including height, schizophrenia, and Alzheimer's disease.
Collapse
Affiliation(s)
- Taibo Li
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole Ferraro
- Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA
| | - Benjamin J. Strober
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Harvard School of Public Health, Epidemiology Department, Boston, MA, USA
| | | | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Marios Arvanitis
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Division of Cardiology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Bohan Ni
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Laurens Wiel
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Dan E. Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca L. Beer
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Robert Gerszten
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - W. Craig Johnson
- Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Henry J. Lin
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - George Papanicolaou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Pankaj Qasba
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ali Shojaie
- Department of Biostatistics, University of Washington School of Public Health, Seattle, WA, USA
| | - Josh Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell P. Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - David Van Den Berg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matthew T. Wheeler
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Malone Center for Engineering of Healthcare, Johns Hopkins University, Baltimore, MD, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| |
Collapse
|
26
|
Leiser CL, Whitsel EA, Reiner A, Rich SS, Rotter JI, Taylor KD, Tracy RP, Kooperberg C, Smith AV, Manson JE, Mychaleckyj JC, Bick AG, Szpiro AA, Kaufman JD. Associations between Ambient Air Pollutants and Clonal Hematopoiesis of Indeterminate Potential. Cancer Epidemiol Biomarkers Prev 2023; 32:1470-1473. [PMID: 37466697 PMCID: PMC10592307 DOI: 10.1158/1055-9965.epi-23-0305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/31/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related somatic mutation associated with incident hematologic cancer. Environmental stressors which, like air pollution, generate oxidative stress at the cellular level, may induce somatic mutations and some mutations may provide a selection advantage for persistence and expansion of specific clones. METHODS We used data from the Multi-Ethnic Study of Atherosclerosis (MESA) N = 4,379 and the Women's Health Initiative (WHI) N = 7,701 to estimate cross-sectional associations between annual average air pollution concentrations at participant address the year before blood draw using validated spatiotemporal models. We used covariate-adjusted logistic regression to estimate risk of CHIP per interquartile range increases in particulate matter (PM2.5; 4 μg/m3) and nitrogen dioxide (NO2; 10 ppb) as ORs (95% confidence intervals). RESULTS Prevalence of CHIP at blood draw (variant allele fraction > 2%) was 4.4% and 8.7% in MESA and WHI, respectively. The most common CHIP driver mutation was in DNMT3A. Neither pollutant was associated with CHIP: ORMESA PM2.5 = 1.00 (0.68-1.45), ORMESA NO2 = 1.05 (0.69-1.61), ORWHI PM2.5 = 0.97 (0.86-1.09), ORWHI NO2 = 0.98 (0.88-1.10); or with DNMT3A-driven CHIP. CONCLUSIONS We did not find evidence that air pollution contributes to CHIP prevalence in two large observational cohorts. IMPACT This is the first study to estimate associations between air pollution and CHIP.
Collapse
Affiliation(s)
- Claire L Leiser
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Eric A. Whitsel
- Departments of Epidemiology and Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC
| | - Alexander Reiner
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Russel P Tracy
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - JoAnn E Manson
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | | | - Adam A Szpiro
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Joel D Kaufman
- Department of Epidemiology, University of Washington, Seattle, WA
- Department of Occupational and Environmental Health Sciences, Seattle, WA
| |
Collapse
|
27
|
Kavousi M, Bos MM, Barnes HJ, Lino Cardenas CL, Wong D, Lu H, Hodonsky CJ, Landsmeer LPL, Turner AW, Kho M, Hasbani NR, de Vries PS, Bowden DW, Chopade S, Deelen J, Benavente ED, Guo X, Hofer E, Hwang SJ, Lutz SM, Lyytikäinen LP, Slenders L, Smith AV, Stanislawski MA, van Setten J, Wong Q, Yanek LR, Becker DM, Beekman M, Budoff MJ, Feitosa MF, Finan C, Hilliard AT, Kardia SLR, Kovacic JC, Kral BG, Langefeld CD, Launer LJ, Malik S, Hoesein FAAM, Mokry M, Schmidt R, Smith JA, Taylor KD, Terry JG, van der Grond J, van Meurs J, Vliegenthart R, Xu J, Young KA, Zilhão NR, Zweiker R, Assimes TL, Becker LC, Bos D, Carr JJ, Cupples LA, de Kleijn DPV, de Winther M, den Ruijter HM, Fornage M, Freedman BI, Gudnason V, Hingorani AD, Hokanson JE, Ikram MA, Išgum I, Jacobs DR, Kähönen M, Lange LA, Lehtimäki T, Pasterkamp G, Raitakari OT, Schmidt H, Slagboom PE, Uitterlinden AG, Vernooij MW, Bis JC, Franceschini N, Psaty BM, Post WS, Rotter JI, Björkegren JLM, O'Donnell CJ, Bielak LF, Peyser PA, Malhotra R, van der Laan SW, Miller CL. Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification. Nat Genet 2023; 55:1651-1664. [PMID: 37770635 PMCID: PMC10601987 DOI: 10.1038/s41588-023-01518-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
Coronary artery calcification (CAC), a measure of subclinical atherosclerosis, predicts future symptomatic coronary artery disease (CAD). Identifying genetic risk factors for CAC may point to new therapeutic avenues for prevention. Currently, there are only four known risk loci for CAC identified from genome-wide association studies (GWAS) in the general population. Here we conducted the largest multi-ancestry GWAS meta-analysis of CAC to date, which comprised 26,909 individuals of European ancestry and 8,867 individuals of African ancestry. We identified 11 independent risk loci, of which eight were new for CAC and five had not been reported for CAD. These new CAC loci are related to bone mineralization, phosphate catabolism and hormone metabolic pathways. Several new loci harbor candidate causal genes supported by multiple lines of functional evidence and are regulators of smooth muscle cell-mediated calcification ex vivo and in vitro. Together, these findings help refine the genetic architecture of CAC and extend our understanding of the biological and potential druggable pathways underlying CAC.
Collapse
Affiliation(s)
- Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Maxime M Bos
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hanna J Barnes
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian L Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Doris Wong
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Haojie Lu
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Lennart P L Landsmeer
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Natalie R Hasbani
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Center at Houston, Houston, TX, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Center at Houston, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Sandesh Chopade
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
| | - Joris Deelen
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Edith Hofer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | | | - Sharon M Lutz
- Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lotte Slenders
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Icelandic Heart Association, Kopavogur, Iceland
| | - Maggie A Stanislawski
- Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica van Setten
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Diane M Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marian Beekman
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthew J Budoff
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Mary F Feitosa
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | | | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jason C Kovacic
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, University of NSW, Sydney, New South Wales, Australia
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Brian G Kral
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences and Data Science, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Shaista Malik
- Susan Samueli Integrative Health Institute, Department of Medicine, University of California Irvine, Irvine, CA, USA
| | | | - Michal Mokry
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - James G Terry
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeroen van der Grond
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Joyce van Meurs
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rozemarijn Vliegenthart
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jianzhao Xu
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado, Anschutz Medical Campus, Denver, CO, USA
| | | | - Robert Zweiker
- Department of Internal Medicine, Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Themistocles L Assimes
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel Bos
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - J Jeffrey Carr
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Menno de Winther
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences: Atherosclerosis and Ischemic syndromes, Amsterdam Infection and Immunity: Inflammatory diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, School of Public Health, University of Iceland, Reykjavik, Iceland
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
| | - John E Hokanson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ivana Išgum
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Biomedical Engineering and Physics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Helena Schmidt
- Gottfried Schatz Research Center (for Cell Signaling, Metabolism and Aging), Medical University of Graz, Graz, Austria
| | - P Eline Slagboom
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Vascular Surgery, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Integrated Cardio Metabolic Centre, Karolinska Institutet, Huddinge, Sweden
| | - Christopher J O'Donnell
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cardiology Section, Department of Medicine, Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Clint L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
28
|
Chen Y, Du X, Kuppa A, Feitosa MF, Bielak LF, O'Connell JR, Musani SK, Guo X, Kahali B, Chen VL, Smith AV, Ryan KA, Eirksdottir G, Allison MA, Bowden DW, Budoff MJ, Carr JJ, Chen YDI, Taylor KD, Oliveri A, Correa A, Crudup BF, Kardia SLR, Mosley TH, Norris JM, Terry JG, Rotter JI, Wagenknecht LE, Halligan BD, Young KA, Hokanson JE, Washko GR, Gudnason V, Province MA, Peyser PA, Palmer ND, Speliotes EK. Genome-wide association meta-analysis identifies 17 loci associated with nonalcoholic fatty liver disease. Nat Genet 2023; 55:1640-1650. [PMID: 37709864 PMCID: PMC10918428 DOI: 10.1038/s41588-023-01497-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is common and partially heritable and has no effective treatments. We carried out a genome-wide association study (GWAS) meta-analysis of imaging (n = 66,814) and diagnostic code (3,584 cases versus 621,081 controls) measured NAFLD across diverse ancestries. We identified NAFLD-associated variants at torsin family 1 member B (TOR1B), fat mass and obesity associated (FTO), cordon-bleu WH2 repeat protein like 1 (COBLL1)/growth factor receptor-bound protein 14 (GRB14), insulin receptor (INSR), sterol regulatory element-binding transcription factor 1 (SREBF1) and patatin-like phospholipase domain-containing protein 2 (PNPLA2), as well as validated NAFLD-associated variants at patatin-like phospholipase domain-containing protein 3 (PNPLA3), transmembrane 6 superfamily 2 (TM6SF2), apolipoprotein E (APOE), glucokinase regulator (GCKR), tribbles homolog 1 (TRIB1), glycerol-3-phosphate acyltransferase (GPAM), mitochondrial amidoxime-reducing component 1 (MARC1), microsomal triglyceride transfer protein large subunit (MTTP), alcohol dehydrogenase 1B (ADH1B), transmembrane channel like 4 (TMC4)/membrane-bound O-acyltransferase domain containing 7 (MBOAT7) and receptor-type tyrosine-protein phosphatase δ (PTPRD). Implicated genes highlight mitochondrial, cholesterol and de novo lipogenesis as causally contributing to NAFLD predisposition. Phenome-wide association study (PheWAS) analyses suggest at least seven subtypes of NAFLD. Individuals in the top 10% and 1% of genetic risk have a 2.5-fold to 6-fold increased risk of NAFLD, cirrhosis and hepatocellular carcinoma. These genetic variants identify subtypes of NAFLD, improve estimates of disease risk and can guide the development of targeted therapeutics.
Collapse
Affiliation(s)
- Yanhua Chen
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Xiaomeng Du
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Annapurna Kuppa
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey R O'Connell
- Department of Endocrinology, Diabetes and Nutrition, University of Maryland - Baltimore, Baltimore, MD, USA
| | - Solomon K Musani
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Bratati Kahali
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Centre for Brain Research, Indian Institute of Science, Bangalore, India
| | - Vincent L Chen
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen A Ryan
- Department of Endocrinology, Diabetes and Nutrition, University of Maryland - Baltimore, Baltimore, MD, USA
| | | | - Matthew A Allison
- Department of Family Medicine, University of California San Diego, San Diego, CA, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Matthew J Budoff
- Department of Internal Medicine, Lundquist Institute at Harbor-UCLA, Torrance, CA, USA
| | - John Jeffrey Carr
- Department of Radiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yii-Der I Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Antonino Oliveri
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Breland F Crudup
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Thomas H Mosley
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - James G Terry
- Department of Radiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Brian D Halligan
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - George R Washko
- Department of Medicine, Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, MA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Elizabeth K Speliotes
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
29
|
Yu Z, Fidler TP, Ruan Y, Vlasschaert C, Nakao T, Uddin MM, Mack T, Niroula A, Heimlich JB, Zekavat SM, Gibson CJ, Griffin GK, Wang Y, Peloso GM, Heard-Costa N, Levy D, Vasan RS, Aguet F, Ardlie KG, Taylor KD, Rich SS, Rotter JI, Libby P, Jaiswal S, Ebert BL, Bick AG, Tall AR, Natarajan P. Genetic modification of inflammation- and clonal hematopoiesis-associated cardiovascular risk. J Clin Invest 2023; 133:e168597. [PMID: 37498674 PMCID: PMC10503804 DOI: 10.1172/jci168597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is associated with an increased risk of cardiovascular diseases (CVDs), putatively via inflammasome activation. We pursued an inflammatory gene modifier scan for CHIP-associated CVD risk among 424,651 UK Biobank participants. We identified CHIP using whole-exome sequencing data of blood DNA and modeled as a composite, considering all driver genes together, as well as separately for common drivers (DNMT3A, TET2, ASXL1, and JAK2). We developed predicted gene expression scores for 26 inflammasome-related genes and assessed how they modify CHIP-associated CVD risk. We identified IL1RAP as a potential key molecule for CHIP-associated CVD risk across genes and increased AIM2 gene expression leading to heightened JAK2- and ASXL1-associated CVD risk. We show that CRISPR-induced Asxl1-mutated murine macrophages had a particularly heightened inflammatory response to AIM2 agonism, associated with an increased DNA damage response, as well as increased IL-10 secretion, mirroring a CVD-protective effect of IL10 expression in ASXL1 CHIP. Our study supports the role of inflammasomes in CHIP-associated CVD and provides evidence to support gene-specific strategies to address CHIP-associated CVD risk.
Collapse
Affiliation(s)
- Zhi Yu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Trevor P. Fidler
- Division of Molecular Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Yunfeng Ruan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Tetsushi Nakao
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Md Mesbah Uddin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Taralynn Mack
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Abhishek Niroula
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - J. Brett Heimlich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seyedeh M. Zekavat
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Ophthalmology, Massachusetts Eye and Ear Institute, Boston, Massachusetts, USA
| | - Christopher J. Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Gabriel K. Griffin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Nancy Heard-Costa
- Department of Medicine, School of Medicine, Boston University, Boston, Massachusetts, USA
- Framingham Heart Study, Framingham, Massachusetts, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, Massachusetts, USA
- Division of Intramural Research, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Ramachandran S. Vasan
- Department of Medicine, School of Medicine, Boston University, Boston, Massachusetts, USA
- Framingham Heart Study, Framingham, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Peter Libby
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Siddhartha Jaiswal
- Department of Pathology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin L. Ebert
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alexander G. Bick
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alan R. Tall
- Division of Molecular Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
30
|
Benson MD, Eisman AS, Tahir UA, Katz DH, Deng S, Ngo D, Robbins JM, Hofmann A, Shi X, Zheng S, Keyes M, Yu Z, Gao Y, Farrell L, Shen D, Chen ZZ, Cruz DE, Sims M, Correa A, Tracy RP, Durda P, Taylor KD, Liu Y, Johnson WC, Guo X, Yao J, Chen YDI, Manichaikul AW, Jain D, Yang Q, Bouchard C, Sarzynski MA, Rich SS, Rotter JI, Wang TJ, Wilson JG, Clish CB, Sarkar IN, Natarajan P, Gerszten RE. Protein-metabolite association studies identify novel proteomic determinants of metabolite levels in human plasma. Cell Metab 2023; 35:1646-1660.e3. [PMID: 37582364 DOI: 10.1016/j.cmet.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 04/12/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023]
Abstract
Although many novel gene-metabolite and gene-protein associations have been identified using high-throughput biochemical profiling, systematic studies that leverage human genetics to illuminate causal relationships between circulating proteins and metabolites are lacking. Here, we performed protein-metabolite association studies in 3,626 plasma samples from three human cohorts. We detected 171,800 significant protein-metabolite pairwise correlations between 1,265 proteins and 365 metabolites, including established relationships in metabolic and signaling pathways such as the protein thyroxine-binding globulin and the metabolite thyroxine, as well as thousands of new findings. In Mendelian randomization (MR) analyses, we identified putative causal protein-to-metabolite associations. We experimentally validated top MR associations in proof-of-concept plasma metabolomics studies in three murine knockout strains of key protein regulators. These analyses identified previously unrecognized associations between bioactive proteins and metabolites in human plasma. We provide publicly available data to be leveraged for studies in human metabolism and disease.
Collapse
Affiliation(s)
- Mark D Benson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Aaron S Eisman
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA; Center for Biomedical Informatics, Brown University, Providence, RI, USA
| | - Usman A Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Daniel H Katz
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Shuliang Deng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Debby Ngo
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jeremy M Robbins
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Alissa Hofmann
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Shuning Zheng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michelle Keyes
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Zhi Yu
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yan Gao
- University of Mississippi Medical Center, Jackson, MS, USA
| | - Laurie Farrell
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Dongxiao Shen
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Zsu-Zsu Chen
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Daniel E Cruz
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Mario Sims
- University of Mississippi Medical Center, Jackson, MS, USA
| | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, MS, USA
| | - Russell P Tracy
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Peter Durda
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yongmei Liu
- Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA; Division of Biostatistics and Epidemiology, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Claude Bouchard
- Human Genomic Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Mark A Sarzynski
- Department of Exercise Science, University of South Carolina, Columbia, Columbia, SC, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Thomas J Wang
- Department of Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Clary B Clish
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Indra Neil Sarkar
- Center for Biomedical Informatics, Brown University, Providence, RI, USA
| | - Pradeep Natarajan
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine Harvard Medical School, Boston, MA, USA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| |
Collapse
|
31
|
Shabani M, Wang M, Jenkins GD, Rotter JI, Rich SS, Batzler A, Taylor KD, Mychaleckyj JC, Liu D, Lima JAC, Pereira NL. Myocardial Fibrosis and Cardiomyopathy Risk: A Genetic Link in the MESA. Circ Heart Fail 2023; 16:e010262. [PMID: 37526028 PMCID: PMC10602591 DOI: 10.1161/circheartfailure.122.010262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/21/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Common genetic variants are associated with risk for hypertrophic cardiomyopathy and dilated cardiomyopathy and with left ventricular (LV) traits. Whether these variants are associated with myocardial fibrosis, an important pathophysiological mediator of cardiomyopathy, is unknown. METHODS Multi-Ethnic Study of Atherosclerosis participants with T1-mapping cardiac magnetic resonance imaging in-whom extracellular volume was assessed, and genotyping information was available were included (N=1255). Log extracellular volume (%) was regressed on 50 candidate single nucleotide polymorphisms (previously identified to be associated with hypertrophic cardiomyopathy, dilated cardiomyopathy, and LV traits) adjusting for age, sex, diabetes, blood pressure, and principal components of ancestry. Ancestry-specific results were pooled by fixed-effect meta-analyses. Gene knockdown experiments were performed in human cardiac fibroblasts. RESULTS The SMARCB1 rs2186370 intronic variant (minor allele frequency: 0.18 in White and 0.50 in Black participants), previously identified as a risk variant for dilated cardiomyopathy and hypertrophic cardiomyopathy, was significantly associated with increased extracellular volume (P=0.0002) after adjusting for confounding clinical variables. The SMARCB1 rs2070458 locus previously associated with increased LV wall thickness and mass was similarly significantly associated with increased extracellular volume (P=0.0002). The direction of effect was similar in all 4 ancestry groups, but the effect was strongest in Black participants. The variants are strong expression quantitative loci in human LV tissue and associated with genotype-dependent decreased expression of SMARCB1 (P=7.3×10-22). SMARCB1 knockdown in human cardiac fibroblasts resulted in increased TGF (transforming growth factor)-β1-mediated α-smooth muscle actin and collagen expression. CONCLUSIONS Common genetic variation in SMARCB1 previously associated with risk for cardiomyopathies and increased LV wall thickness is associated with increased cardiac magnetic resonance imaging-based myocardial fibrosis and increased TGF-β1 mediated myocardial fibrosis in vitro. Whether these findings suggest a pathophysiologic link between myocardial fibrosis and cardiomyopathy risk remains to be proven.
Collapse
Affiliation(s)
- Mahsima Shabani
- Division of Cardiology, Department of Medicine (M.S., J.A.C.L.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Min Wang
- Department of Molecular Pharmacology and Experimental Therapeutics (M.W., D.L., N.L.P.), Mayo Clinic, Rochester, MN
| | - Gregory D Jenkins
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (G.D.J., A.B.), Mayo Clinic, Rochester, MN
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA (J.I.R., K.D.T.)
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville (S.S.R., J.C.M.)
| | - Anthony Batzler
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (G.D.J., A.B.), Mayo Clinic, Rochester, MN
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA (J.I.R., K.D.T.)
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville (S.S.R., J.C.M.)
| | - Duan Liu
- Department of Molecular Pharmacology and Experimental Therapeutics (M.W., D.L., N.L.P.), Mayo Clinic, Rochester, MN
| | - Joao A C Lima
- Division of Cardiology, Department of Medicine (M.S., J.A.C.L.), Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Radiology and Radiological Science (J.A.C.L.), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Naveen L Pereira
- Department of Molecular Pharmacology and Experimental Therapeutics (M.W., D.L., N.L.P.), Mayo Clinic, Rochester, MN
- Department of Cardiovascular Medicine (N.L.P.), Mayo Clinic, Rochester, MN
| |
Collapse
|
32
|
Zhang X, Brody JA, Graff M, Highland HM, Chami N, Xu H, Wang Z, Ferrier K, Chittoor G, Josyula NS, Li X, Li Z, Allison MA, Becker DM, Bielak LF, Bis JC, Boorgula MP, Bowden DW, Broome JG, Buth EJ, Carlson CS, Chang KM, Chavan S, Chiu YF, Chuang LM, Conomos MP, DeMeo DL, Du M, Duggirala R, Eng C, Fohner AE, Freedman BI, Garrett ME, Guo X, Haiman C, Heavner BD, Hidalgo B, Hixson JE, Ho YL, Hobbs BD, Hu D, Hui Q, Hwu CM, Jackson RD, Jain D, Kalyani RR, Kardia SL, Kelly TN, Lange EM, LeNoir M, Li C, Marchand LL, McDonald MLN, McHugh CP, Morrison AC, Naseri T, O’Connell J, O’Donnell CJ, Palmer ND, Pankow JS, Perry JA, Peters U, Preuss MH, Rao D, Regan EA, Reupena SM, Roden DM, Rodriguez-Santana J, Sitlani CM, Smith JA, Tiwari HK, Vasan RS, Wang Z, Weeks DE, Wessel J, Wiggins KL, Wilkens LR, Wilson PW, Yanek LR, Yoneda ZT, Zhao W, Zöllner S, Arnett DK, Ashley-Koch AE, Barnes KC, Blangero J, Boerwinkle E, Burchard EG, Carson AP, Chasman DI, Chen YDI, Curran JE, Fornage M, Gordeuk VR, He J, Heckbert SR, Hou L, Irvin MR, Kooperberg C, Minster RL, Mitchell BD, Nouraie M, Psaty BM, Raffield LM, Reiner AP, Rich SS, Rotter JI, Shoemaker MB, Smith NL, Taylor KD, Telen MJ, Weiss ST, Zhang Y, Heard-Costa N, Sun YV, Lin X, Adrienne Cupples L, Lange LA, Liu CT, Loos RJ, North KE, Justice AE. WHOLE GENOME SEQUENCING ANALYSIS OF BODY MASS INDEX IDENTIFIES NOVEL AFRICAN ANCESTRY-SPECIFIC RISK ALLELE. medRxiv 2023:2023.08.21.23293271. [PMID: 37662265 PMCID: PMC10473809 DOI: 10.1101/2023.08.21.23293271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Obesity is a major public health crisis associated with high mortality rates. Previous genome-wide association studies (GWAS) investigating body mass index (BMI) have largely relied on imputed data from European individuals. This study leveraged whole-genome sequencing (WGS) data from 88,873 participants from the Trans-Omics for Precision Medicine (TOPMed) Program, of which 51% were of non-European population groups. We discovered 18 BMI-associated signals (P < 5 × 10-9). Notably, we identified and replicated a novel low frequency single nucleotide polymorphism (SNP) in MTMR3 that was common in individuals of African descent. Using a diverse study population, we further identified two novel secondary signals in known BMI loci and pinpointed two likely causal variants in the POC5 and DMD loci. Our work demonstrates the benefits of combining WGS and diverse cohorts in expanding current catalog of variants and genes confer risk for obesity, bringing us one step closer to personalized medicine.
Collapse
Affiliation(s)
- Xinruo Zhang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heather M. Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hanfei Xu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kendra Ferrier
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | | | | | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zilin Li
- Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Matthew A. Allison
- Department of Family Medicine, Division of Preventive Medicine, The University of California San Diego, La Jolla, CA, USA
| | - Diane M. Becker
- Department of Medicine, General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jai G. Broome
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Erin J. Buth
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kyong-Mi Chang
- The Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sameer Chavan
- Department of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Yen-Feng Chiu
- Institute of Population Health Sciences, National Health Research Institutes, Taipei, Taiwan
| | - Lee-Ming Chuang
- Department of Internal Medicine, Division of Metabolism/Endocrinology, National Taiwan University Hospital, Taipei, Taiwan
| | - Matthew P. Conomos
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Dawn L. DeMeo
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Margaret Du
- Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ravindranath Duggirala
- Life Sciences, College of Arts and Sciences, Texas A&M University-San Antonio, San Antonio, TX, USA
| | - Celeste Eng
- Department of Medicine, Lung Biology Center, University of California, San Francisco, San Francisco, CA, USA
| | - Alison E. Fohner
- Epidemiology, Institute of Public Health Genetics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Barry I. Freedman
- Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Melanie E. Garrett
- Department of Medicine, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Xiuqing Guo
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Chris Haiman
- Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Benjamin D. Heavner
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Bertha Hidalgo
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - James E. Hixson
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yuk-Lam Ho
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Brian D. Hobbs
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Donglei Hu
- Department of Medicine, Lung Biology Center, University of California, San Francisco, San Francisco, CA, USA
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Chii-Min Hwu
- Department of Medicine, Division of Endocrinology and Metabolism, Taipei Veterans General Hospital, Taipei, Taiwan, Taiwan
| | | | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Rita R. Kalyani
- Department of Medicine, Endocrinology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tanika N. Kelly
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Ethan M. Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Michael LeNoir
- Department of Pediatrics, Bay Area Pediatrics, Oakland, CA, USA
| | - Changwei Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Loic Le. Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Merry-Lynn N. McDonald
- Department of Medicine, Pulmonary, Allergy and Critical Care, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Caitlin P. McHugh
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Alanna C. Morrison
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | | | - Jeffrey O’Connell
- Department of Medicine, Program for Personalized and Genomic Medicine, University of Maryland, Baltimore, MD, USA
| | - Christopher J. O’Donnell
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - James A. Perry
- Department of Medicine, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D.C. Rao
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO, USA
| | - Elizabeth A. Regan
- Department of Medicine, Rheumatology, National Jewish Health, Denver, CO, USA
| | | | - Dan M. Roden
- Medicine, Pharmacology, and Biomedical Informatics, Clinical Pharmacology and Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Hemant K. Tiwari
- Department of Biostatistics, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | | | - Zeyuan Wang
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Daniel E. Weeks
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jennifer Wessel
- Department of Epidemiology, Indiana University, Indianapolis, IN, USA
- Department of Medicine, Indiana University, Indianapolis, IN, USA
- Diabaetes Translational Research Center, Indiana University, Indianapolis, IN, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Peter W.F. Wilson
- Atlanta VA Health Care System, Decatur, GA, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Lisa R. Yanek
- Department of Medicine, General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zachary T. Yoneda
- Department of Medicine, Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Sebastian Zöllner
- Department of Biostatistics, Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Donna K. Arnett
- Department of Epidemiology, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Allison E. Ashley-Koch
- Department of Medicine, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Kathleen C. Barnes
- Department of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA
| | - John Blangero
- Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Esteban G. Burchard
- Bioengineering and Therapeutic Sciences and Medicine, Lung Biology Center, University of California, San Francisco, San Francisco, CA, USA
| | - April P. Carson
- Department of Medicine, University of Mississippi, Jackson, MI, USA
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yii-Der Ida Chen
- Department of Medical Genetics, Genomic Outcomes, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Myriam Fornage
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Victor R. Gordeuk
- Department of Medicine, School of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Jiang He
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Lifang Hou
- Northwestern University, Chicago, IL, USA
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ryan L. Minster
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Braxton D. Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland, Baltimore, MD, USA
| | - Mehdi Nouraie
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Stephen S. Rich
- Public Health Science, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I. Rotter
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - M. Benjamin Shoemaker
- Department of Medicine, Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicholas L. Smith
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Office of Research and Development, Department of Veterans Affairs, Seattle, WA, USA
| | - Kent D. Taylor
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J. Telen
- Department of Medicine, Hematology, Duke University Medical Center, Durham, NC, USA
| | - Scott T. Weiss
- Department of Medicine, Channing Division of Network Medicine, Harvard Medical School, Boston, MA, USA
| | - Yingze Zhang
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nancy Heard-Costa
- Framingham Heart Study, School of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Yan V. Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Atlanta VA Health Care System, Decatur, GA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, Harvard University, Boston, MA, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | |
Collapse
|
33
|
Zhang D, Gao B, Feng Q, Manichaikul A, Peloso GM, Tracy RP, Durda P, Taylor KD, Liu Y, Johnson WC, Gabriel S, Gupta N, Smith JD, Aguet F, Ardlie KG, Blackwell TW, Gerszten RE, Rich SS, Rotter JI, Scott LJ, Zhou X, Lee S. Proteome-Wide Association Studies for Blood Lipids and Comparison with Transcriptome-Wide Association Studies. bioRxiv 2023:2023.08.17.553749. [PMID: 37662416 PMCID: PMC10473643 DOI: 10.1101/2023.08.17.553749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Blood lipid traits are treatable and heritable risk factors for heart disease, a leading cause of mortality worldwide. Although genome-wide association studies (GWAS) have discovered hundreds of variants associated with lipids in humans, most of the causal mechanisms of lipids remain unknown. To better understand the biological processes underlying lipid metabolism, we investigated the associations of plasma protein levels with total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL), and low-density lipoprotein cholesterol (LDL) in blood. We trained protein prediction models based on samples in the Multi-Ethnic Study of Atherosclerosis (MESA) and applied them to conduct proteome-wide association studies (PWAS) for lipids using the Global Lipids Genetics Consortium (GLGC) data. Of the 749 proteins tested, 42 were significantly associated with at least one lipid trait. Furthermore, we performed transcriptome-wide association studies (TWAS) for lipids using 9,714 gene expression prediction models trained on samples from peripheral blood mononuclear cells (PBMCs) in MESA and 49 tissues in the Genotype-Tissue Expression (GTEx) project. We found that although PWAS and TWAS can show different directions of associations in an individual gene, 40 out of 49 tissues showed a positive correlation between PWAS and TWAS signed p-values across all the genes, which suggests a high-level consistency between proteome-lipid associations and transcriptome-lipid associations.
Collapse
Affiliation(s)
- Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Boran Gao
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Qidi Feng
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine, and Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT USA
| | - Peter Durda
- Departments of Pathology & Laboratory Medicine, Larner College of Medicine, The University of Vermont, Burlington, VT USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Yongmei Liu
- Department of Medicine, Divisions of Cardiology and Neurology, Duke University Medical Center, Durham, NC USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA USA
| | - Stacey Gabriel
- Genomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Namrata Gupta
- Genomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Joshua D Smith
- Department of Genome Sciences, Human Genetics and Translational Genomics, The University of Washington, Seattle, WA, USA
| | - Francois Aguet
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Kristin G Ardlie
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Thomas W Blackwell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO USA
| | - Robert E Gerszten
- Genomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Xiang Zhou
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| |
Collapse
|
34
|
Georgakis MK, Malik R, Hasbani NR, Shakt G, Morrison AC, Tsao NL, Judy R, Mitchell BD, Xu H, Montasser ME, Do R, Kenny EE, Loos RJ, Terry JG, Carr JJ, Bis JC, Psaty BM, Longstreth WT, Young KA, Lutz SM, Cho MH, Broome J, Khan AT, Wang FF, Heard-Costa N, Seshadri S, Vasan RS, Palmer ND, Freedman BI, Bowden DW, Yanek LR, Kral BG, Becker LC, Peyser PA, Bielak LF, Ammous F, Carson AP, Hall ME, Raffield LM, Rich SS, Post WS, Tracy RP, Taylor KD, Guo X, Mahaney MC, Curran JE, Blangero J, Clarke SL, Haessler JW, Hu Y, Assimes TL, Kooperberg C, Damrauer SM, Rotter JI, de Vries PS, Dichgans M. Carriers of rare damaging CCR2 genetic variants are at lower risk of atherosclerotic disease. medRxiv 2023:2023.08.14.23294063. [PMID: 37645892 PMCID: PMC10462211 DOI: 10.1101/2023.08.14.23294063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Background The CCL2/CCR2 axis governs monocyte trafficking and recruitment to atherosclerotic lesions. Human genetic analyses and population-based studies support an association between circulating CCL2 levels and atherosclerosis. Still, it remains unknown whether pharmacological targeting of CCR2, the main CCL2 receptor, would provide protection against human atherosclerotic disease. Methods In whole-exome sequencing data from 454,775 UK Biobank participants (40-69 years), we identified predicted loss-of-function (LoF) or damaging missense (REVEL score >0.5) variants within the CCR2 gene. We prioritized variants associated with lower monocyte count (p<0.05) and tested associations with vascular risk factors and risk of atherosclerotic disease over a mean follow-up of 14 years. The results were replicated in a pooled cohort of three independent datasets (TOPMed, deCODE and Penn Medicine BioBank; total n=441,445) and the effect of the most frequent damaging variant was experimentally validated. Results A total of 45 predicted LoF or damaging missense variants were identified in the CCR2 gene, 4 of which were also significantly associated with lower monocyte count, but not with other white blood cell counts. Heterozygous carriers of these variants were at a lower risk of a combined atherosclerosis outcome, showed a lower burden of atherosclerosis across four vascular beds, and were at a lower lifetime risk of coronary artery disease and myocardial infarction. There was no evidence of association with vascular risk factors including LDL-cholesterol, blood pressure, glycemic status, or C-reactive protein. Using a cAMP assay, we found that cells transfected with the most frequent CCR2 damaging variant (3:46358273:T:A, M249K, 547 carriers, frequency: 0.14%) show a decrease in signaling in response to CCL2. The associations of the M249K variant with myocardial infarction were consistent across cohorts (ORUKB: 0.62 95%CI: 0.39-0.96; ORexternal: 0.64 95%CI: 0.34-1.19; ORpooled: 0.64 95%CI: 0.450.90). In a phenome-wide association study, we found no evidence for higher risk of common infections or mortality among carriers of damaging CCR2 variants. Conclusions Heterozygous carriers of damaging CCR2 variants have a lower burden of atherosclerosis and lower lifetime risk of myocardial infarction. In conjunction with previous evidence from experimental and epidemiological studies, our findings highlight the translational potential of CCR2-targeting as an atheroprotective approach.
Collapse
Affiliation(s)
- Marios K. Georgakis
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Natalie R. Hasbani
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Gabrielle Shakt
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Noah L. Tsao
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Renae Judy
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD
| | - Huichun Xu
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - May E. Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E. Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James G. Terry
- Department of Radiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Jeffrey Carr
- Department of Radiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - W. T. Longstreth
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora CO, USA
| | - Sharon M Lutz
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Alyna T. Khan
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Fei Fei Wang
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nancy Heard-Costa
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Boston University and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
| | - Sudha Seshadri
- Bigg’s Institute for Alzheimer’s Disease and neurodegenerative disorders, University of Texas Health Science Center, San Antonio, TX, USA
| | - Ramachandran S. Vasan
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Boston University and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Barry I. Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian G. Kral
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lewis C. Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Michael E. Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Wendy S. Post
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - Russel P. Tracy
- Departments of Pathology & Laboratory Medicine, and Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Michael C. Mahaney
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville TX USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville TX USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville TX USA
| | - Shoa L. Clarke
- Department of Medicine (Division of Cardiovascular Medicine), Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Jeffrey W. Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle WA 98109 USA
| | - Yao Hu
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle WA 98109 USA
| | - Themistocles L. Assimes
- Department of Medicine (Division of Cardiovascular Medicine), Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle WA 98109 USA
| | - Scott M. Damrauer
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jerome I. Rotter
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville TX USA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Munich, Germany
| |
Collapse
|
35
|
Brown BC, Wang C, Kasela S, Aguet F, Nachun DC, Taylor KD, Tracy RP, Durda P, Liu Y, Johnson WC, Van Den Berg D, Gupta N, Gabriel S, Smith JD, Gerzsten R, Clish C, Wong Q, Papanicolau G, Blackwell TW, Rotter JI, Rich SS, Barr RG, Ardlie KG, Knowles DA, Lappalainen T. Multiset correlation and factor analysis enables exploration of multi-omics data. Cell Genom 2023; 3:100359. [PMID: 37601969 PMCID: PMC10435377 DOI: 10.1016/j.xgen.2023.100359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/26/2023] [Accepted: 06/14/2023] [Indexed: 08/22/2023]
Abstract
Multi-omics datasets are becoming more common, necessitating better integration methods to realize their revolutionary potential. Here, we introduce multi-set correlation and factor analysis (MCFA), an unsupervised integration method tailored to the unique challenges of high-dimensional genomics data that enables fast inference of shared and private factors. We used MCFA to integrate methylation markers, protein expression, RNA expression, and metabolite levels in 614 diverse samples from the Trans-Omics for Precision Medicine/Multi-Ethnic Study of Atherosclerosis multi-omics pilot. Samples cluster strongly by ancestry in the shared space, even in the absence of genetic information, while private spaces frequently capture dataset-specific technical variation. Finally, we integrated genetic data by conducting a genome-wide association study (GWAS) of our inferred factors, observing that several factors are enriched for GWAS hits and trans-expression quantitative trait loci. Two of these factors appear to be related to metabolic disease. Our study provides a foundation and framework for further integrative analysis of ever larger multi-modal genomic datasets.
Collapse
Affiliation(s)
- Brielin C. Brown
- New York Genome Center, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
| | - Collin Wang
- New York Genome Center, New York, NY, USA
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - François Aguet
- Illumina Incorporated, San Francisco, CA, USA
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - Kent D. Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Yongmei Liu
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David Van Den Berg
- Department of Clinical Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Namrata Gupta
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Stacy Gabriel
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Joshua D. Smith
- Northwest Genomics Center, University of Washington, Seattle, WA, USA
| | - Robert Gerzsten
- Beth Israel Deaconess Medical Center, Division of Cardiovascular Medicine, Boston, MA, USA
| | - Clary Clish
- The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - George Papanicolau
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jerome I. Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R. Graham Barr
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | | | - David A. Knowles
- New York Genome Center, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
- Department of Computer Science, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
36
|
Ha ET, Taylor KD, Raffield LM, Briggs M, Yee A, Elemento O, Parikh M, Peterson SJ, Frishman W, Gerszten RE, Wilson JG, Kelsey K, Tahir UA, Reiner A, Auer P, Seeman T, Rich SS, Carson AP, Post WS, Rotter JI, Aronow WS. The Relationship of Duffy Gene Polymorphism, High Sensitivity C-Reactive Protein, and Long-term Outcomes. medRxiv 2023:2023.08.03.23293626. [PMID: 37609271 PMCID: PMC10441500 DOI: 10.1101/2023.08.03.23293626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Background Black adults have higher incidence of all-cause death and worse cardiovascular outcomes when compared to other populations. The Duffy chemokine receptor is not expressed in a large majority of Black adults and the clinical implications of this are unclear. Methods Here, we investigated the relationship of Duffy receptor status, high-sensitivity C-reactive protein (hs-CRP), and long-term cardiovascular outcomes in Black members of two contemporary, longitudinal cohort studies (the Jackson Heart Study and Multi-Ethnic Study of Atherosclerosis). Data on 4,307 Black participants (2,942 Duffy null and 1,365 Duffy receptor positive, as defined using Single Nucleotide Polymorphism (SNP) rs2814778) were included in this analysis. Results Duffy null was not independently associated with elevated levels of serum hs-CRP levels once conditioning for known CRP locus alleles in linkage disequilibrium with the Duffy gene. Duffy null status was not found to be independently associated with higher incidence of all-cause mortality or secondary outcomes after adjusting for possible confounders in Black participants. Conclusions These findings suggest that increased levels of hs-CRP found in Duffy null individuals is due to co-inheritance of CRP alleles known to influence circulating levels hs-CRP and that Duffy null status was not associated with worse adverse outcomes over the follow-up period in this cohort of well-balanced Black participants.
Collapse
|
37
|
van de Vegte YJ, Eppinga RN, van der Ende MY, Hagemeijer YP, Mahendran Y, Salfati E, Smith AV, Tan VY, Arking DE, Ntalla I, Appel EV, Schurmann C, Brody JA, Rueedi R, Polasek O, Sveinbjornsson G, Lecoeur C, Ladenvall C, Zhao JH, Isaacs A, Wang L, Luan J, Hwang SJ, Mononen N, Auro K, Jackson AU, Bielak LF, Zeng L, Shah N, Nethander M, Campbell A, Rankinen T, Pechlivanis S, Qi L, Zhao W, Rizzi F, Tanaka T, Robino A, Cocca M, Lange L, Müller-Nurasyid M, Roselli C, Zhang W, Kleber ME, Guo X, Lin HJ, Pavani F, Galesloot TE, Noordam R, Milaneschi Y, Schraut KE, den Hoed M, Degenhardt F, Trompet S, van den Berg ME, Pistis G, Tham YC, Weiss S, Sim XS, Li HL, van der Most PJ, Nolte IM, Lyytikäinen LP, Said MA, Witte DR, Iribarren C, Launer L, Ring SM, de Vries PS, Sever P, Linneberg A, Bottinger EP, Padmanabhan S, Psaty BM, Sotoodehnia N, Kolcic I, Arnar DO, Gudbjartsson DF, Holm H, Balkau B, Silva CT, Newton-Cheh CH, Nikus K, Salo P, Mohlke KL, Peyser PA, Schunkert H, Lorentzon M, Lahti J, Rao DC, Cornelis MC, Faul JD, Smith JA, Stolarz-Skrzypek K, Bandinelli S, Concas MP, Sinagra G, Meitinger T, Waldenberger M, Sinner MF, Strauch K, Delgado GE, Taylor KD, Yao J, Foco L, Melander O, de Graaf J, de Mutsert R, de Geus EJC, Johansson Å, Joshi PK, Lind L, Franke A, Macfarlane PW, Tarasov KV, Tan N, Felix SB, Tai ES, Quek DQ, Snieder H, Ormel J, Ingelsson M, Lindgren C, Morris AP, Raitakari OT, Hansen T, Assimes T, Gudnason V, Timpson NJ, Morrison AC, Munroe PB, Strachan DP, Grarup N, Loos RJF, Heckbert SR, Vollenweider P, Hayward C, Stefansson K, Froguel P, Groop L, Wareham NJ, van Duijn CM, Feitosa MF, O'Donnell CJ, Kähönen M, Perola M, Boehnke M, Kardia SLR, Erdmann J, Palmer CNA, Ohlsson C, Porteous DJ, Eriksson JG, Bouchard C, Moebus S, Kraft P, Weir DR, Cusi D, Ferrucci L, Ulivi S, Girotto G, Correa A, Kääb S, Peters A, Chambers JC, Kooner JS, März W, Rotter JI, Hicks AA, Smith JG, Kiemeney LALM, Mook-Kanamori DO, Penninx BWJH, Gyllensten U, Wilson JF, Burgess S, Sundström J, Lieb W, Jukema JW, Eijgelsheim M, Lakatta ELM, Cheng CY, Dörr M, Wong TY, Sabanayagam C, Oldehinkel AJ, Riese H, Lehtimäki T, Verweij N, van der Harst P. Genetic insights into resting heart rate and its role in cardiovascular disease. Nat Commun 2023; 14:4646. [PMID: 37532724 PMCID: PMC10397318 DOI: 10.1038/s41467-023-39521-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/16/2023] [Indexed: 08/04/2023] Open
Abstract
Resting heart rate is associated with cardiovascular diseases and mortality in observational and Mendelian randomization studies. The aims of this study are to extend the number of resting heart rate associated genetic variants and to obtain further insights in resting heart rate biology and its clinical consequences. A genome-wide meta-analysis of 100 studies in up to 835,465 individuals reveals 493 independent genetic variants in 352 loci, including 68 genetic variants outside previously identified resting heart rate associated loci. We prioritize 670 genes and in silico annotations point to their enrichment in cardiomyocytes and provide insights in their ECG signature. Two-sample Mendelian randomization analyses indicate that higher genetically predicted resting heart rate increases risk of dilated cardiomyopathy, but decreases risk of developing atrial fibrillation, ischemic stroke, and cardio-embolic stroke. We do not find evidence for a linear or non-linear genetic association between resting heart rate and all-cause mortality in contrast to our previous Mendelian randomization study. Systematic alteration of key differences between the current and previous Mendelian randomization study indicates that the most likely cause of the discrepancy between these studies arises from false positive findings in previous one-sample MR analyses caused by weak-instrument bias at lower P-value thresholds. The results extend our understanding of resting heart rate biology and give additional insights in its role in cardiovascular disease development.
Collapse
Affiliation(s)
- Yordi J van de Vegte
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
| | - Ruben N Eppinga
- Department of Cardiology, Isala Zwolle ziekenhuis, Zwolle, 8025 AB, the Netherlands
| | - M Yldau van der Ende
- Department of Cardiology, University medical Center Utrecht, Utrecht, 3584 Cx, the Netherlands
| | - Yanick P Hagemeijer
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
- Analytical Biochemistry, University of Groningen, Groningen, 9713 AV, the Netherlands
| | - Yuvaraj Mahendran
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Elias Salfati
- Department of Medicine, Stanford University School of Medicine, Stanford, 94305, USA
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI48109, USA
| | - Vanessa Y Tan
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, BS82BN, UK
- MRC Integrative Epidemiology, University of Bristol, Bristol, BS82BN, UK
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21215, USA
| | - Ioanna Ntalla
- Clinical Pharmacology and Precision Medicine, William Harvey Research Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Emil V Appel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | | | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Ozren Polasek
- Department of Public Health, University of Split School of Medicine, Split, 21000, Croatia
- Algebra LAB, Algebra University College, Zagreb, 10000, Croatia
| | | | - Cecile Lecoeur
- UMR 8199, University of Lille Nord de France, Lille, 59000, France
| | - Claes Ladenvall
- Clinial Genomics Uppsala, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, 75185, Sweden
- Lund University Diabetes Center, Department of Clinical Sciences, Lund University, Malmö, 20502, Sweden
| | - Jing Hua Zhao
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
| | - Aaron Isaacs
- CARIM School for Cardiovascular Diseases, Maastricht Centre for Systems Biology (MaCSBio), Department of Physiology, Maastricht University, Maastricht, 6229ER, Netherlands
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63108-2212, Campus Box 8506, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Shih-Jen Hwang
- Division of Intramural Research, National Heart Lung and Blood Institute, NIH, USA, Framingham, 1702, USA
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, FI-33014, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Kirsi Auro
- Department of Health, unit of genetics and biomarkers, , National Institute for Health and Welfare, Finland, Helsinki, FI-00290, Finland
- Department of molecular medicine, University of Helsinki, Helsinki, FI-00290, Finland
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Linyao Zeng
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, 80636, Germany
| | - Nabi Shah
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
- Pharmacogenetics Research Lab, Department of Pharmacy, COMSATS University Islamabad, Abbottabad, 22060, Pakistan
| | - Maria Nethander
- Sahlgrenska Osteoporosis Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Usher Institute for Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, 70808, USA
| | - Sonali Pechlivanis
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, 45122, Germany
| | - Lu Qi
- Department of Epidemiology, Tulane University, New Orleans, LA, 70112, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Federica Rizzi
- Unit of Biomedicine, Bio4Dreams-Business Nursery for Life Sciences, Milano, 20121, Italy
| | - Toshiko Tanaka
- Longitudinal Study Section, National Institute on Aging, Baltimore, 21224, USA
| | - Antonietta Robino
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
| | - Massimiliano Cocca
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
| | - Leslie Lange
- Medicine, University of Colorado Anschutz Medical Campus, Aurora, 80045, USA
| | - Martina Müller-Nurasyid
- IBE, Ludwig-Maximilians-University Munich, LMU Munich, Munich, 81377, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, 55101, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Carolina Roselli
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, 02142, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, 68167, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, 68163, Germany
| | - Xiuqing Guo
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Henry J Lin
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Francesca Pavani
- Institute for Biomedicine, Eurac Research, Bolzano, 39100, Italy
| | | | - Raymond Noordam
- Department of Internal Medicine, section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health, Amsterdam UMC, Amsterdam UMC, Vrije Universiteit, Amsterdam, Amsterdam, 1081 HL, the Netherlands
| | - Katharina E Schraut
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, Scotland, UK
| | - Marcel den Hoed
- The Beijer laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, Uppsala, 75237, Sweden
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, 24105, Germany
| | - Stella Trompet
- Department of Internal Medicine, section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, ZA, 2333, the Netherlands
| | - Marten E van den Berg
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, 3015GD, the Netherlands
| | - Giorgio Pistis
- Institute of Genetics and Biomedic Research (IRGB), Italian National Research Council (CNR), Monserrato, (CA), 9042, Italy
- Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, USA
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, 17475, Germany
| | - Xueling S Sim
- Saw Swee Hock School of Public Health, National University Health System and National University of Singapore, Singapore, 117549, Singapore
| | - Hengtong L Li
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, FI-33014, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB2 0SL, UK
| | - M Abdullah Said
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus C, 8000, Denmark
| | - Carlos Iribarren
- Division of Research, Kaiser Permenente of Northern California, Oakland, 94612, USA
- The Scripps Research Institute, La Jolla, 10550, USA
| | | | - Susan M Ring
- Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, BS82BN, UK
- MRC Integrative Epidemiology, University of Bristol, Bristol, BS82BN, UK
| | - Paul S de Vries
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Science Center at Houston, School of Public Health, Houston, 77030, USA
| | - Peter Sever
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, 2400, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
- Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Bruce M Psaty
- Departments of Medicine, Epidemiology and Health Systems and Population Health, University of Washington, Seattle, 98195, USA
| | - Nona Sotoodehnia
- Medicine and Epidemiology, University of Washington, Seattle, 98195, USA
| | - Ivana Kolcic
- Department of Public Health, University of Split School of Medicine, Split, 21000, Croatia
- Algebra LAB, Algebra University College, Zagreb, 10000, Croatia
| | - David O Arnar
- deCODE genetics / Amgen Inc., Reykjavik, 102, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, 101, Iceland
- Department of Medicine, Landspitali-The National University Hospital of Iceland, Reykjavik, 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics / Amgen Inc., Reykjavik, 102, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Hilma Holm
- deCODE genetics / Amgen Inc., Reykjavik, 102, Iceland
| | - Beverley Balkau
- Centre for Research in Epidemiology and Population Health, Institut national de la santé et de la recherche médicale, Villejuif, 94800, France
- UMRS 1018, University Versailles Saint-Quentin-en-Yvelines, Versailles, 78035, France
- UMRS 1018, University Paris Sud, Villejuif, 94807, France
| | - Claudia T Silva
- Genetic Epidemiology Unit, Dept. of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000CA, Netherlands
| | | | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, FI-33521, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Perttu Salo
- Department of Health, unit of genetics and biomarkers, , National Institute for Health and Welfare, Finland, Helsinki, FI-00290, Finland
- Department of molecular medicine, University of Helsinki, Helsinki, FI-00290, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, 80636, Germany
- Deutsches Zentrum für Herz- und Kreislauferkrankungen (DZHK), Partner Site Munich Heart Alliance, Munich, 80636, Germany
| | - Mattias Lorentzon
- Sahlgrenska Osteoporosis Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
- Region Västra Götaland, Geriatric Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Mölndal, 43180, Sweden
- Mary McKillop Institute for Health Research, Australian Catholic University, Melbourne, 3000, Australia
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, 00014, Finland
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University, St. Louis, MO, 63110, USA
| | | | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Katarzyna Stolarz-Skrzypek
- Department of Cardiology, Interventional Electrocardiology and Hypertension, Jagiellonian University Medical College, Kraków, 31-008, Poland
| | - Stefania Bandinelli
- Geriatric Unit, Unità sanitaria locale Toscana Centro, Florence, 50142, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
| | - Gianfranco Sinagra
- Cardiovascular Department, "Ospedali Riuniti and University of Trieste", Trieste, 34149, Italy
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, München, 81675, Germany
- Institute of Human Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, 80802, Germany
| | - Moritz F Sinner
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, 80802, Germany
- Department of Cardiology, University Hospital, LMU Munich, Munich, 81377, Germany
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, 55101, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
| | - Graciela E Delgado
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, 68167, Germany
| | - Kent D Taylor
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Jie Yao
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Luisa Foco
- Institute for Biomedicine, Eurac Research, Bolzano, 39100, Italy
| | - Olle Melander
- Department of Internal Medicine, Clinical Sciences, Lund University and Skåne University Hospital, Malmo, 221 85, Sweden
- Lund University Diabetes Center, Lund University, Malmö, 221 85, Sweden
| | | | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Eco J C de Geus
- Biological Psychology, EMGO+ Institute for Health and Care Research and Neuroscience Campus Amsterdam, VU University, Amsterdam, 1081 BT, the Netherlands
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 75108, Sweden
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, Scotland, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University Hospital, Uppsala, 75237, Sweden
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, 24105, Germany
| | - Peter W Macfarlane
- Institute of Health and Wellbeing, Faculty of Medicine, University of Glasgow, Glasgow, G12 0XH, UK
| | - Kirill V Tarasov
- Laboratory of Cardiovascular Sciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Nicholas Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Stephan B Felix
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | - E-Shyong Tai
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Debra Q Quek
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Johan Ormel
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Uppsala University, Uppsala, 75237, Sweden
| | - Cecilia Lindgren
- Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew P Morris
- Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, FI-20521, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, FI-20521, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, FI-20521, Finland
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Themistocles Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, 94305, USA
| | - Vilmundur Gudnason
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Icelandic Heart Association, Kopavogur, 201, Iceland
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School,, University of Bristol, Bristol, BS8 2BN, UK
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Science Center at Houston, School of Public Health, Houston, 77030, USA
| | - Patricia B Munroe
- Clinical Pharmacology and Precision Medicine, William Harvey Research Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Biomedical Research Centre, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Ruth J F Loos
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine Science, University of Copenhagen, Copenhagen Ø, 2100, Denmark
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
- The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, 98195, USA
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University hospital, Lausanne, 1015, Switzerland
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland, UK
| | - Kari Stefansson
- deCODE genetics / Amgen Inc., Reykjavik, 102, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Philippe Froguel
- Department of Metabolism, Imperial College London, London, W12 0HS, UK
- Inserm/CNRS UMR 1283/8199, Pasteur Institute of Lille, Lille University Hospital, EGID, Lille, 59000, France
- University of Lille, Lille, 59000, France
| | - Leif Groop
- Lund University Diabetes Center, Department of Clinical Sciences, Lund University, Malmö, 20502, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00290, Finland
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Dept. of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000CA, Netherlands
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63108-2212, Campus Box 8506, USA
| | - Christopher J O'Donnell
- Cardiology Section, VA Boston Healthcare System, Harvard Medical School, Boston, MA, 02132, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, FI-33521, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33521, Finland
| | - Markus Perola
- Department of Health, unit of genetics and biomarkers, , National Institute for Health and Welfare, Finland, Helsinki, FI-00290, Finland
- Department of molecular medicine, University of Helsinki, Helsinki, FI-00290, Finland
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Lübeck, 23562, Germany
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, DD1 9SY, UK
| | - Claes Ohlsson
- Sahlgrenska Osteoporosis Centre, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 41345, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Gothenburg, 41345, Sweden
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Johan G Eriksson
- Department of General practice and primary care, University of Helsinki, Helsinki, 00014, Finland
- Department of Obstetrics and Gynecology, National University of Singapore, Singapore, 119228, Singapore
- Public health Research Program, Folkhalsan Research Center, Helsinki, 000250, Finland
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, 70808, USA
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, 45122, Germany
- Centre for Urban Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, 45122, Germany
| | - Peter Kraft
- Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02112, USA
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Daniele Cusi
- Unit of Biomedicine, Bio4Dreams-Business Nursery for Life Sciences, Milano, 20121, Italy
- Institute of Biomedical Technologies, National Research Council of Italy, Segrate, (MI), 20090, Italy
| | - Luigi Ferrucci
- Longitudinal Study Section, National Institute on Aging, Baltimore, 21224, USA
| | - Sheila Ulivi
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
| | - Giorgia Girotto
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, 34137, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, 34149, Italy
| | - Adolfo Correa
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, 39216, USA
| | - Stefan Kääb
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, 80802, Germany
- Department of Cardiology, University Hospital, LMU Munich, Munich, 81377, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, 80802, Germany
- Chair of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, 81377, Germany
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, W12 0HS, UK
| | - Winfried März
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, 68167, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, 68161, Germany
| | - Jerome I Rotter
- Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Bolzano, 39100, Italy
| | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, 221 85, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, 221 84, Sweden
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, 413 45, Sweden
| | | | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health, Amsterdam UMC, Amsterdam UMC, Vrije Universiteit, Amsterdam, Amsterdam, 1081 HL, the Netherlands
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 75108, Sweden
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, Scotland, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Johan Sundström
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University Hospital, Uppsala, 75237, Sweden
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Kiel University, Kiel, 24105, Germany
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, ZA, 2333, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, ZA, 2333, the Netherlands
- Netherlands Heart Institute, Utrecht, 3511 EP, the Netherlands
| | - Mark Eijgelsheim
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, 3015GD, the Netherlands
- Department of Nephrology, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
| | - Edward L M Lakatta
- Laboratory of Cardiovascular Sciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Marcus Dörr
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857, Singapore
- Tsinghua Medicine, Tsinghua University, Beijing, 100084, China
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, 169856, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Harriette Riese
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, The Netherlands
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, FI-33014, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands.
- Department of Cardiology, University medical Center Utrecht, Utrecht, 3584 Cx, the Netherlands.
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9700RB, the Netherlands.
| |
Collapse
|
38
|
Ngo D, Pratte KA, Flexeder C, Petersen H, Dang H, Ma Y, Keyes MJ, Gao Y, Deng S, Peterson BD, Farrell LA, Bhambhani VM, Palacios C, Quadir J, Gillenwater L, Xu H, Emson C, Gieger C, Suhre K, Graumann J, Jain D, Conomos MP, Tracy RP, Guo X, Liu Y, Johnson WC, Cornell E, Durda P, Taylor KD, Papanicolaou GJ, Rich SS, Rotter JI, Rennard SI, Curtis JL, Woodruff PG, Comellas AP, Silverman EK, Crapo JD, Larson MG, Vasan RS, Wang TJ, Correa A, Sims M, Wilson JG, Gerszten RE, O’Connor GT, Barr RG, Couper D, Dupuis J, Manichaikul A, O’Neal WK, Tesfaigzi Y, Schulz H, Bowler RP. Systemic Markers of Lung Function and Forced Expiratory Volume in 1 Second Decline across Diverse Cohorts. Ann Am Thorac Soc 2023; 20:1124-1135. [PMID: 37351609 PMCID: PMC10405603 DOI: 10.1513/annalsats.202210-857oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airway obstruction and accelerated lung function decline. Our understanding of systemic protein biomarkers associated with COPD remains incomplete. Objectives: To determine what proteins and pathways are associated with impaired pulmonary function in a diverse population. Methods: We studied 6,722 participants across six cohort studies with both aptamer-based proteomic and spirometry data (4,566 predominantly White participants in a discovery analysis and 2,156 African American cohort participants in a validation). In linear regression models, we examined protein associations with baseline forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity (FVC). In linear mixed effects models, we investigated the associations of baseline protein levels with rate of FEV1 decline (ml/yr) in 2,777 participants with up to 7 years of follow-up spirometry. Results: We identified 254 proteins associated with FEV1 in our discovery analyses, with 80 proteins validated in the Jackson Heart Study. Novel validated protein associations include kallistatin serine protease inhibitor, growth differentiation factor 2, and tumor necrosis factor-like weak inducer of apoptosis (discovery β = 0.0561, Q = 4.05 × 10-10; β = 0.0421, Q = 1.12 × 10-3; and β = 0.0358, Q = 1.67 × 10-3, respectively). In longitudinal analyses within cohorts with follow-up spirometry, we identified 15 proteins associated with FEV1 decline (Q < 0.05), including elafin leukocyte elastase inhibitor and mucin-associated TFF2 (trefoil factor 2; β = -4.3 ml/yr, Q = 0.049; β = -6.1 ml/yr, Q = 0.032, respectively). Pathways and processes highlighted by our study include aberrant extracellular matrix remodeling, enhanced innate immune response, dysregulation of angiogenesis, and coagulation. Conclusions: In this study, we identify and validate novel biomarkers and pathways associated with lung function traits in a racially diverse population. In addition, we identify novel protein markers associated with FEV1 decline. Several protein findings are supported by previously reported genetic signals, highlighting the plausibility of certain biologic pathways. These novel proteins might represent markers for risk stratification, as well as novel molecular targets for treatment of COPD.
Collapse
Affiliation(s)
- Debby Ngo
- Cardiovascular Research Institute
- Division of Pulmonary, Critical Care, and Sleep Medicine, and
| | | | - Claudia Flexeder
- Institute of Epidemiology and
- Comprehensive Pneumology Center Munich (CPC-M) as member of the German Center for Lung Research (DZL), Munich, Germany
- Institute and Clinic for Occupational, Social, and Environmental Medicine, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Hans Petersen
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Hong Dang
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yanlin Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Yan Gao
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi; and
- Institute and Clinic for Occupational, Social, and Environmental Medicine, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | | | | | | | | | | | | | | | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Claire Emson
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Christian Gieger
- Institute of Epidemiology and
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine Qatar, Education City, Doha, Qatar
| | | | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Matthew P. Conomos
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA (University of California, Los Angeles) Medical Center, Torrance, California
| | - Yongmei Liu
- Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Elaine Cornell
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA (University of California, Los Angeles) Medical Center, Torrance, California
| | - George J. Papanicolaou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA (University of California, Los Angeles) Medical Center, Torrance, California
| | - Steven I. Rennard
- Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Prescott G. Woodruff
- Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | | | | | - Martin G. Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
| | - Ramachandran S. Vasan
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Division of Preventive Medicine and
- Division of Cardiology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Thomas J. Wang
- Department of Medicine, UT (University of Texas) Southwestern Medical Center, Dallas, Texas
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, and
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi; and
| | - Mario Sims
- Jackson Heart Study, Department of Medicine, and
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi; and
| | - James G. Wilson
- Cardiovascular Research Institute
- Jackson Heart Study, Department of Medicine, and
| | - Robert E. Gerszten
- Cardiovascular Research Institute
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - George T. O’Connor
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Pulmonary Center, Department of Medicine, Boston University, Boston, Massachusetts
| | - R. Graham Barr
- Department of Medicine and
- Department of Epidemiology, Columbia University, New York, New York
| | - David Couper
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Wanda K. O’Neal
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yohannes Tesfaigzi
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Holger Schulz
- Institute of Epidemiology and
- Comprehensive Pneumology Center Munich (CPC-M) as member of the German Center for Lung Research (DZL), Munich, Germany
| | | |
Collapse
|
39
|
Kwak SH, Hernandez-Cancela RB, DiCorpo DA, Condon DE, Merino J, Wu P, Brody JA, Yao J, Guo X, Ahmadizar F, Meyer M, Sincan M, Mercader JM, Lee S, Haessler J, Vy HMT, Lin Z, Armstrong ND, Gu S, Tsao NL, Lange LA, Wang N, Wiggins KL, Trompet S, Liu S, Loos RJ, Judy R, Schroeder PH, Hasbani NR, Bos MM, Morrison AC, Jackson RD, Reiner AP, Manson JE, Chaudhary NS, Carmichael LK, Chen YDI, Taylor KD, Ghanbari M, van Meurs J, Pitsillides AN, Psaty BM, Noordam R, Do R, Park KS, Jukema JW, Kavousi M, Correa A, Rich SS, Damrauer SM, Hajek C, Cho NH, Irvin MR, Pankow JS, Nadkarni GN, Sladek R, Goodarzi MO, Florez JC, Chasman DI, Heckbert SR, Kooperberg C, Dupuis J, Malhotra R, de Vries PS, Liu CT, Rotter JI, Meigs JB. Time-to-Event Genome-Wide Association Study for Incident Cardiovascular Disease in People with Type 2 Diabetes Mellitus. medRxiv 2023:2023.07.25.23293180. [PMID: 37546893 PMCID: PMC10402212 DOI: 10.1101/2023.07.25.23293180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
BACKGROUND Type 2 diabetes mellitus (T2D) confers a two- to three-fold increased risk of cardiovascular disease (CVD). However, the mechanisms underlying increased CVD risk among people with T2D are only partially understood. We hypothesized that a genetic association study among people with T2D at risk for developing incident cardiovascular complications could provide insights into molecular genetic aspects underlying CVD. METHODS From 16 studies of the Cohorts for Heart & Aging Research in Genomic Epidemiology (CHARGE) Consortium, we conducted a multi-ancestry time-to-event genome-wide association study (GWAS) for incident CVD among people with T2D using Cox proportional hazards models. Incident CVD was defined based on a composite of coronary artery disease (CAD), stroke, and cardiovascular death that occurred at least one year after the diagnosis of T2D. Cohort-level estimated effect sizes were combined using inverse variance weighted fixed effects meta-analysis. We also tested 204 known CAD variants for association with incident CVD among patients with T2D. RESULTS A total of 49,230 participants with T2D were included in the analyses (31,118 European ancestries and 18,112 non-European ancestries) which consisted of 8,956 incident CVD cases over a range of mean follow-up duration between 3.2 and 33.7 years (event rate 18.2%). We identified three novel, distinct genetic loci for incident CVD among individuals with T2D that reached the threshold for genome-wide significance (P<5.0×10-8): rs147138607 (intergenic variant between CACNA1E and ZNF648) with a hazard ratio (HR) 1.23, 95% confidence interval (CI) 1.15 - 1.32, P=3.6×10-9, rs11444867 (intergenic variant near HS3ST1) with HR 1.89, 95% CI 1.52 - 2.35, P=9.9×10-9, and rs335407 (intergenic variant between TFB1M and NOX3) HR 1.25, 95% CI 1.16 - 1.35, P=1.5×10-8. Among 204 known CAD loci, 32 were associated with incident CVD in people with T2D with P<0.05, and 5 were significant after Bonferroni correction (P<0.00024, 0.05/204). A polygenic score of these 204 variants was significantly associated with incident CVD with HR 1.14 (95% CI 1.12 - 1.16) per 1 standard deviation increase (P=1.0×10-16). CONCLUSIONS The data point to novel and known genomic regions associated with incident CVD among individuals with T2D.
Collapse
Affiliation(s)
- Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | | | - Daniel A DiCorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | | | - Jordi Merino
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Jie Yao
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Fariba Ahmadizar
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Data Science and Biostatistics, Julius Global Health, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mariah Meyer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Murat Sincan
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Josep M. Mercader
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Sujin Lee
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Ha My T. Vy
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zhaotong Lin
- Department of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Nicole D. Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL
| | - Shaopeng Gu
- Department of Internal Medicine, Sanford Health, Sioux Falls, SD
| | - Noah L. Tsao
- Corporal Michael Crescenz VA Medical Center, and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
| | - Leslie A. Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ningyuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Simin Liu
- Department of Epidemiology, Brown University, Providence, RI
| | - Ruth J.F. Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Renae Judy
- Corporal Michael Crescenz VA Medical Center, and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
| | - Philip H. Schroeder
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Natalie R. Hasbani
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Maxime M. Bos
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Rebecca D. Jackson
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, Ohio State University, Columbus, OH
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Ninad S. Chaudhary
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL
| | | | - Yii-Der Ida Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Kent D. Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Joyce van Meurs
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Ron Do
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- The Netherlands Heart Institute, Utrecht, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Scott M. Damrauer
- Corporal Michael Crescenz VA Medical Center, and Department of Surgery, Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, Perelman School of Medicine, Philadelphia, PA
| | - Catherine Hajek
- Department of Internal Medicine, Sanford Health, Sioux Falls, SD
| | - Nam H. Cho
- Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Korea
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL
| | - James S. Pankow
- Department of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Girish N. Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Robert Sladek
- Department of Medicine and Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center
| | - Jose C. Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Daniel I. Chasman
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division of the Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Jerome I. Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Science, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - James B. Meigs
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Department of General Internal Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, MA
| |
Collapse
|
40
|
Ji Y, Temprano-Sagrera G, Holle LA, Bebo A, Brody JA, Le NQ, Kangro K, Brown MR, Martinez-Perez A, Sitlani CM, Suchon P, Kleber ME, Emmert DB, Ozel AB, Dobson DA, Tang W, Llobet D, Tracy RP, Deleuze JF, Delgado GE, Gögele M, Wiggins KL, Souto JC, Pankow JS, Taylor KD, Trégouët DA, Moissl AP, Fuchsberger C, Rosendaal FR, Morrison AC, Soria JM, Cushman M, Morange PE, März W, Hicks AA, Desch KC, Johnson AD, de Vries PS, Wolberg AS, Smith NL, Sabater-Lleal M. Antithrombin, Protein C, and Protein S: Genome and Transcriptome-Wide Association Studies Identify 7 Novel Loci Regulating Plasma Levels. Arterioscler Thromb Vasc Biol 2023; 43:e254-e269. [PMID: 37128921 PMCID: PMC10330350 DOI: 10.1161/atvbaha.122.318213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Antithrombin, PC (protein C), and PS (protein S) are circulating natural anticoagulant proteins that regulate hemostasis and of which partial deficiencies are causes of venous thromboembolism. Previous genetic association studies involving antithrombin, PC, and PS were limited by modest sample sizes or by being restricted to candidate genes. In the setting of the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, we meta-analyzed across ancestries the results from 10 genome-wide association studies of plasma levels of antithrombin, PC, PS free, and PS total. METHODS Study participants were of European and African ancestries, and genotype data were imputed to TOPMed, a dense multiancestry reference panel. Each of the 10 studies conducted a genome-wide association studies for each phenotype and summary results were meta-analyzed, stratified by ancestry. Analysis of antithrombin included 25 243 European ancestry and 2688 African ancestry participants, PC analysis included 16 597 European ancestry and 2688 African ancestry participants, PSF and PST analysis included 4113 and 6409 European ancestry participants. We also conducted transcriptome-wide association analyses and multiphenotype analysis to discover additional associations. Novel genome-wide association studies and transcriptome-wide association analyses findings were validated by in vitro functional experiments. Mendelian randomization was performed to assess the causal relationship between these proteins and cardiovascular outcomes. RESULTS Genome-wide association studies meta-analyses identified 4 newly associated loci: 3 with antithrombin levels (GCKR, BAZ1B, and HP-TXNL4B) and 1 with PS levels (ORM1-ORM2). transcriptome-wide association analyses identified 3 newly associated genes: 1 with antithrombin level (FCGRT), 1 with PC (GOLM2), and 1 with PS (MYL7). In addition, we replicated 7 independent loci reported in previous studies. Functional experiments provided evidence for the involvement of GCKR, SNX17, and HP genes in antithrombin regulation. CONCLUSIONS The use of larger sample sizes, diverse populations, and a denser imputation reference panel allowed the detection of 7 novel genomic loci associated with plasma antithrombin, PC, and PS levels.
Collapse
Affiliation(s)
- Yuekai Ji
- Cardiovascular Division, Department of Medicine, University of Minnesota, MN, USA
| | - Gerard Temprano-Sagrera
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Lori A Holle
- Department of Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, NC, USA
| | - Allison Bebo
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
| | | | - Ngoc-Quynh Le
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Kadri Kangro
- Department of Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, NC, USA
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
| | - Angel Martinez-Perez
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, WA, USA
| | - Pierre Suchon
- C2VN, INSERM, INRAE, Aix Marseille Univ, France
- Laboratory of Haematology, La Timone Hospital, France
| | - Marcus E Kleber
- SYNLAB MVZ für Humangenetik Mannheim, Germany
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Germany
| | - David B Emmert
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Italy
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, C.S. Mott Children’s Hospital, MI, USA
| | - Dre’Von A Dobson
- Department of Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, NC, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN, USA
| | - Dolors Llobet
- Unit of Thrombosis and Hemostasis, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, VT, USA
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, CEA, France
- Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, France
- Laboratory of Excellence on Medical Genomics (GenMed), France
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Germany
| | - Martin Gögele
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Italy
| | | | - Juan Carlos Souto
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
- Unit of Thrombosis and Hemostasis, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, CA, USA
| | - David-Alexandre Trégouët
- Laboratory of Excellence on Medical Genomics (GenMed), France
- INSERM UMR 1219, Bordeaux Population Health Research Center, France
| | - Angela P Moissl
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Germany
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Germany
- Competence Cluster for Nutrition and Cardiovascular Health(nutriCARD) Halle-Jena-Leipzig, Germany
| | - Christian Fuchsberger
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Italy
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, the Netherlands
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
| | - Jose Manuel Soria
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
| | - Mary Cushman
- Larner College of Medicine, University of Vermont, VT, USA
| | - Pierre-Emmanuel Morange
- C2VN, INSERM, INRAE, Aix Marseille Univ, France
- Laboratory of Haematology, La Timone Hospital, France
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, Germany
| | - Andrew A Hicks
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Italy
| | - Karl C Desch
- Department of Pediatrics, University of Michigan, C.S. Mott Children’s Hospital, MI, USA
| | - Andrew D Johnson
- National Heart Lung and Blood Institute, Division of Intramural Research, Population Sciences Branch, The Framingham Heart Study, MA, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, TX, USA
| | | | | | - Alisa S Wolberg
- Department of Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, NC, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, WA, USA
| | - Maria Sabater-Lleal
- Unit of genomics of Complex Disease, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, Sweden
| |
Collapse
|
41
|
Kasela S, Aguet F, Kim-Hellmuth S, Brown BC, Nachun DC, Tracy RP, Durda P, Liu Y, Taylor KD, Craig Johnson W, Berg DVD, Gabriel S, Gupta N, Smith JD, Blackwell TW, Rotter JI, Ardlie KG, Manichaikul A, Rich SS, Graham Barr R, Lappalainen T. Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects. bioRxiv 2023:2023.06.26.546528. [PMID: 37425716 PMCID: PMC10326995 DOI: 10.1101/2023.06.26.546528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Bulk tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, while context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs (iQTLs) for cell type, age, and other phenotypic variables in multi-omic, longitudinal data from blood of individuals of diverse ancestries. By modeling the interaction between genotype and estimated cell type proportions, we demonstrate that cell type iQTLs could be considered as proxies for cell type-specific QTL effects. The interpretation of age iQTLs, however, warrants caution as the moderation effect of age on the genotype and molecular phenotype association may be mediated by changes in cell type composition. Finally, we show that cell type iQTLs contribute to cell type-specific enrichment of diseases that, in combination with additional functional data, may guide future functional studies. Overall, this study highlights iQTLs to gain insights into the context-specificity of regulatory effects.
Collapse
Affiliation(s)
- Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Sarah Kim-Hellmuth
- New York Genome Center, New York, NY, USA
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
- Computational Health Center, Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Brielin C. Brown
- New York Genome Center, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
| | | | - Russell P. Tracy
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Peter Durda
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Yongmei Liu
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kent D. Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David Van Den Berg
- Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua D. Smith
- Northwest Genomic Center, University of Washington, Seattle, WA, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jerome I. Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Ani Manichaikul
- Center for Public health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen S. Rich
- Center for Public health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R. Graham Barr
- Epidemiology and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
42
|
Williamson A, Norris DM, Yin X, Broadaway KA, Moxley AH, Vadlamudi S, Wilson EP, Jackson AU, Ahuja V, Andersen MK, Arzumanyan Z, Bonnycastle LL, Bornstein SR, Bretschneider MP, Buchanan TA, Chang YC, Chuang LM, Chung RH, Clausen TD, Damm P, Delgado GE, de Mello VD, Dupuis J, Dwivedi OP, Erdos MR, Fernandes Silva L, Frayling TM, Gieger C, Goodarzi MO, Guo X, Gustafsson S, Hakaste L, Hammar U, Hatem G, Herrmann S, Højlund K, Horn K, Hsueh WA, Hung YJ, Hwu CM, Jonsson A, Kårhus LL, Kleber ME, Kovacs P, Lakka TA, Lauzon M, Lee IT, Lindgren CM, Lindström J, Linneberg A, Liu CT, Luan J, Aly DM, Mathiesen E, Moissl AP, Morris AP, Narisu N, Perakakis N, Peters A, Prasad RB, Rodionov RN, Roll K, Rundsten CF, Sarnowski C, Savonen K, Scholz M, Sharma S, Stinson SE, Suleman S, Tan J, Taylor KD, Uusitupa M, Vistisen D, Witte DR, Walther R, Wu P, Xiang AH, Zethelius B, Ahlqvist E, Bergman RN, Chen YDI, Collins FS, Fall T, Florez JC, Fritsche A, Grallert H, Groop L, Hansen T, Koistinen HA, Komulainen P, Laakso M, Lind L, Loeffler M, März W, Meigs JB, Raffel LJ, Rauramaa R, Rotter JI, Schwarz PEH, Stumvoll M, Sundström J, Tönjes A, Tuomi T, Tuomilehto J, Wagner R, Barroso I, Walker M, Grarup N, Boehnke M, Wareham NJ, Mohlke KL, Wheeler E, O'Rahilly S, Fazakerley DJ, Langenberg C. Genome-wide association study and functional characterization identifies candidate genes for insulin-stimulated glucose uptake. Nat Genet 2023; 55:973-983. [PMID: 37291194 PMCID: PMC7614755 DOI: 10.1038/s41588-023-01408-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/26/2023] [Indexed: 06/10/2023]
Abstract
Distinct tissue-specific mechanisms mediate insulin action in fasting and postprandial states. Previous genetic studies have largely focused on insulin resistance in the fasting state, where hepatic insulin action dominates. Here we studied genetic variants influencing insulin levels measured 2 h after a glucose challenge in >55,000 participants from three ancestry groups. We identified ten new loci (P < 5 × 10-8) not previously associated with postchallenge insulin resistance, eight of which were shown to share their genetic architecture with type 2 diabetes in colocalization analyses. We investigated candidate genes at a subset of associated loci in cultured cells and identified nine candidate genes newly implicated in the expression or trafficking of GLUT4, the key glucose transporter in postprandial glucose uptake in muscle and fat. By focusing on postprandial insulin resistance, we highlighted the mechanisms of action at type 2 diabetes loci that are not adequately captured by studies of fasting glycemic traits.
Collapse
Affiliation(s)
- Alice Williamson
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Metabolic Research Laboratories Wellcome Trust-MRC Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK
| | - Dougall M Norris
- Metabolic Research Laboratories Wellcome Trust-MRC Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK
| | - Xianyong Yin
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - K Alaine Broadaway
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Anne H Moxley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | | | - Emma P Wilson
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Anne U Jackson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Vasudha Ahuja
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mette K Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zorayr Arzumanyan
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lori L Bonnycastle
- Center for Precision Health Research National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stefan R Bornstein
- Department of Internal Medicine III, Metabolic and Vascular Medicine, Medical Faculty Carl Gustav Carus, Dresden, Germany
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Maxi P Bretschneider
- Department of Internal Medicine III, Metabolic and Vascular Medicine, Medical Faculty Carl Gustav Carus, Dresden, Germany
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Thomas A Buchanan
- Department of Medicine, Division of Endocrinology and Diabetes, Keck School of Medicine USC, Los Angeles, CA, USA
| | - Yi-Cheng Chang
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei City, Taiwan
- Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Lee-Ming Chuang
- Department of Internal Medicine, Division of Endocrinology and Metabolism, National Taiwan University Hospital, Taipei City, Taiwan
| | - Ren-Hua Chung
- Institute of Population Health Sciences, National Health Research Institutes, Toufen, Taiwan
| | - Tine D Clausen
- Department of Gynecology and Obstetrics, Nordsjaellands Hospital, Hillerød, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Damm
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark
- Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vanessa D de Mello
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - Om P Dwivedi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Michael R Erdos
- Center for Precision Health Research National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Christian Gieger
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Mark O Goodarzi
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiuqing Guo
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stefan Gustafsson
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Liisa Hakaste
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Ulf Hammar
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Gad Hatem
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Sandra Herrmann
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- Department of Internal Medicine III, Prevention and Care of Diabetes, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Kurt Højlund
- Steno Diabetes Center Odense, Odense University Hospital, Odense, Denmark
| | - Katrin Horn
- Medical Faculty Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, Medical Faculty, Leipzig, Germany
| | - Willa A Hsueh
- Internal Medicine, Endocrinology, Diabetes and Metabolism, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Chii-Min Hwu
- Department of Medicine Section of Endocrinology and Metabolism, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Anna Jonsson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Line L Kårhus
- Center for Clinical Research and Prevention, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Marcus E Kleber
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Peter Kovacs
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Marie Lauzon
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - I-Te Lee
- Department of Internal Medicine Division of Endocrinology and Metabolism, Taichung Veterans General Hospital, Taichung City, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei City, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung City, Taiwan
| | - Cecilia M Lindgren
- Big Data Institute Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Wellcome Trust Centre Human Genetics, University of Oxford, Oxford, UK
- Broad Institute, Cambridge, MA, USA
| | | | - Allan Linneberg
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Research and Prevention, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jian'an Luan
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Dina Mansour Aly
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Elisabeth Mathiesen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark
- Department of Endocrinology Rigshospitalet, Copenhagen, Denmark
| | - Angela P Moissl
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Institute of Nutritional Sciences, Friedrich-Schiller-University, Jena, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena, Jena, Germany
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Narisu Narisu
- Center for Precision Health Research National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nikolaos Perakakis
- Department of Internal Medicine III, Metabolic and Vascular Medicine, Medical Faculty Carl Gustav Carus, Dresden, Germany
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Annette Peters
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Rashmi B Prasad
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Roman N Rodionov
- Department of Internal Medicine III, University Center for Vascular Medicine, Medical Faculty Carl Gustav Carus, Dresden, Germany
- College of Medicine and Public Health, Flinders University and Flinders Medical Centre, Adelaide, Australia
| | - Kathryn Roll
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Carsten F Rundsten
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chloé Sarnowski
- Department of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center, Houston, TX, USA
| | - Kai Savonen
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Markus Scholz
- Medical Faculty Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, Medical Faculty, Leipzig, Germany
| | - Sapna Sharma
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Freising-Weihenstephan, München, Germany
| | - Sara E Stinson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sufyan Suleman
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jingyi Tan
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Matti Uusitupa
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Dorte Vistisen
- Clinical Research, Steno Diabetes Center Copenhagen, Herlev, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Daniel R Witte
- Steno Diabetes Center Aarhus, Aarhus, Denmark
- Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Romy Walther
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- Department of Internal Medicine III, Pathobiochemistry, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Anny H Xiang
- Research and Evaluation, Division of Biostatistics, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Björn Zethelius
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, Sweden
| | - Emma Ahlqvist
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Malmö, Sweden
| | - Richard N Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Francis S Collins
- Center for Precision Health Research National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Jose C Florez
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, The Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andreas Fritsche
- Department of Internal Medicine IV, University Hospital Tübingen, Tübingen, Germany
| | - Harald Grallert
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Leif Groop
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Lund, Sweden
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heikki A Koistinen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Pirjo Komulainen
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Lars Lind
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Markus Loeffler
- Medical Faculty Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, Medical Faculty, Leipzig, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Synlab Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany
| | - James B Meigs
- Department of Internal Medicine IV, University Hospital Tübingen, Tübingen, Germany
- Clinical Sciences Malmö, Genomics, Diabetes and Endocrinology, Lund University, Lund, Sweden
- Department of Medicine Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Leslie J Raffel
- Department of Pediatrics, Genetic and Genomic Medicine, University of California, Irvine, CA, USA
| | - Rainer Rauramaa
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Peter E H Schwarz
- Helmholtz Zentrum München Paul Langerhans Institute Dresden (PLID), University Hospital and Faculty of Medicine TU Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Department of Internal Medicine III, Prevention and Care of Diabetes, Medical Faculty Carl Gustav Carus, Dresden, Germany
| | - Michael Stumvoll
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Johan Sundström
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Anke Tönjes
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Jaakko Tuomilehto
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Robert Wagner
- Department of Internal Medicine IV, University Hospital Tübingen, Tübingen, Germany
| | - Inês Barroso
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Mark Walker
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas J Wareham
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
| | - Eleanor Wheeler
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK.
| | - Stephen O'Rahilly
- Metabolic Research Laboratories Wellcome Trust-MRC Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK.
| | - Daniel J Fazakerley
- Metabolic Research Laboratories Wellcome Trust-MRC Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK.
| | - Claudia Langenberg
- MRC Epidemiology Unit Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK.
- Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin, Berlin, Germany.
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
| |
Collapse
|
43
|
Araujo DS, Nguyen C, Hu X, Mikhaylova AV, Gignoux C, Ardlie K, Taylor KD, Durda P, Liu Y, Papanicolaou G, Cho MH, Rich SS, Rotter JI, Im HK, Manichaikul A, Wheeler HE. Multivariate adaptive shrinkage improves cross-population transcriptome prediction for transcriptome-wide association studies in underrepresented populations. bioRxiv 2023:2023.02.09.527747. [PMID: 36798214 PMCID: PMC9934635 DOI: 10.1101/2023.02.09.527747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Transcriptome prediction models built with data from European-descent individuals are less accurate when applied to different populations because of differences in linkage disequilibrium patterns and allele frequencies. We hypothesized methods that leverage shared regulatory effects across different conditions, in this case, across different populations may improve cross-population transcriptome prediction. To test this hypothesis, we made transcriptome prediction models for use in transcriptome-wide association studies (TWAS) using different methods (Elastic Net, Joint-Tissue Imputation (JTI), Matrix eQTL, Multivariate Adaptive Shrinkage in R (MASHR), and Transcriptome-Integrated Genetic Association Resource (TIGAR)) and tested their out-of-sample transcriptome prediction accuracy in population-matched and cross-population scenarios. Additionally, to evaluate model applicability in TWAS, we integrated publicly available multi-ethnic genome-wide association study (GWAS) summary statistics from the Population Architecture using Genomics and Epidemiology Study (PAGE) and Pan-UK Biobank with our developed transcriptome prediction models. In regard to transcriptome prediction accuracy, MASHR models performed better or the same as other methods in both population-matched and cross-population transcriptome predictions. Furthermore, in multi-ethnic TWAS, MASHR models yielded more discoveries that replicate in both PAGE and PanUKBB across all methods analyzed, including loci previously mapped in GWAS and new loci previously not found in GWAS. Overall, our study demonstrates the importance of using methods that benefit from different populations' effect size estimates in order to improve TWAS for multi-ethnic or underrepresented populations.
Collapse
Affiliation(s)
- Daniel S. Araujo
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Chris Nguyen
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Xiaowei Hu
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | - Anna V. Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Chris Gignoux
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, UC Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kristin Ardlie
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Colchester, VT, 05446, USA
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - George Papanicolaou
- Epidemiology Branch, Division of Cardiovascular Sciences, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | | | - Hae Kyung Im
- Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | - Heather E. Wheeler
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, 60660, USA
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| |
Collapse
|
44
|
Hahn J, Bressler J, Domingo-Relloso A, Chen MH, McCartney DL, Teumer A, van Dongen J, Kleber ME, Aïssi D, Swenson BR, Yao J, Zhao W, Huang J, Xia Y, Brown MR, Costeira R, de Geus EJC, Delgado GE, Dobson DA, Elliott P, Grabe HJ, Guo X, Harris SE, Huffman JE, Kardia SLR, Liu Y, Lorkowski S, Marioni RE, Nauck M, Ratliff SM, Sabater-Lleal M, Spector TD, Suchon P, Taylor KD, Thibord F, Trégouët DA, Wiggins KL, Willemsen G, Bell JT, Boomsma DI, Cole SA, Cox SR, Dehghan A, Greinacher A, Haack K, März W, Morange PE, Rotter JI, Sotoodehnia N, Tellez-Plaza M, Navas-Acien A, Smith JA, Johnson AD, Fornage M, Smith NL, Wolberg AS, Morrison AC, de Vries PS. DNA methylation analysis is used to identify novel genetic loci associated with circulating fibrinogen levels in blood. J Thromb Haemost 2023; 21:1135-1147. [PMID: 36716967 DOI: 10.1016/j.jtha.2023.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/04/2022] [Accepted: 01/17/2023] [Indexed: 01/30/2023]
Abstract
BACKGROUND Fibrinogen plays an essential role in blood coagulation and inflammation. Circulating fibrinogen levels may be determined based on interindividual differences in DNA methylation at cytosine-phosphate-guanine (CpG) sites and vice versa. OBJECTIVES To perform an EWAS to examine an association between blood DNA methylation levels and circulating fibrinogen levels to better understand its biological and pathophysiological actions. METHODS We performed an epigenome-wide association study of circulating fibrinogen levels in 18 037 White, Black, American Indian, and Hispanic participants, representing 14 studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium. Circulating leukocyte DNA methylation was measured using the Illumina 450K array in 12 904 participants and using the EPIC array in 5133 participants. In each study, an epigenome-wide association study of fibrinogen was performed using linear mixed models adjusted for potential confounders. Study-specific results were combined using array-specific meta-analysis, followed by cross-replication of epigenome-wide significant associations. We compared models with and without CRP adjustment to examine the role of inflammation. RESULTS We identified 208 and 87 significant CpG sites associated with fibrinogen levels from the 450K (p < 1.03 × 10-7) and EPIC arrays (p < 5.78 × 10-8), respectively. There were 78 associations from the 450K array that replicated in the EPIC array and 26 vice versa. After accounting for overlapping sites, there were 83 replicated CpG sites located in 61 loci, of which only 4 have been previously reported for fibrinogen. The examples of genes located near these CpG sites were SOCS3 and AIM2, which are involved in inflammatory pathways. The associations of all 83 replicated CpG sites were attenuated after CRP adjustment, although many remained significant. CONCLUSION We identified 83 CpG sites associated with circulating fibrinogen levels. These associations are partially driven by inflammatory pathways shared by both fibrinogen and CRP.
Collapse
Affiliation(s)
- Julie Hahn
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA.
| | - Jan Bressler
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Arce Domingo-Relloso
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA; Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institutes, Madrid, Spain; Department of Statistics and Operations Research, University of Valencia, Burjassot, Spain
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, Massachusetts, USA
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Alexander Teumer
- Department SHIP/Clinical-Epidemiological Research, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany; Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Dylan Aïssi
- Univ. Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, Molecular Epidemiology of Vascular and Brain Disorders, Bordeaux, France
| | - Brenton R Swenson
- Cardiovascular Health Research Unit, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Jie Yao
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA; Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Jian Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Yujing Xia
- Department of Twin Research and Genetic Epidemiology, St Thomas Hospital Campus, King's College London, London, United Kingdom
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, St Thomas Hospital Campus, King's College London, London, United Kingdom
| | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Dre'Von A Dobson
- Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom; UK Dementia Research Institute, Imperial College London, London, United Kingdom; British Heart Foundation Centre for Research Excellence, Imperial College London, London, United Kingdom
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, Germany
| | - Xiuqing Guo
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Jennifer E Huffman
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Yongmei Liu
- Medicine, Cardiology, Duke Molecular Physiology Institute, Durham, North Carolina, USA
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany; Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, Germany
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Matthias Nauck
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Scott M Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Maria Sabater-Lleal
- Genomics of Complex Disease Unit, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain; Department of Medicine, Cardiovascular Medicine Unit, Karolinska Institutet, Stockholm, Sweden
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, St Thomas Hospital Campus, King's College London, London, United Kingdom
| | - Pierre Suchon
- Center for CardioVascular and Nutrition research (C2VN), INSERM 1263, INRAE 1260, Hematology Laboratory, La Timone University Hospital of Marseille, Aix-Marseille University, Marseille, France
| | - Kent D Taylor
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Florian Thibord
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham, Massachusetts, USA
| | - David-Alexandre Trégouët
- Univ. Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, Molecular Epidemiology of Vascular and Brain Disorders, Bordeaux, France
| | - Kerri L Wiggins
- Department of Medicine, Division of General Internal Medicine, University of Washington, Seattle, Washington, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, St Thomas Hospital Campus, King's College London, London, United Kingdom
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Andreas Greinacher
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Pierre-Emmanuel Morange
- Cardiovascular and Nutrition Reserach Center (C2VN), INSERM, INRAE, Aix-Marseille University, Marseille, France
| | - Jerome I Rotter
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Nona Sotoodehnia
- Department of Medicine, Division of Cardiology, University of Washington, Seattle, Washington, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institutes, Madrid, Spain
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA; Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, Massachusetts, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA; Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Nicholas L Smith
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA; Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, Washington, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, Washington, USA
| | - Alisa S Wolberg
- Pathology and Laboratory Medicine and UNC Blood Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA.
| |
Collapse
|
45
|
Jiang MZ, Aguet F, Ardlie K, Chen J, Cornell E, Cruz D, Durda P, Gabriel SB, Gerszten RE, Guo X, Johnson CW, Kasela S, Lange LA, Lappalainen T, Liu Y, Reiner AP, Smith J, Sofer T, Taylor KD, Tracy RP, VanDenBerg DJ, Wilson JG, Rich SS, Rotter JI, Love MI, Raffield LM, Li Y. Canonical correlation analysis for multi-omics: Application to cross-cohort analysis. PLoS Genet 2023; 19:e1010517. [PMID: 37216410 PMCID: PMC10237647 DOI: 10.1371/journal.pgen.1010517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 06/02/2023] [Accepted: 05/01/2023] [Indexed: 05/24/2023] Open
Abstract
Integrative approaches that simultaneously model multi-omics data have gained increasing popularity because they provide holistic system biology views of multiple or all components in a biological system of interest. Canonical correlation analysis (CCA) is a correlation-based integrative method designed to extract latent features shared between multiple assays by finding the linear combinations of features-referred to as canonical variables (CVs)-within each assay that achieve maximal across-assay correlation. Although widely acknowledged as a powerful approach for multi-omics data, CCA has not been systematically applied to multi-omics data in large cohort studies, which has only recently become available. Here, we adapted sparse multiple CCA (SMCCA), a widely-used derivative of CCA, to proteomics and methylomics data from the Multi-Ethnic Study of Atherosclerosis (MESA) and Jackson Heart Study (JHS). To tackle challenges encountered when applying SMCCA to MESA and JHS, our adaptations include the incorporation of the Gram-Schmidt (GS) algorithm with SMCCA to improve orthogonality among CVs, and the development of Sparse Supervised Multiple CCA (SSMCCA) to allow supervised integration analysis for more than two assays. Effective application of SMCCA to the two real datasets reveals important findings. Applying our SMCCA-GS to MESA and JHS, we identified strong associations between blood cell counts and protein abundance, suggesting that adjustment of blood cell composition should be considered in protein-based association studies. Importantly, CVs obtained from two independent cohorts also demonstrate transferability across the cohorts. For example, proteomic CVs learned from JHS, when transferred to MESA, explain similar amounts of blood cell count phenotypic variance in MESA, explaining 39.0% ~ 50.0% variation in JHS and 38.9% ~ 49.1% in MESA. Similar transferability was observed for other omics-CV-trait pairs. This suggests that biologically meaningful and cohort-agnostic variation is captured by CVs. We anticipate that applying our SMCCA-GS and SSMCCA on various cohorts would help identify cohort-agnostic biologically meaningful relationships between multi-omics data and phenotypic traits.
Collapse
Affiliation(s)
- Min-Zhi Jiang
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - François Aguet
- Illumina Artificial Intelligence Laboratory, Illumina, Inc., San Diego, California, United States of America
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elaine Cornell
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, Vermont, United States of America
| | - Dan Cruz
- Department of Medicine, Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Peter Durda
- Department of Pathology & Laboratory Medicine, University of Vermont, Colchester, Vermont, United States of America
| | - Stacey B. Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Robert E. Gerszten
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, University of California at Los Angeles, Torrance, California, United States of America
| | - Craig W. Johnson
- Department of Biostatistics, University of Washington at Seattle, Seattle, Washington, United States of America
| | - Silva Kasela
- New York Genome Center, New York, New York, United States of America
| | - Leslie A. Lange
- Department of Epidemiology, Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, Lifecourse Epidemiology of Adiposity & Diabetes Center, Aurora, Colorado, United States of America
| | - Tuuli Lappalainen
- New York Genome Center, New York, New York, United States of America
| | - Yongmei Liu
- Department of Medicine, Cardiology and Neurology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Josh Smith
- Northwest Genomic Center, University of Washington, Seattle, Washington, United States of America
| | - Tamar Sofer
- Department of Biostatistics, Harvard Medical School, Medicine-Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Kent D. Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, University of California at Los Angeles, Torrance, California, United States of America
| | - Russell P. Tracy
- Department of Pathology & Laboratory Medicine, University of Vermont, Colchester, Vermont, United States of America
| | - David J. VanDenBerg
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - James G. Wilson
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jerome I. Rotter
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, University of California at Los Angeles, Torrance, California, United States of America
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | |
Collapse
|
46
|
Weinstock JS, Laurie CA, Broome JG, Taylor KD, Guo X, Shuldiner AR, O’Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJ, Fornage M, Redline S, Cade BE, Gilliland FD, Chen Z, Gauderman WJ, Kumar R, Grammer L, Schleimer RP, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Weiss ST, Lasky-Su J, DeMeo DL, Palmer ND, Freedman BI, Bowden DW, Cho MH, Vasan RS, Johnson AD, Yanek LR, Becker LC, Kardia S, He J, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Manichaikul AW, Konkle BA, Johnsen JM, Wheeler MM, Custer BS, Duggirala R, Curran JE, Blangero J, Gui H, Xiao S, Williams LK, Meyers DA, Li X, Ortega V, McGarvey S, Gu CC, Chen YDI, Lee WJ, Shoemaker MB, Darbar D, Roden D, Albert C, Kooperberg C, Desai P, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Mathias R, Natarajan P, Jaiswal S, Reiner AP, Bick AG. The genetic determinants of recurrent somatic mutations in 43,693 blood genomes. Sci Adv 2023; 9:eabm4945. [PMID: 37126548 PMCID: PMC10132750 DOI: 10.1126/sciadv.abm4945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Nononcogenic somatic mutations are thought to be uncommon and inconsequential. To test this, we analyzed 43,693 National Heart, Lung and Blood Institute Trans-Omics for Precision Medicine blood whole genomes from 37 cohorts and identified 7131 non-missense somatic mutations that are recurrently mutated in at least 50 individuals. These recurrent non-missense somatic mutations (RNMSMs) are not clearly explained by other clonal phenomena such as clonal hematopoiesis. RNMSM prevalence increased with age, with an average 50-year-old having 27 RNMSMs. Inherited germline variation associated with RNMSM acquisition. These variants were found in genes involved in adaptive immune function, proinflammatory cytokine production, and lymphoid lineage commitment. In addition, the presence of eight specific RNMSMs associated with blood cell traits at effect sizes comparable to Mendelian genetic mutations. Overall, we found that somatic mutations in blood are an unexpectedly common phenomenon with ancestry-specific determinants and human health consequences.
Collapse
Affiliation(s)
- Joshua S. Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Cecelia A. Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jai G. Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Alan R. Shuldiner
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Jeffrey R. O’Connell
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Joshua P. Lewis
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kathleen C. Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nathalie Chami
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth J. F. Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Brian E. Cade
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Frank D. Gilliland
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhanghua Chen
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - W. James Gauderman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Rajesh Kumar
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Leslie Grammer
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jeong H. Yun
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Scott T. Weiss
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jessica Lasky-Su
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Dawn L. DeMeo
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Michael H. Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ramachandran S. Vasan
- National Heart, Lung, and Blood Institute’s, Boston University’s Framingham Heart Study, Framingham, MA 01701, USA
| | - Andrew D. Johnson
- National Heart, Lung, and Blood Institute’s, Boston University’s Framingham Heart Study, Framingham, MA 01701, USA
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA 01701, USA
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lewis C. Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sharon Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98108, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Donna K. Arnett
- Dean’s Office, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
| | | | - Hemant Tiwari
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yan Gao
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Stephen S. Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Ani W. Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Barbara A. Konkle
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jill M. Johnsen
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Research Institute, Bloodworks Northwest, Seattle, WA 98102, USA
| | | | | | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Joanne E. Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - Deborah A. Meyers
- Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Victor Ortega
- Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
| | - Stephen McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI 02903, USA
| | - C. Charles Gu
- Division of Biostatistics, Washington University School of Medicine, Campus Box 8067, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, 1650, Sec. 4, Taiwan Boulevard, Taichung City, Taiwan
| | - M. Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Dan Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christine Albert
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA 90048, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York 10065, NY, USA
| | - Thomas W. Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Goncalo R. Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Albert V. Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Hyun M. Kang
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Rasika Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- National Heart, Lung, and Blood Institute’s, Boston University’s Framingham Heart Study, Framingham, MA 01701, USA
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA 01701, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98108, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Dean’s Office, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Research Institute, Bloodworks Northwest, Seattle, WA 98102, USA
- Genome Science, University of Washington, Seattle, WA 98195, USA
- Vitalant Research Institute, San Francisco, CA 94105, USA
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
- Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ 85721, USA
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
- Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI 02903, USA
- Division of Biostatistics, Washington University School of Medicine, Campus Box 8067, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Medical Research, Taichung Veterans General Hospital, 1650, Sec. 4, Taiwan Boulevard, Taichung City, Taiwan
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL 60607, USA
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA 90048, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York 10065, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| |
Collapse
|
47
|
Okut H, Lu Y, Palmer ND, Chen YDI, Taylor KD, Norris JM, Lorenzo C, Rotter JI, Langefeld CD, Wagenknecht LE, Bowden DW, Ng MCY. Metabolomic profiling of glucose homeostasis in African Americans: the Insulin Resistance Atherosclerosis Family Study (IRAS-FS). Metabolomics 2023; 19:35. [PMID: 37005925 PMCID: PMC10068644 DOI: 10.1007/s11306-023-01984-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/04/2023] [Indexed: 04/04/2023]
Abstract
INTRODUCTION African Americans are at increased risk for type 2 diabetes. OBJECTIVES This work aimed to examine metabolomic signature of glucose homeostasis in African Americans. METHODS We used an untargeted liquid chromatography-mass spectrometry metabolomic approach to comprehensively profile 727 plasma metabolites among 571 African Americans from the Insulin Resistance Atherosclerosis Family Study (IRAS-FS) and investigate the associations between these metabolites and both the dynamic (SI, insulin sensitivity; AIR, acute insulin response; DI, disposition index; and SG, glucose effectiveness) and basal (HOMA-IR and HOMA-B) measures of glucose homeostasis using univariate and regularized regression models. We also compared the results with our previous findings in the IRAS-FS Mexican Americans. RESULTS We confirmed increased plasma metabolite levels of branched-chain amino acids and their metabolic derivatives, 2-aminoadipate, 2-hydroxybutyrate, glutamate, arginine and its metabolic derivatives, carbohydrate metabolites, and medium- and long-chain fatty acids were associated with insulin resistance, while increased plasma metabolite levels in the glycine, serine and threonine metabolic pathway were associated with insulin sensitivity. We also observed a differential ancestral effect of glutamate on glucose homeostasis with significantly stronger effects observed in African Americans than those previously observed in Mexican Americans. CONCLUSION We extended the observations that metabolites are useful biomarkers in the identification of prediabetes in individuals at risk of type 2 diabetes in African Americans. We revealed, for the first time, differential ancestral effect of certain metabolites (i.e., glutamate) on glucose homeostasis traits. Our study highlights the need for additional comprehensive metabolomic studies in well-characterized multiethnic cohorts.
Collapse
Affiliation(s)
- Hayrettin Okut
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Population Health, University of Kansas School of Medicine-Wichita, Wichita, KS, USA
| | - Yingchang Lu
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Nicholette D Palmer
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jill M Norris
- Departments of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Carlos Lorenzo
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Donald W Bowden
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Maggie C Y Ng
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
| |
Collapse
|
48
|
Weinstock JS, Gopakumar J, Burugula BB, Uddin MM, Jahn N, Belk JA, Bouzid H, Daniel B, Miao Z, Ly N, Mack TM, Luna SE, Prothro KP, Mitchell SR, Laurie CA, Broome JG, Taylor KD, Guo X, Sinner MF, von Falkenhausen AS, Kääb S, Shuldiner AR, O'Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJF, Fornage M, Hou L, Lloyd-Jones DM, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Palmer ND, Freedman BI, Bowden DW, Cho MH, DeMeo DL, Vasan RS, Yanek LR, Becker LC, Kardia SLR, Peyser PA, He J, Rienstra M, Van der Harst P, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Cutler MJ, Knight S, Muhlestein JB, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Tracy RP, Konkle BA, Johnsen JM, Wheeler MM, Smith JG, Melander O, Nilsson PM, Custer BS, Duggirala R, Curran JE, Blangero J, McGarvey S, Williams LK, Xiao S, Yang M, Gu CC, Chen YDI, Lee WJ, Marcus GM, Kane JP, Pullinger CR, Shoemaker MB, Darbar D, Roden DM, Albert C, Kooperberg C, Zhou Y, Manson JE, Desai P, Johnson AD, Mathias RA, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Satpathy AT, Natarajan P, Kitzman JO, Whitsel EA, Reiner AP, Bick AG, Jaiswal S. Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis. Nature 2023; 616:755-763. [PMID: 37046083 PMCID: PMC10360040 DOI: 10.1038/s41586-023-05806-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/08/2023] [Indexed: 04/14/2023]
Abstract
Mutations in a diverse set of driver genes increase the fitness of haematopoietic stem cells (HSCs), leading to clonal haematopoiesis1. These lesions are precursors for blood cancers2-6, but the basis of their fitness advantage remains largely unknown, partly owing to a paucity of large cohorts in which the clonal expansion rate has been assessed by longitudinal sampling. Here, to circumvent this limitation, we developed a method to infer the expansion rate from data from a single time point. We applied this method to 5,071 people with clonal haematopoiesis. A genome-wide association study revealed that a common inherited polymorphism in the TCL1A promoter was associated with a slower expansion rate in clonal haematopoiesis overall, but the effect varied by driver gene. Those carrying this protective allele exhibited markedly reduced growth rates or prevalence of clones with driver mutations in TET2, ASXL1, SF3B1 and SRSF2, but this effect was not seen in clones with driver mutations in DNMT3A. TCL1A was not expressed in normal or DNMT3A-mutated HSCs, but the introduction of mutations in TET2 or ASXL1 led to the expression of TCL1A protein and the expansion of HSCs in vitro. The protective allele restricted TCL1A expression and expansion of mutant HSCs, as did experimental knockdown of TCL1A expression. Forced expression of TCL1A promoted the expansion of human HSCs in vitro and mouse HSCs in vivo. Our results indicate that the fitness advantage of several commonly mutated driver genes in clonal haematopoiesis may be mediated by TCL1A activation.
Collapse
Affiliation(s)
- Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | | | - Md Mesbah Uddin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nikolaus Jahn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hind Bouzid
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bence Daniel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhuang Miao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nghi Ly
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taralynn M Mack
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine P Prothro
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaneice R Mitchell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Institute for Translational Genomics and Populations Sciences, Lundquist Institute, Torrance, CA, USA
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Lundquist Institute, Torrance, CA, USA
| | - Moritz F Sinner
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Aenne S von Falkenhausen
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Stefan Kääb
- Department of Medicine I, University Hospital, LMU Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Joshua P Lewis
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
- University of Maryland, Baltimore, MD, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- University of Texas Health at Houston, Houston, TX, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nathalie Chami
- The Charles Bronfman Institute of Personalized Medicine, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E Kenny
- Institute for Genomic Health, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Myriam Fornage
- University of Texas Health at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northeastern University, Chicago, IL, USA
| | | | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Brian E Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce M Psaty
- University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest Baptist Health, Winston-Salem, NC, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest Baptist Health, Winston-Salem, NC, USA
| | - Michael H Cho
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's, Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University, New Orleans, LA, USA
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pim Van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Albert Einstein College of Medicine, New York, NY, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
- Broad Institute, Cambridge, MA, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
- University of Kentucky, Lexington, KY, USA
| | | | - Hemant Tiwari
- Department of Biostatistics, University of Alabama, Birmingham, AL, USA
| | - Michael J Cutler
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Stacey Knight
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - J Brent Muhlestein
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, USA
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Population Health Science, University of Mississippi, Jackson, MS, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yan Gao
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- University of Mississippi, Jackson, MS, USA
| | - Mariza de Andrade
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Lundquist Institute, Torrance, CA, USA
| | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- University of Virginia, Charlottesville, VA, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, USA
| | - Barbara A Konkle
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Blood Works Northwest, Seattle, WA, USA
| | - Jill M Johnsen
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- Research Institute, Bloodworks Northwest, Seattle, WA, USA
| | | | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University, Gothenburg, Sweden
- Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Olle Melander
- Department of Internal Medicine, Clinical Sciences, Lund University and Skane University Hospital, Malmo, Sweden
| | - Peter M Nilsson
- Department of Internal Medicine, Clinical Sciences, Lund University and Skane University Hospital, Malmo, Sweden
| | | | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Stephen McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
- Henry Ford Health System, Detroit, MI, USA
| | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Mao Yang
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St Louis, MO, USA
- Washington University in St Louis, St Louis, MO, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Lundquist Institute, Torrance, CA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Taichung Veterans General Hospital Taiwan, Taichung City, Taiwan
| | - Gregory M Marcus
- Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA
| | - John P Kane
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California, San Francisco, USA
| | - M Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine and Cardiology, Vanderbilt University, Nashville, TN, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois at Chicago, Chicago, IL, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christine Albert
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA, USA
- Cedars-Sinai, Boston, MA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ying Zhou
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - JoAnn E Manson
- Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | - Thomas W Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Albert V Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Hyun M Kang
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Alexander P Reiner
- Broad Institute, Cambridge, MA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA.
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
49
|
Suzuki K, Hatzikotoulas K, Southam L, Taylor HJ, Yin X, Lorenz KM, Mandla R, Huerta-Chagoya A, Rayner NW, Bocher O, Arruda ALDSV, Sonehara K, Namba S, Lee SSK, Preuss MH, Petty LE, Schroeder P, Vanderwerff B, Kals M, Bragg F, Lin K, Guo X, Zhang W, Yao J, Kim YJ, Graff M, Takeuchi F, Nano J, Lamri A, Nakatochi M, Moon S, Scott RA, Cook JP, Lee JJ, Pan I, Taliun D, Parra EJ, Chai JF, Bielak LF, Tabara Y, Hai Y, Thorleifsson G, Grarup N, Sofer T, Wuttke M, Sarnowski C, Gieger C, Nousome D, Trompet S, Kwak SH, Long J, Sun M, Tong L, Chen WM, Nongmaithem SS, Noordam R, Lim VJY, Tam CHT, Joo YY, Chen CH, Raffield LM, Prins BP, Nicolas A, Yanek LR, Chen G, Brody JA, Kabagambe E, An P, Xiang AH, Choi HS, Cade BE, Tan J, Broadaway KA, Williamson A, Kamali Z, Cui J, Adair LS, Adeyemo A, Aguilar-Salinas CA, Ahluwalia TS, Anand SS, Bertoni A, Bork-Jensen J, Brandslund I, Buchanan TA, Burant CF, Butterworth AS, Canouil M, Chan JCN, Chang LC, Chee ML, Chen J, Chen SH, Chen YT, Chen Z, Chuang LM, Cushman M, Danesh J, Das SK, de Silva HJ, Dedoussis G, Dimitrov L, Doumatey AP, Du S, Duan Q, Eckardt KU, Emery LS, Evans DS, Evans MK, Fischer K, Floyd JS, Ford I, Franco OH, Frayling TM, Freedman BI, Genter P, Gerstein HC, Giedraitis V, González-Villalpando C, González-Villalpando ME, Gordon-Larsen P, Gross M, Guare LA, Hackinger S, Han S, Hattersley AT, Herder C, Horikoshi M, Howard AG, Hsueh W, Huang M, Huang W, Hung YJ, Hwang MY, Hwu CM, Ichihara S, Ikram MA, Ingelsson M, Islam MT, Isono M, Jang HM, Jasmine F, Jiang G, Jonas JB, Jørgensen T, Kandeel FR, Kasturiratne A, Katsuya T, Kaur V, Kawaguchi T, Keaton JM, Kho AN, Khor CC, Kibriya MG, Kim DH, Kronenberg F, Kuusisto J, Läll K, Lange LA, Lee KM, Lee MS, Lee NR, Leong A, Li L, Li Y, Li-Gao R, Lithgart S, Lindgren CM, Linneberg A, Liu CT, Liu J, Locke AE, Louie T, Luan J, Luk AO, Luo X, Lv J, Lynch JA, Lyssenko V, Maeda S, Mamakou V, Mansuri SR, Matsuda K, Meitinger T, Metspalu A, Mo H, Morris AD, Nadler JL, Nalls MA, Nayak U, Ntalla I, Okada Y, Orozco L, Patel SR, Patil S, Pei P, Pereira MA, Peters A, Pirie FJ, Polikowsky HG, Porneala B, Prasad G, Rasmussen-Torvik LJ, Reiner AP, Roden M, Rohde R, Roll K, Sabanayagam C, Sandow K, Sankareswaran A, Sattar N, Schönherr S, Shahriar M, Shen B, Shi J, Shin DM, Shojima N, Smith JA, So WY, Stančáková A, Steinthorsdottir V, Stilp AM, Strauch K, Taylor KD, Thorand B, Thorsteinsdottir U, Tomlinson B, Tran TC, Tsai FJ, Tuomilehto J, Tusie-Luna T, Udler MS, Valladares-Salgado A, van Dam RM, van Klinken JB, Varma R, Wacher-Rodarte N, Wheeler E, Wickremasinghe AR, van Dijk KW, Witte DR, Yajnik CS, Yamamoto K, Yamamoto K, Yoon K, Yu C, Yuan JM, Yusuf S, Zawistowski M, Zhang L, Zheng W, Raffel LJ, Igase M, Ipp E, Redline S, Cho YS, Lind L, Province MA, Fornage M, Hanis CL, Ingelsson E, Zonderman AB, Psaty BM, Wang YX, Rotimi CN, Becker DM, Matsuda F, Liu Y, Yokota M, Kardia SLR, Peyser PA, Pankow JS, Engert JC, Bonnefond A, Froguel P, Wilson JG, Sheu WHH, Wu JY, Hayes MG, Ma RCW, Wong TY, Mook-Kanamori DO, Tuomi T, Chandak GR, Collins FS, Bharadwaj D, Paré G, Sale MM, Ahsan H, Motala AA, Shu XO, Park KS, Jukema JW, Cruz M, Chen YDI, Rich SS, McKean-Cowdin R, Grallert H, Cheng CY, Ghanbari M, Tai ES, Dupuis J, Kato N, Laakso M, Köttgen A, Koh WP, Bowden DW, Palmer CNA, Kooner JS, Kooperberg C, Liu S, North KE, Saleheen D, Hansen T, Pedersen O, Wareham NJ, Lee J, Kim BJ, Millwood IY, Walters RG, Stefansson K, Goodarzi MO, Mohlke KL, Langenberg C, Haiman CA, Loos RJF, Florez JC, Rader DJ, Ritchie MD, Zöllner S, Mägi R, Denny JC, Yamauchi T, Kadowaki T, Chambers JC, Ng MCY, Sim X, Below JE, Tsao PS, Chang KM, McCarthy MI, Meigs JB, Mahajan A, Spracklen CN, Mercader JM, Boehnke M, Rotter JI, Vujkovic M, Voight BF, Morris AP, Zeggini E. Multi-ancestry genome-wide study in >2.5 million individuals reveals heterogeneity in mechanistic pathways of type 2 diabetes and complications. medRxiv 2023:2023.03.31.23287839. [PMID: 37034649 PMCID: PMC10081410 DOI: 10.1101/2023.03.31.23287839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes. To characterise the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study (GWAS) data from 2,535,601 individuals (39.7% non-European ancestry), including 428,452 T2D cases. We identify 1,289 independent association signals at genome-wide significance (P<5×10-8) that map to 611 loci, of which 145 loci are previously unreported. We define eight non-overlapping clusters of T2D signals characterised by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial, and enteroendocrine cells. We build cluster-specific partitioned genetic risk scores (GRS) in an additional 137,559 individuals of diverse ancestry, including 10,159 T2D cases, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned GRS are more strongly associated with coronary artery disease and end-stage diabetic nephropathy than an overall T2D GRS across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings demonstrate the value of integrating multi-ancestry GWAS with single-cell epigenomics to disentangle the aetiological heterogeneity driving the development and progression of T2D, which may offer a route to optimise global access to genetically-informed diabetes care.
Collapse
Affiliation(s)
- Ken Suzuki
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Konstantinos Hatzikotoulas
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Henry J. Taylor
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing City, China
| | - Kim M. Lorenz
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ravi Mandla
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alicia Huerta-Chagoya
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Nigel W. Rayner
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ozvan Bocher
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ana Luiza de S. V. Arruda
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Simon S. K. Lee
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren E. Petty
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip Schroeder
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brett Vanderwerff
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Mart Kals
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fiona Bragg
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hosptial, London NorthWest Healthcare NHS Trust, Middlesex, UK
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jana Nano
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Amel Lamri
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sanghoon Moon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | - Robert A. Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - James P. Cook
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Jung-Jin Lee
- Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian Pan
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto at Mississsauga, Mississauga, ON, Canada
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yang Hai
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tamar Sofer
- Department of Biostatistics, Harvard University, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard University, Boston, MA, USA
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Chloé Sarnowski
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Darryl Nousome
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Soo-Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Meng Sun
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Lin Tong
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Wei-Min Chen
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Suraj S. Nongmaithem
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Victor J. Y. Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Claudia H. T. Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yoonjung Yoonie Joo
- Institute of Data Science, Korea University, Seoul, South Korea
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bram Peter Prins
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Aude Nicolas
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Edmond Kabagambe
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Academics, Ochsner Health, New Orleans, LA, USA
| | - Ping An
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Anny H. Xiang
- Department of Research and Evaluation, Division of Biostatistics Research, Kaiser Permanente of Southern California, Pasadena, CA, USA
| | - Hyeok Sun Choi
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - K. Alaine Broadaway
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alice Williamson
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK
| | - Zoha Kamali
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jinrui Cui
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Linda S. Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carlos A. Aguilar-Salinas
- Unidad de Investigación en Enfermedades Metabólicas and Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Tarunveer S. Ahluwalia
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sonia S. Anand
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Alain Bertoni
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Brandslund
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Biochemistry, Vejle Hospital, Vejle, Denmark
| | - Thomas A. Buchanan
- Department of Medicine, Division of Endocrinology and Diabetes, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Charles F. Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
- National Institute for Health and Care Research (NIHR) Blood and Transplant Unit (BTRU) in Donor Health and Behaviour, Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Mickaël Canouil
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- University of Lille, Lille, France
| | - Juliana C. N. Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Miao-Li Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Ji Chen
- Exeter Centre of Excellence in Diabetes (ExCEeD), Exeter Medical School, University of Exeter, Exeter, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shyh-Huei Chen
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Lee-Ming Chuang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Mary Cushman
- Department of Medicine, University of Vermont, Colchester, VT, USA
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- British Heart Foundation Centre of Research Excellence, School of Clinical Medicine, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
- National Institute for Health and Care Research (NIHR) Blood and Transplant Unit (BTRU) in Donor Health and Behaviour, Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Swapan K. Das
- Section on Endocrinology and Metabolism, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - H. Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | - Latchezar Dimitrov
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ayo P. Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shufa Du
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qing Duan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Leslie S. Emery
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - James S. Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
| | - Oscar H. Franco
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Timothy M. Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Barry I. Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Pauline Genter
- Department of Medicine, Division of Endocrinology and Metabolism, Lundquist Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hertzel C. Gerstein
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Mexico City, Mexico
| | - Maria Elena González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Mexico City, Mexico
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Lindsay A. Guare
- Genomics and Computational Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sophie Hackinger
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sohee Han
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, South Korea
| | | | - Christian Herder
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Dusseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Momoko Horikoshi
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Annie-Green Howard
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Willa Hsueh
- Department of Internal Medicine, Diabetes and Metabolism Research Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Mengna Huang
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
- Center for Global Cardiometabolic Health, Brown University, Providence, RI, USA
| | - Wei Huang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Yi-Jen Hung
- Division of Endocrine and Metabolism, Tri-Service General Hospital Songshan Branch, Taipei, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - Mohammad Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | | | - Masato Isono
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hye-Mi Jang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Farzana Jasmine
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Guozhi Jiang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Jost B. Jonas
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Torben Jørgensen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Fouad R. Kandeel
- Department of Clinical Diabetes, Endocrinology and Metabolism, Department of Translational Research and Cellular Therapeutics, City of Hope, Duarte, CA, USA
| | | | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Geriatric and General Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Varinderpal Kaur
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jacob M. Keaton
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Abel N. Kho
- Division of General Internal Medicine and Geriatrics, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Health Information Partnerships, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Muhammad G. Kibriya
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Leslie A. Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Kyung Min Lee
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Myung-Shik Lee
- Severance Biomedical Science Institute and Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nanette R. Lee
- USC-Office of Population Studies Foundation Inc., University of San Carlos, Cebu City, Philippines
| | - Aaron Leong
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Symen Lithgart
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Cecilia M. Lindgren
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Big Data Institute, Li Ka Shing Centre For Health Information and Discovery, University of Oxford, Oxford, UK
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Adam E. Locke
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, Division of Genomics and Bioinformatics, Washington University School of Medicine, St Louis, MO, USA
- Present address: Regeneron Genetics Center, Tarrytown, NY, USA
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jian’an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Andrea O. Luk
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Xi Luo
- Department of Biostatistics and Data Science, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Julie A. Lynch
- VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
- Department of Clinical Science, Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Shiro Maeda
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Vasiliki Mamakou
- Dromokaiteio Psychiatric Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Sohail Rafik Mansuri
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Koichi Matsuda
- Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Huan Mo
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D. Morris
- The Usher Institute to the Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Jerry L. Nadler
- Department of Medicine and Pharmacology, New York Medical College, Valhalla, NY, USA
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Glen Echo, MD, USA
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Uma Nayak
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Sanjay R. Patel
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Snehal Patil
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pei Pei
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Mark A Pereira
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig Maximilians Universität München, Munich, Germany
| | - Fraser J. Pirie
- Department of Diabetes and Endocrinology, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hannah G. Polikowsky
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bianca Porneala
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gauri Prasad
- Academy of Scientific and Innovative Research, CSIR-Human Resource Development Campus, Ghaziabad, India
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Laura J. Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Michael Roden
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Dusseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebecca Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katheryn Roll
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Kevin Sandow
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alagu Sankareswaran
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Mohammad Shahriar
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Botong Shen
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jinxiu Shi
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Institute for Biomedical and Pharmaceutical Technologies (SIBPT), Shanghai, China
| | - Dong Mun Shin
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Nobuhiro Shojima
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Wing Yee So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Alena Stančáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
- Chair of Genetic Epidemiology, Institute of Medical Information Processing, Biometry, and Epidemiology, Faculty of Medicine, Ludwig Maximilians Universität München, Munich, Germany
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Brian Tomlinson
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Tam C. Tran
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fuu-Jen Tsai
- Department of Medical Genetics and Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Jaakko Tuomilehto
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland, Finnish Institute for Health and Welfare, Helsinki, Finland
- National School of Public Health, Madrid, Spain
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Teresa Tusie-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Departamento de Medicina Genómica y Toxiología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Miriam S. Udler
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Adan Valladares-Salgado
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rob M. van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Jan B. van Klinken
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Chemistry, Laboratory of Genetic Metabolic Disease, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Hospital, Los Angeles, CA, USA
| | - Niels Wacher-Rodarte
- Unidad de Investigación Médica en Epidemiologia Clinica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | | | - Ko Willems van Dijk
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniel R. Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Chittaranjan S. Yajnik
- Diabetology Research Centre, King Edward Memorial Hospital and Research Centre, Pune, India
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kyungheon Yoon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Salim Yusuf
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Liang Zhang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | | | | | | | | | | | - Leslie J Raffel
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UCI Irvine School of Medicine, Irvine, CA, USA
| | - Michiya Igase
- Department of Anti-Aging Medicine, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Eli Ipp
- Department of Medicine, Division of Endocrinology and Metabolism, Lundquist Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, South Korea
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael A. Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Craig L. Hanis
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, US
| | - Erik Ingelsson
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Ya-Xing Wang
- Beijing Institute of Ophthalmology, Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Diane M. Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - James C. Engert
- Department of Medicine, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Amélie Bonnefond
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Philippe Froguel
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- University of Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Wayne H. H. Sheu
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - M. Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Ronald C. W. Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Chinese University of Hong Kong-Shanghai Jiao Tong University Joint Research Centre in Diabetes Genomics and Precision Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tiinamaija Tuomi
- Department of Endocrinology, Helsinki University Hospital, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
- Lund University Diabetes Centre, Malmö, Sweden
| | - Giriraj R. Chandak
- Genomic Research on Complex Diseases (GRC-Group), CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Francis S. Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dwaipayan Bharadwaj
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Guillaume Paré
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Michèle M. Sale
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Deceased
| | - Habibul Ahsan
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Ayesha A. Motala
- Department of Diabetes and Endocrinology, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kyong-Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Miguel Cruz
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Roberta McKean-Cowdin
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Harald Grallert
- Institute of Epidemiology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Josee Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Woon-Puay Koh
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Colin N. A. Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, University of Dundee, Dundee, UK
| | - Jaspal S. Kooner
- Department of Cardiology, Ealing Hosptial, London NorthWest Healthcare NHS Trust, Middlesex, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Simin Liu
- Department of Epidemiology, Brown University School of Public Health, Providence, RI, USA
- Center for Global Cardiometabolic Health, Brown University, Providence, RI, USA
- Department of Medicine, Brown University Alpert School of Medicine, Providence, RI, USA
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Danish Saleheen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicholas J. Wareham
- The Usher Institute to the Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Juyoung Lee
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Korea
| | - Iona Y. Millwood
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Robin G. Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Kari Stefansson
- deCODE Genetics, Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Mark O. Goodarzi
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité Universitätsmedizin, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose C. Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Daniel J. Rader
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Translational Medicine and Therapeutics, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marylyn D. Ritchie
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Center for Precision Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sebastian Zöllner
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Joshua C. Denny
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Toranomon Hospital, Tokyo, Japan
| | - John C. Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hosptial, London NorthWest Healthcare NHS Trust, Middlesex, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Maggie C. Y. Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Jennifer E. Below
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip S. Tsao
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyong-Mi Chang
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark I. McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hosptial, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Present address: Genentech, South San Francisco, CA, USA
| | - James B. Meigs
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Present address: Genentech, South San Francisco, CA, USA
| | - Cassandra N. Spracklen
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Josep M. Mercader
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marijana Vujkovic
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Epidemiology, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin F. Voight
- Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Andrew P. Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
| |
Collapse
|
50
|
Dron JS, Patel AP, Zhang Y, Jurgens SJ, Maamari DJ, Wang M, Boerwinkle E, Morrison AC, de Vries PS, Fornage M, Hou L, Lloyd-Jones DM, Psaty BM, Tracy RP, Bis JC, Vasan RS, Levy D, Heard-Costa N, Rich SS, Guo X, Taylor KD, Gibbs RA, Rotter JI, Willer CJ, Oelsner EC, Moran AE, Peloso GM, Natarajan P, Khera AV. Association of Rare Protein-Truncating DNA Variants in APOB or PCSK9 With Low-density Lipoprotein Cholesterol Level and Risk of Coronary Heart Disease. JAMA Cardiol 2023; 8:258-267. [PMID: 36723951 PMCID: PMC9996405 DOI: 10.1001/jamacardio.2022.5271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/29/2022] [Indexed: 02/02/2023]
Abstract
Importance Protein-truncating variants (PTVs) in apolipoprotein B (APOB) and proprotein convertase subtilisin/kexin type 9 (PCSK9) are associated with significantly lower low-density lipoprotein (LDL) cholesterol concentrations. The association of these PTVs with coronary heart disease (CHD) warrants further characterization in large, multiracial prospective cohort studies. Objective To evaluate the association of PTVs in APOB and PCSK9 with LDL cholesterol concentrations and CHD risk. Design, Setting, and Participants This studied included participants from 5 National Heart, Lung, and Blood Institute (NHLBI) studies and the UK Biobank. NHLBI study participants aged 5 to 84 years were recruited between 1971 and 2002 across the US and underwent whole-genome sequencing. UK Biobank participants aged 40 to 69 years were recruited between 2006 and 2010 in the UK and underwent whole-exome sequencing. Data were analyzed from June 2021 to October 2022. Exposures PTVs in APOB and PCSK9. Main Outcomes and Measures Estimated untreated LDL cholesterol levels and CHD. Results Among 19 073 NHLBI participants (10 598 [55.6%] female; mean [SD] age, 52 [17] years), 139 (0.7%) carried an APOB or PCSK9 PTV, which was associated with 49 mg/dL (95% CI, 43-56) lower estimated untreated LDL cholesterol level. Over a median (IQR) follow-up of 21.5 (13.9-29.4) years, incident CHD was observed in 12 of 139 carriers (8.6%) vs 3029 of 18 934 noncarriers (16.0%), corresponding to an adjusted hazard ratio of 0.51 (95% CI, 0.28-0.89; P = .02). Among 190 464 UK Biobank participants (104 831 [55.0%] female; mean [SD] age, 57 [8] years), 662 (0.4%) carried a PTV, which was associated with 45 mg/dL (95% CI, 42-47) lower estimated untreated LDL cholesterol level. Estimated CHD risk by age 75 years was 3.7% (95% CI, 2.0-5.3) in carriers vs 7.0% (95% CI, 6.9-7.2) in noncarriers, corresponding to an adjusted hazard ratio of 0.51 (95% CI, 0.32-0.81; P = .004). Conclusions and Relevance Among 209 537 individuals in this study, 0.4% carried an APOB or PCSK9 PTV that was associated with less exposure to LDL cholesterol and a 49% lower risk of CHD.
Collapse
Affiliation(s)
- Jacqueline S. Dron
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Aniruddh P. Patel
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston
| | - Yiyi Zhang
- Division of General Medicine, Columbia University, New York, New York
| | - Sean J. Jurgens
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Experimental Cardiology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Dimitri J. Maamari
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Minxian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Donald M. Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle
- Department of Epidemiology, University of Washington, Seattle
- Department of Health Systems and Population Health, University of Washington, Seattle
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine at the University of Vermont, Colchester, Vermont
- Department of Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, Vermont
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle
| | - Ramachandran S. Vasan
- Sections of Preventive Medicine and Epidemiology, Cardiovascular Medicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
- Framingham Heart Study, Framingham, Massachusetts
| | - Daniel Levy
- Framingham Heart Study, Framingham, Massachusetts
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Nancy Heard-Costa
- Framingham Heart Study, Framingham, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | | | | | - Andrew E. Moran
- Division of General Medicine, Columbia University, New York, New York
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Pradeep Natarajan
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston
| | - Amit V. Khera
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Verve Therapeutics, Boston, Massachusetts
| |
Collapse
|