1
|
Antikainen AA, Haukka JK, Kumar A, Syreeni A, Hägg-Holmberg S, Ylinen A, Kilpeläinen E, Kytölä A, Palotie A, Putaala J, Thorn LM, Harjutsalo V, Groop PH, Sandholm N. Whole-genome sequencing identifies variants in ANK1, LRRN1, HAS1, and other genes and regulatory regions for stroke in type 1 diabetes. Sci Rep 2024; 14:13453. [PMID: 38862513 PMCID: PMC11166668 DOI: 10.1038/s41598-024-61840-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/10/2024] [Indexed: 06/13/2024] Open
Abstract
Individuals with type 1 diabetes (T1D) carry a markedly increased risk of stroke, with distinct clinical and neuroimaging characteristics as compared to those without diabetes. Using whole-exome or whole-genome sequencing of 1,051 individuals with T1D, we aimed to find rare and low-frequency genomic variants associated with stroke in T1D. We analysed the genome comprehensively with single-variant analyses, gene aggregate analyses, and aggregate analyses on genomic windows, enhancers and promoters. In addition, we attempted replication in T1D using a genome-wide association study (N = 3,945) and direct genotyping (N = 3,263), and in the general population from the large-scale population-wide FinnGen project and UK Biobank summary statistics. We identified a rare missense variant on SREBF1 exome-wide significantly associated with stroke (rs114001633, p.Pro227Leu, p-value = 7.30 × 10-8), which replicated for hemorrhagic stroke in T1D. Using gene aggregate analysis, we identified exome-wide significant genes: ANK1 and LRRN1 displayed replication evidence in T1D, and LRRN1, HAS1 and UACA in the general population (UK Biobank). Furthermore, we performed sliding-window analyses and identified 14 genome-wide significant windows for stroke on 4q33-34.1, of which two replicated in T1D, and a suggestive genomic window on LINC01500, which replicated in T1D. Finally, we identified a suggestively stroke-associated TRPM2-AS promoter (p-value = 5.78 × 10-6) with borderline significant replication in T1D, which we validated with an in vitro cell-based assay. Due to the rarity of the identified genetic variants, future replication of the genomic regions represented here is required with sequencing of individuals with T1D. Nevertheless, we here report the first genome-wide analysis on stroke in individuals with diabetes.
Collapse
Affiliation(s)
- Anni A Antikainen
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jani K Haukka
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anmol Kumar
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Stefanie Hägg-Holmberg
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anni Ylinen
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Anastasia Kytölä
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology and Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- The Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jukka Putaala
- Neurology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Lena M Thorn
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia.
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
2
|
Li JC, Huang ST, Feng F, Wang LJ, Chen TT, Li M, Liu LP. Relationship between low molecular weight heparin calcium therapy and prognosis in severe acute kidney injury in sepsis: Mendelian randomized analysis and retrospective study. Front Pharmacol 2024; 15:1389354. [PMID: 38915464 PMCID: PMC11194406 DOI: 10.3389/fphar.2024.1389354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/22/2024] [Indexed: 06/26/2024] Open
Abstract
Background Sepsis-associated acute kidney injury (SA-AKI) poses an independent risk for mortality due to the absence of highly sensitive biomarkers and a specific treatment plan. Objective Investigate the association between low molecular weight heparin (LMWH) calcium therapy and prognosis in critically ill SA-AKI patients, and assess the causal relationship through Mendelian randomization (MR) analysis. Methods A single-center, retrospective, cross-sectional study included 90 SA-AKI patients and 30 septic patients without acute kidney injury (AKI) from the intensive care unit (ICU) of the First Hospital of Lanzhou University. SA-AKI patients were categorized into control or LMWH groups based on LMWH calcium usage. Primary outcome was renal function recovery, with secondary outcomes including 28-day mortality, ICU stay length, number of renal replacement therapy (RRT) recipients, and 90-day survival. MR and related sensitivity analyses explored causal effects. Results The combination of heparin-binding protein (HBP), heparanase (HPA), and neutrophil gelatinase-associated lipocalin (NGAL) demonstrated high diagnostic value for SA-AKI. MR analysis suggested a potential causal link between gene-predicted HBP and AKI (OR: 1.369, 95%CI: 1.040-1.801, p = 0.024). In the retrospective study, LMWH-treated patients exhibited improved renal function, reduced levels of HPA, HBP, Syndecan-1, and inflammation, along with enhanced immune function compared to controls. However, LMWH did not impact 28-day mortality, 90-day survival, or ICU stay length. Conclusion LMWH could enhance renal function in SA-AKI patients. MR analysis supports this causal link, underscoring the need for further validation in randomized controlled trials.
Collapse
Affiliation(s)
- Jian-Chun Li
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Shi-Tao Huang
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Fei Feng
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Lin-Jun Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Ting-Ting Chen
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Min Li
- Department of Emergency Critical Care Medicine, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Li-Ping Liu
- Department of Emergency Critical Care Medicine, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| |
Collapse
|
3
|
Landfors F, Henneman P, Chorell E, Nilsson SK, Kersten S. Drug-target Mendelian randomization analysis supports lowering plasma ANGPTL3, ANGPTL4, and APOC3 levels as strategies for reducing cardiovascular disease risk. EUROPEAN HEART JOURNAL OPEN 2024; 4:oeae035. [PMID: 38895109 PMCID: PMC11182694 DOI: 10.1093/ehjopen/oeae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/30/2024] [Accepted: 04/26/2024] [Indexed: 06/21/2024]
Abstract
Aims APOC3, ANGPTL3, and ANGPTL4 are circulating proteins that are actively pursued as pharmacological targets to treat dyslipidaemia and reduce the risk of atherosclerotic cardiovascular disease. Here, we used human genetic data to compare the predicted therapeutic and adverse effects of APOC3, ANGPTL3, and ANGPTL4 inactivation. Methods and results We conducted drug-target Mendelian randomization analyses using variants in proximity to the genes associated with circulating protein levels to compare APOC3, ANGPTL3, and ANGPTL4 as drug targets. We obtained exposure and outcome data from large-scale genome-wide association studies and used generalized least squares to correct for linkage disequilibrium-related correlation. We evaluated five primary cardiometabolic endpoints and screened for potential side effects across 694 disease-related endpoints, 43 clinical laboratory tests, and 11 internal organ MRI measurements. Genetically lowering circulating ANGPTL4 levels reduced the odds of coronary artery disease (CAD) [odds ratio, 0.57 per s.d. protein (95% CI 0.47-0.70)] and Type 2 diabetes (T2D) [odds ratio, 0.73 per s.d. protein (95% CI 0.57-0.94)]. Genetically lowering circulating APOC3 levels also reduced the odds of CAD [odds ratio, 0.90 per s.d. protein (95% CI 0.82-0.99)]. Genetically lowered ANGPTL3 levels via common variants were not associated with CAD. However, meta-analysis of protein-truncating variants revealed that ANGPTL3 inactivation protected against CAD (odds ratio, 0.71 per allele [95%CI, 0.58-0.85]). Analysis of lowered ANGPTL3, ANGPTL4, and APOC3 levels did not identify important safety concerns. Conclusion Human genetic evidence suggests that therapies aimed at reducing circulating levels of ANGPTL3, ANGPTL4, and APOC3 reduce the risk of CAD. ANGPTL4 lowering may also reduce the risk of T2D.
Collapse
Affiliation(s)
- Fredrik Landfors
- Department of Public Health and Clinical Medicine, Section of Medicine, Umeå University, B41, Norrlands universitetssjukhus, S-901 87 Umeå, Sweden
- Lipigon Pharmaceuticals AB, Tvistevägen 48C, S-907 36 Umeå, Sweden
| | - Peter Henneman
- Department of Human Genetics, Amsterdam University Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Elin Chorell
- Department of Public Health and Clinical Medicine, Section of Medicine, Umeå University, B41, Norrlands universitetssjukhus, S-901 87 Umeå, Sweden
| | - Stefan K Nilsson
- Lipigon Pharmaceuticals AB, Tvistevägen 48C, S-907 36 Umeå, Sweden
- Department of Medical Biosciences, Umeå University, B41, Norrlands universitetssjukhus, S-901 87 Umeå, Sweden
| | - Sander Kersten
- Nutrition, Metabolism, and Genomics group, Division of Human Nutrition and Health, Wageningen University, 6708WE Wageningen, the Netherlands
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
4
|
Karjalainen MK, Karthikeyan S, Oliver-Williams C, Sliz E, Allara E, Fung WT, Surendran P, Zhang W, Jousilahti P, Kristiansson K, Salomaa V, Goodwin M, Hughes DA, Boehnke M, Fernandes Silva L, Yin X, Mahajan A, Neville MJ, van Zuydam NR, de Mutsert R, Li-Gao R, Mook-Kanamori DO, Demirkan A, Liu J, Noordam R, Trompet S, Chen Z, Kartsonaki C, Li L, Lin K, Hagenbeek FA, Hottenga JJ, Pool R, Ikram MA, van Meurs J, Haller T, Milaneschi Y, Kähönen M, Mishra PP, Joshi PK, Macdonald-Dunlop E, Mangino M, Zierer J, Acar IE, Hoyng CB, Lechanteur YTE, Franke L, Kurilshikov A, Zhernakova A, Beekman M, van den Akker EB, Kolcic I, Polasek O, Rudan I, Gieger C, Waldenberger M, Asselbergs FW, Hayward C, Fu J, den Hollander AI, Menni C, Spector TD, Wilson JF, Lehtimäki T, Raitakari OT, Penninx BWJH, Esko T, Walters RG, Jukema JW, Sattar N, Ghanbari M, Willems van Dijk K, Karpe F, McCarthy MI, Laakso M, Järvelin MR, Timpson NJ, Perola M, Kooner JS, Chambers JC, van Duijn C, Slagboom PE, Boomsma DI, Danesh J, Ala-Korpela M, Butterworth AS, Kettunen J. Genome-wide characterization of circulating metabolic biomarkers. Nature 2024; 628:130-138. [PMID: 38448586 PMCID: PMC10990933 DOI: 10.1038/s41586-024-07148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
Genome-wide association analyses using high-throughput metabolomics platforms have led to novel insights into the biology of human metabolism1-7. This detailed knowledge of the genetic determinants of systemic metabolism has been pivotal for uncovering how genetic pathways influence biological mechanisms and complex diseases8-11. Here we present a genome-wide association study for 233 circulating metabolic traits quantified by nuclear magnetic resonance spectroscopy in up to 136,016 participants from 33 cohorts. We identify more than 400 independent loci and assign probable causal genes at two-thirds of these using manual curation of plausible biological candidates. We highlight the importance of sample and participant characteristics that can have significant effects on genetic associations. We use detailed metabolic profiling of lipoprotein- and lipid-associated variants to better characterize how known lipid loci and novel loci affect lipoprotein metabolism at a granular level. We demonstrate the translational utility of comprehensively phenotyped molecular data, characterizing the metabolic associations of intrahepatic cholestasis of pregnancy. Finally, we observe substantial genetic pleiotropy for multiple metabolic pathways and illustrate the importance of careful instrument selection in Mendelian randomization analysis, revealing a putative causal relationship between acetone and hypertension. Our publicly available results provide a foundational resource for the community to examine the role of metabolism across diverse diseases.
Collapse
Affiliation(s)
- Minna K Karjalainen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland.
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland.
- Northern Finland Birth Cohorts, Arctic Biobank, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland.
| | - Savita Karthikeyan
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Clare Oliver-Williams
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Public Health Specialty Training Programme, Cambridge, UK
| | - Eeva Sliz
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elias Allara
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Wing Tung Fung
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kati Kristiansson
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matt Goodwin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Lilian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - 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, Jiangsu, China
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Matt J Neville
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie R van Zuydam
- 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
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - 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
| | - Ayse Demirkan
- Surrey Institute for People-Centred AI, University of Surrey, Guildford, UK
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - 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
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Christiana Kartsonaki
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - 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
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Toomas Haller
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Pashupati P Mishra
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Peter K Joshi
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Erin Macdonald-Dunlop
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Jonas Zierer
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yara T E Lechanteur
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marian Beekman
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B van den Akker
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Center for Computational Biology, Leiden University Medical Center, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ivana Kolcic
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Ozren Polasek
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Igor Rudan
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Christian Gieger
- Research Unit Molecular Epidemiology, 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
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, 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
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Genomics Research Center, Abbvie, Cambridge, MA, USA
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - James F Wilson
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Olli T Raitakari
- 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
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tonu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Fredrik Karpe
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - 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
- Genentech, South San Francisco, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Marjo-Riitta Järvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Markus Perola
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University 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
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University 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
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Cornelia van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Mika Ala-Korpela
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Johannes Kettunen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| |
Collapse
|
5
|
Melton HJ, Zhang Z, Wu C. SUMMIT-FA: a new resource for improved transcriptome imputation using functional annotations. Hum Mol Genet 2024; 33:624-635. [PMID: 38129112 PMCID: PMC10954367 DOI: 10.1093/hmg/ddad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Transcriptome-wide association studies (TWAS) integrate gene expression prediction models and genome-wide association studies (GWAS) to identify gene-trait associations. The power of TWAS is determined by the sample size of GWAS and the accuracy of the expression prediction model. Here, we present a new method, the Summary-level Unified Method for Modeling Integrated Transcriptome using Functional Annotations (SUMMIT-FA), which improves gene expression prediction accuracy by leveraging functional annotation resources and a large expression quantitative trait loci (eQTL) summary-level dataset. We build gene expression prediction models in whole blood using SUMMIT-FA with the comprehensive functional database MACIE and eQTL summary-level data from the eQTLGen consortium. We apply these models to GWAS for 24 complex traits and show that SUMMIT-FA identifies significantly more gene-trait associations and improves predictive power for identifying "silver standard" genes compared to several benchmark methods. We further conduct a simulation study to demonstrate the effectiveness of SUMMIT-FA.
Collapse
Affiliation(s)
- Hunter J Melton
- Department of Statistics, Florida State University, 214 Rogers Building, 117 N. Woodward Avenue, Tallahassee, FL 32306, United States
| | - Zichen Zhang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 7007 Bertner Avenue, Unit 1689, Houston, TX 77030, United States
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 7007 Bertner Avenue, Unit 1689, Houston, TX 77030, United States
| |
Collapse
|
6
|
Li H, Du S, Dai J, Jiang Y, Li Z, Fan Q, Zhang Y, You D, Zhang R, Zhao Y, Christiani DC, Shen S, Chen F. Proteome-wide Mendelian randomization identifies causal plasma proteins in lung cancer. iScience 2024; 27:108985. [PMID: 38333712 PMCID: PMC10850776 DOI: 10.1016/j.isci.2024.108985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Plasma proteins are promising biomarkers and potential drug targets in lung cancer. To evaluate the causal association between plasma proteins and lung cancer, we performed proteome-wide Mendelian randomization meta-analysis (PW-MR-meta) based on lung cancer genome-wide association studies (GWASs), protein quantitative trait loci (pQTLs) of 4,719 plasma proteins in deCODE and 4,775 in Fenland. Further, causal-protein risk score (CPRS) was developed based on causal proteins and validated in the UK Biobank. 270 plasma proteins were identified using PW-MR meta-analysis, including 39 robust causal proteins (both FDR-q < 0.05) and 78 moderate causal proteins (FDR-q < 0.05 in one and p < 0.05 in another). The CPRS had satisfactory performance in risk stratification for lung cancer (top 10% CPRS:Hazard ratio (HR) (95%CI):4.33(2.65-7.06)). The CPRS [AUC (95%CI): 65.93 (62.91-68.78)] outperformed the traditional polygenic risk score (PRS) [AUC (95%CI): 55.71(52.67-58.59)]. Our findings offer further insight into the genetic architecture of plasma proteins for lung cancer susceptibility.
Collapse
Affiliation(s)
- Hongru Li
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Sha Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Jinglan Dai
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yunke Jiang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zaiming Li
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Qihan Fan
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yixin Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Dongfang You
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing 211166, China
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing 211166, China
| | - Yang Zhao
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing 211166, China
| | - David C. Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Pulmonary and Critical Care Division, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Sipeng Shen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing 211166, China
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing 211166, China
| |
Collapse
|
7
|
Shen J, Xu L, Wu X, Ding Y. Mineral Metabolism and Polycystic Ovary Syndrome and Metabolic Risk Factors: A Mendelian Randomization Study. Reprod Sci 2024:10.1007/s43032-024-01476-0. [PMID: 38366089 DOI: 10.1007/s43032-024-01476-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/31/2024] [Indexed: 02/18/2024]
Abstract
Observational investigations recommend that mineral supplements were associated with a higher risk of polycystic ovary syndrome (PCOS) and its risk factors (insulin resistance, hyperandrogenism, and obesity), but the relationship with risk of PCOS, hyperandrogenism, obesity, and insulin resistance was unclear. This study was to investigate the potential causal impact of genetically predicted levels of magnesium (Mg), calcium (Ca), selenium (Se), zinc (Zn), iron (Fe), and omega-3 (ω-3) on polycystic ovary syndrome (PCOS) and its associated risk factors. A two-sample Mendelian randomization (MR) analysis was conducted. The genetic variations obtained from GWAS of individuals with European ancestry were found to be associated with the genetically predicted levels of Ca, Mg, Zn, Se, Fe, or ω-3. The data obtained from the FinnGen Consortium and MAGIC were utilized for the outcome of GWAS. The study found that there was a correlation between genetically predicted higher levels of Se and a reduced risk of insulin resistance, with a decrease of 2.2% according to random-effect IVW (OR 0.978, 95% CI 0.960-0.996, p = 0.015). The association between genetically determined mineral levels and PCOS was found to be limited, with an odds ratio (OR) ranging from 0.875 (95% CI: 0.637-1.202, p value = 0.411) for Ca. Limited scientific proof was found for the efficacy of other genetically determined mineral levels on hyperandrogenism, obesity, and insulin resistance. These findings suggested a causal relationship between genetically predicted higher levels of Se and a reduced risk of insulin resistance. Nonetheless, there is limited evidence supporting a causal association between various genetically determined mineral levels and the risk factors associated with PCOS.
Collapse
Affiliation(s)
- Jiayan Shen
- Department of Reproductive Medicine, Huzhou Maternity & Child Health Care Hospital, Huzhou, 313000, Zhejiang Province, China
| | - Li Xu
- Department of Obstetrics and Gynecology, Huzhou Maternity & Child Health Care Hospital, Huzhou, 313000, Zhejiang Province, China
| | - Xiaoyun Wu
- Department of Reproductive Medicine, Huzhou Maternity & Child Health Care Hospital, Huzhou, 313000, Zhejiang Province, China.
| | - Yang Ding
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, No. 158, Shangtang Road, Hangzhou, 310014, China.
| |
Collapse
|
8
|
Li T, Ihanus A, Ohukainen P, Järvelin MR, Kähönen M, Kettunen J, Raitakari OT, Lehtimäki T, Mäkinen VP, Tynkkynen T, Ala-Korpela M. Clinical and biochemical associations of urinary metabolites: quantitative epidemiological approach on renal-cardiometabolic biomarkers. Int J Epidemiol 2024; 53:dyad162. [PMID: 38030573 PMCID: PMC10859141 DOI: 10.1093/ije/dyad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Urinary metabolomics has demonstrated considerable potential to assess kidney function and its metabolic corollaries in health and disease. However, applications in epidemiology remain sparse due to technical challenges. METHODS We added 17 metabolites to an open-access urinary nuclear magnetic resonance metabolomics platform, extending the panel to 61 metabolites (n = 994). We also introduced automated quantification for 11 metabolites, extending the panel to 12 metabolites (+creatinine). Epidemiological associations between these 12 metabolites and 49 clinical measures were studied in three independent cohorts (up to 5989 participants). Detailed regression analyses with various confounding factors are presented for body mass index (BMI) and smoking. RESULTS Sex-specific population reference concentrations and distributions are provided for 61 urinary metabolites (419 men and 575 women), together with methodological intra-assay metabolite variations as well as the biological intra-individual and epidemiological population variations. For the 12 metabolites, 362 associations were found. These are mostly novel and reflect potential molecular proxies to estimate kidney function, as the associations cannot be simply explained by estimated glomerular filtration rate. Unspecific renal excretion results in leakage of amino acids (and glucose) to urine in all individuals. Seven urinary metabolites associated with smoking, providing questionnaire-independent proxy measures of smoking status in epidemiological studies. Common confounders did not affect metabolite associations with smoking, but insulin had a clear effect on most associations with BMI, including strong effects on 2-hydroxyisobutyrate, valine, alanine, trigonelline and hippurate. CONCLUSIONS Urinary metabolomics provides new insight on kidney function and related biomarkers on the renal-cardiometabolic system, supporting large-scale applications in epidemiology.
Collapse
Affiliation(s)
- Tianqi Li
- Systems Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Andrei Ihanus
- Systems Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Pauli Ohukainen
- Systems Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Marjo-Riitta Järvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center Tampere, Tampere University, Tampere, Finland
| | - Johannes Kettunen
- Systems Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- 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
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center Tampere, Tampere University, Tampere, Finland
| | - Ville-Petteri Mäkinen
- Systems Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tuulia Tynkkynen
- Systems Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Mika Ala-Korpela
- Systems Epidemiology, Faculty of Medicine, University of Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
9
|
Lin S, Wu S, Zhao W, Fang Z, Kang H, Liu X, Pan S, Yu F, Bao Y, Jia P. TargetGene: a comprehensive database of cell-type-specific target genes for genetic variants. Nucleic Acids Res 2024; 52:D1072-D1081. [PMID: 37870478 PMCID: PMC10767789 DOI: 10.1093/nar/gkad901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023] Open
Abstract
Annotating genetic variants to their target genes is of great importance in unraveling the causal variants and genetic mechanisms that underlie complex diseases. However, disease-associated genetic variants are often located in non-coding regions and manifest context-specific effects, making it challenging to accurately identify the target genes and regulatory mechanisms. Here, we present TargetGene (https://ngdc.cncb.ac.cn/targetgene/), a comprehensive database reporting target genes for human genetic variants from various aspects. Specifically, we collected a comprehensive catalog of multi-omics data at the single-cell and bulk levels and from various human tissues, cell types and developmental stages. To facilitate the identification of Single Nucleotide Polymorphism (SNP)-to-gene connections, we have implemented multiple analytical tools based on chromatin co-accessibility, 3D interaction, enhancer activities and quantitative trait loci, among others. We applied the pipeline to evaluate variants from nearly 1300 Genome-wide association studies (GWAS) and assembled a comprehensive atlas of multiscale regulation of genetic variants. TargetGene is equipped with user-friendly web interfaces that enable intuitive searching, navigation and browsing through the results. Overall, TargetGene provides a unique resource to empower researchers to study the regulatory mechanisms of genetic variants in complex human traits.
Collapse
Affiliation(s)
- Shiqi Lin
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wu
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Wei Zhao
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhanjie Fang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongen Kang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinxuan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyu Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fudong Yu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200237, China
| | - Yiming Bao
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
10
|
Gagnon L, Moreau C, Laprise C, Vézina H, Girard SL. Deciphering the genetic structure of the Quebec founder population using genealogies. Eur J Hum Genet 2024; 32:91-97. [PMID: 37016017 PMCID: PMC10772069 DOI: 10.1038/s41431-023-01356-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 04/06/2023] Open
Abstract
Using genealogy to study the demographic history of a population makes it possible to overcome the models and assumptions often used in population genetics. The Quebec founder population is one of the few populations in the world having access to the complete genealogy of the last 400 years. The goal of this study is to follow the evolution of the Quebec population structure over time from the beginning of European colonization until the present day. To do so, we calculated the kinship coefficients of all ancestors' pairs in the ascending genealogy of 665 subjects from eight regional and ethnocultural groups per 25-year period. We show that the Quebec population structure appeared progressively in the St. Lawrence valley as early as 1750 with the distinction of the Saguenay and Gaspesian groups. At that time, the ancestors of two groups, the Sagueneans and the Acadians from the Gaspé Peninsula, experienced a marked increase in kinship and inbreeding levels which have shaped the structure and led to the contemporary population structure. Interestingly, this structure arose before the colonization of the Saguenay region and at the very beginning of the Gaspé Peninsula settlement. The resulting regional founder effects in these groups led to differences in the present-day identity-by-descent sharing, the Gaspé and North Shore groups sharing more large segments and the Sagueneans more short segments. This is also reflected by the distribution of the number of most recent common ancestors at different generations and their genetic contribution to the studied subjects.
Collapse
Affiliation(s)
- Laurence Gagnon
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Centre Intersectoriel en Santé Durable (CISD), Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
| | - Claudia Moreau
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Centre Intersectoriel en Santé Durable (CISD), Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Centre Intersectoriel en Santé Durable (CISD), Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Centre Intégré Universitaire en Santé et Services Sociaux du Saguenay-Lac-Saint-Jean, Saguenay, Québec, G7H 7K9, Canada
| | - Hélène Vézina
- Centre Intersectoriel en Santé Durable (CISD), Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Département des Sciences Humaines et Sociales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
- Projet BALSAC, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
| | - Simon L Girard
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada.
- Centre Intersectoriel en Santé Durable (CISD), Université du Québec à Chicoutimi, Saguenay, Québec, G7H 2B1, Canada.
- Centre de Recherche CERVO, Université Laval, Québec, Québec, G1V 0A6, Canada.
| |
Collapse
|
11
|
Hu X, Zhao Y, He T, Gao ZX, Zhang P, Fang Y, Ge M, Xu YQ, Pan HF, Wang P. Causal Relationships between Air Pollutant Exposure and Bone Mineral Density and the Risk of Bone Fractures: Evidence from a Two-Stage Mendelian Randomization Analysis. TOXICS 2023; 12:27. [PMID: 38250984 PMCID: PMC10820864 DOI: 10.3390/toxics12010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/25/2023] [Accepted: 12/26/2023] [Indexed: 01/23/2024]
Abstract
A number of studies from the literature have suggested that exposure to air pollutants is associated with a declined bone mineral density (BMD), and increased risks of osteoporosis (OP) and bone fractures. This study was performed to systemically assess the genetically causal associations of air pollutants with site-/age-specific BMD and risk of bone fractures with the implementation of two-sample Mendelian randomization (TSMR) and multivariate Mendelian randomization (MVMR). The TSMR analysis was implemented to infer the causal associations between air pollutants and BMD and the risk of bone fractures, additional MVMR analysis was used to further estimate the direct causal effects between air pollutants and BMD, the occurrence of OP, and bone fractures. The results showed that NOx exposure contributed to lower femoral neck BMD (FN-BMD) (β = -0.71, 95%CI: -1.22, -0.20, p = 0.006) and total body BMD (TB-BMD) (β = -0.55, 95%CI: -0.90, -0.21, p = 0.002). Additionally, exposure to PM10 was found to be associated with a decreased TB-BMD (B β = -0.42, 95%CI: -0.66, -0.18, p = 0.001), further age-specific subgroup analysis demonstrated the causal effect of PM10 exposure on the decreased TB-BMD in a subgroup aged 45 to 60 years (β = -0.70, 95%CI: -1.12, -0.29, p = 0.001). Moreover, the findings of the MVMR analysis implied that there was a direct causal effect between PM10 exposure and the decreased TB-BMD (45 < age < 60), after adjusting for PM2.5 and PM2.5 -10 exposure. Our study provides additional evidence to support the causal associations of higher concentrations of air pollutant exposure with decreased BMD, especially in those populations aged between 45 to 60 years, suggesting that early intervention measures and public policy should be considered to improve public health awareness and promote bone health.
Collapse
Affiliation(s)
- Xiao Hu
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China;
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
| | - Yan Zhao
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Tian He
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Zhao-Xing Gao
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Peng Zhang
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Yang Fang
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Man Ge
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Yi-Qing Xu
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Hai-Feng Pan
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China
| | - Peng Wang
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, China;
- Institute of Kidney Disease, Inflammation & Immunity Mediated Diseases, The Second Hospital of Anhui Medical University, Hefei 230032, China; (Y.Z.); (T.H.); (Z.-X.G.); (P.Z.); (Y.F.); (M.G.); (Y.-Q.X.)
| |
Collapse
|
12
|
Koivisto AP, Szallasi A. Targeting TRP Channels for Pain, Itch and Neurogenic Inflammation. Int J Mol Sci 2023; 25:320. [PMID: 38203491 PMCID: PMC10779384 DOI: 10.3390/ijms25010320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Transient receptor potential (TRP) channels are multifunctional signaling molecules with important roles in health and disease [...].
Collapse
Affiliation(s)
| | - Arpad Szallasi
- Department of Pathology and Experimental Cancer Research, Semmelweis University, 1083 Budapest, Hungary
| |
Collapse
|
13
|
Detera-Wadleigh SD, Kassem L, Besancon E, Lopes F, Akula N, Sung H, Blattner M, Sheridan L, Lacbawan LN, Garcia J, Gordovez F, Hosey K, Donner C, Salvini C, Schulze T, Chen DTW, England B, Cross J, Jiang X, Corona W, Russ J, Mallon B, Dutra A, Pak E, Steiner J, Malik N, de Guzman T, Horato N, Mallmann MB, Mendes V, Dűck AL, Nardi AE, McMahon FJ. A resource of induced pluripotent stem cell (iPSC) lines including clinical, genomic, and cellular data from genetically isolated families with mood and psychotic disorders. Transl Psychiatry 2023; 13:397. [PMID: 38104115 PMCID: PMC10725500 DOI: 10.1038/s41398-023-02641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/05/2023] [Accepted: 10/30/2023] [Indexed: 12/19/2023] Open
Abstract
Genome-wide (GWAS) and copy number variant (CNV) association studies have reproducibly identified numerous risk alleles associated with bipolar disorder (BD), major depressive disorder (MDD), and schizophrenia (SCZ), but biological characterization of these alleles lags gene discovery, owing to the inaccessibility of live human brain cells and inadequate animal models for human psychiatric conditions. Human-derived induced pluripotent stem cells (iPSCs) provide a renewable cellular reagent that can be differentiated into living, disease-relevant cells and 3D brain organoids carrying the full complement of genetic variants present in the donor germline. Experimental studies of iPSC-derived cells allow functional characterization of risk alleles, establishment of causal relationships between genes and neurobiology, and screening for novel therapeutics. Here we report the creation and availability of an iPSC resource comprising clinical, genomic, and cellular data obtained from genetically isolated families with BD and related conditions. Results from the first 324 study participants, 61 of whom have validated pluripotent clones, show enrichment of rare single nucleotide variants and CNVs overlapping many known risk genes and pathogenic CNVs. This growing iPSC resource is available to scientists pursuing functional genomic studies of BD and related conditions.
Collapse
Affiliation(s)
- Sevilla D Detera-Wadleigh
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA.
| | - Layla Kassem
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA.
| | - Emily Besancon
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Fabiana Lopes
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Nirmala Akula
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Heejong Sung
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Meghan Blattner
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Laura Sheridan
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Ley Nadine Lacbawan
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Joshua Garcia
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Francis Gordovez
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Katherine Hosey
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Cassandra Donner
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Claudio Salvini
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Thomas Schulze
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Institute of Psychiatric Phenomics and Genomics, LMU Munich, 80336, München, Germany
- Department of Psychiatry and Behavioral Sciences, Upstate University Hospital, Syracuse, NY, 13210, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - David T W Chen
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Bryce England
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Joanna Cross
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Xueying Jiang
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Winston Corona
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Jill Russ
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Barbara Mallon
- Center for Scientific Review, Neurotechnology and Vision Branch, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joe Steiner
- Neurotherapeutics Development Unit, NINDS, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nasir Malik
- Neurotherapeutics Development Unit, NINDS, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Theresa de Guzman
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Natia Horato
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Mariana B Mallmann
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Victoria Mendes
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Amanda L Dűck
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Antonio E Nardi
- Laboratorio de Panico e Respiracao, Instituto de Psiquiatria, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 22410-003, Brazil
| | - Francis J McMahon
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| |
Collapse
|
14
|
Li L, Wang S, Zhang T, Lv B, Jin Y, Wang Y, Chen X, Li N, Han N, Wu Y, Yuan J. Walnut peptide alleviates obesity, inflammation and dyslipidemia in mice fed a high-fat diet by modulating the intestinal flora and metabolites. Front Immunol 2023; 14:1305656. [PMID: 38162665 PMCID: PMC10755907 DOI: 10.3389/fimmu.2023.1305656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Obesity is a chronic disease in which the body stores excess energy in the form of fat, and intestinal bacterial metabolism and inflammatory host phenotypes influence the development of obesity. Walnut peptide (WP) is a small molecule biopeptide, and the mechanism of action of WP against metabolic disorders has not been fully elucidated. In this study, we explored the potential intervention mechanism of WP on high-fat diet (HFD)-induced obesity through bioinformatics combined with animal experiments. Methods PPI networks of Amino acids and their metabolites in WP (AMWP) and "obesity" and "inflammation" diseases were searched and constructed by using the database, and their core targets were enriched and analyzed. Subsequently, Cytoscape software was used to construct the network diagram of the AMWP-core target-KEGG pathway and analyze the topological parameters. MOE2019.0102 was used to verify the molecular docking of core AMWP and core target. Subsequently, an obese Mice model induced by an HFD was established, and the effects of WP on obesity were verified by observing weight changes, glucose, and lipid metabolism levels, liver pathological changes, the size of adipocytes in groin adipose tissue, inflammatory infiltration of colon tissue, and intestinal microorganisms and their metabolites. Results The network pharmacology and molecular docking showed that glutathione oxide may be the main active component of AMWP, and its main targets may be EGFR, NOS3, MMP2, PLG, PTGS2, AR. Animal experiments showed that WP could reduce weight gain and improve glucose-lipid metabolism in HFD-induced obesity model mice, attenuate hepatic lesions reduce the size of adipocytes in inguinal adipose tissue, and reduce the inflammatory infiltration in colonic tissue. In addition, the abundance and diversity of intestinal flora were remodeled, reducing the phylum Firmicutes/Bacteroidetes (F/B) ratio, while the intestinal mucosal barrier was repaired, altering the content of short-chain fatty acids (SCFAs), and alleviating intestinal inflammation in HFD-fed mice. These results suggest that WP intervenes in HFD-induced obesity and dyslipidemia by repairing the intestinal microenvironment, regulating flora metabolism and anti-inflammation. Discussion Our findings suggest that WP intervenes in HFD-induced obesity and dyslipidemia by repairing the intestinal microenvironment, regulating flora metabolism, and exerting anti-inflammatory effects. Thus, WP may be a potential therapeutic strategy for preventing and treating metabolic diseases, and for alleviating the intestinal flora disorders induced by these diseases. This provides valuable insights for the development of WP therapies.
Collapse
Affiliation(s)
- Lei Li
- College of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Si Wang
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- First Clinical School of Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Tong Zhang
- College of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Bijun Lv
- College of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Yanling Jin
- College of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Yue Wang
- College of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Xiaojiao Chen
- College of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Ning Li
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- First Clinical School of Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Niping Han
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Yueying Wu
- College of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Jiali Yuan
- College of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| |
Collapse
|
15
|
Upadhyay KK, Du X, Chen Y, Buscher B, Chen VL, Oliveri A, Zhao R, Speliotes EK, Brady GF. A common variant that alters SUN1 degradation associates with hepatic steatosis and metabolic traits in multiple cohorts. J Hepatol 2023; 79:1226-1235. [PMID: 37567366 PMCID: PMC10618955 DOI: 10.1016/j.jhep.2023.07.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND & AIMS Non-alcoholic fatty liver disease (NAFLD), and its progressive form steatohepatitis (NASH), represent a genetically and phenotypically diverse entity for which there is no approved therapy, making it imperative to define the spectrum of pathways contributing to its pathogenesis. Rare variants in genes encoding nuclear envelope proteins cause lipodystrophy with early-onset NAFLD/NASH; we hypothesized that common variants in nuclear envelope-related genes might also contribute to hepatic steatosis and NAFLD. METHODS Using hepatic steatosis as the outcome of interest, we performed an association meta-analysis of nuclear envelope-related coding variants in three large discovery cohorts (N >120,000 participants), followed by phenotype association studies in large validation cohorts (N >600,000) and functional testing of the top steatosis-associated variant in cell culture. RESULTS A common protein-coding variant, rs6461378 (SUN1 H118Y), was the top steatosis-associated variant in our association meta-analysis (p <0.001). In ancestrally distinct validation cohorts, rs6461378 associated with histologic NAFLD and with NAFLD-related metabolic traits including increased serum fatty acids, type 2 diabetes, hypertension, cardiovascular disease, and decreased HDL. SUN1 H118Y was subject to increased proteasomal degradation relative to wild-type SUN1 in cells, and SUN1 H118Y-expressing cells exhibited insulin resistance and increased lipid accumulation. CONCLUSIONS Collectively, these data support a potential causal role for the common SUN1 variant rs6461378 in NAFLD and metabolic disease. IMPACT AND IMPLICATIONS Non-alcoholic fatty liver disease (NAFLD), with an estimated global prevalence of nearly 30%, is a growing cause of morbidity and mortality for which there is no approved pharmacologic therapy. Our data provide a rationale for broadening current concepts of NAFLD genetics and pathophysiology to include the nuclear envelope, and particularly Sad1 and UNC84 domain containing 1 (SUN1), as novel contributors to this common liver disease. Furthermore, if future studies confirm causality of the common SUN1 H118Y variant, it has the potential to become a broadly relevant therapeutic target in NAFLD and metabolic disease.
Collapse
Affiliation(s)
- Kapil K Upadhyay
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Ann Arbor, Michigan, USA
| | - Xiaomeng Du
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Ann Arbor, Michigan, USA
| | - Yanhua Chen
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Ann Arbor, Michigan, USA
| | - Brandon Buscher
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Ann Arbor, Michigan, USA
| | - Vincent L Chen
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Ann Arbor, Michigan, USA
| | - Antonino Oliveri
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Ann Arbor, Michigan, USA
| | - Raymond Zhao
- University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Elizabeth K Speliotes
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Graham F Brady
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Ann Arbor, Michigan, USA.
| |
Collapse
|
16
|
Patchen BK, Balte P, Bartz TM, Barr RG, Fornage M, Graff M, Jacobs DR, Kalhan R, Lemaitre RN, O'Connor G, Psaty B, Seo J, Tsai MY, Wood AC, Xu H, Zhang J, Gharib SA, Manichaikul A, North K, Steffen LM, Dupuis J, Oelsner E, Hancock DB, Cassano PA. Investigating Associations of Omega-3 Fatty Acids, Lung Function Decline, and Airway Obstruction. Am J Respir Crit Care Med 2023; 208:846-857. [PMID: 37470492 DOI: 10.1164/rccm.202301-0074oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/26/2023] [Indexed: 07/21/2023] Open
Abstract
Rationale: Inflammation contributes to lung function decline and the development of chronic obstructive pulmonary disease. Omega-3 fatty acids have antiinflammatory properties and may benefit lung health. Objectives: To investigate associations of omega-3 fatty acids with lung function decline and incident airway obstruction in a diverse sample of adults from general-population cohorts. Methods: Complementary study designs: 1) longitudinal study of plasma phospholipid omega-3 fatty acids and repeated FEV1 and FVC measures in the NHLBI Pooled Cohorts Study and 2) two-sample Mendelian randomization (MR) study of genetically predicted omega-3 fatty acids and lung function parameters. Measurements and Main Results: The longitudinal study found that higher omega-3 fatty acid levels were associated with attenuated lung function decline in 15,063 participants, with the largest effect sizes for the most metabolically downstream omega-3 fatty acid, docosahexaenoic acid (DHA). An increase in DHA of 1% of total fatty acids was associated with attenuations of 1.4 ml/yr for FEV1 (95% confidence interval [CI], 1.1-1.8) and 2.0 ml/yr for FVC (95% CI, 1.6-2.4) and a 7% lower incidence of spirometry-defined airway obstruction (95% CI, 0.89-0.97). DHA associations persisted across sexes and smoking histories and in Black, White, and Hispanic participants, with associations of the largest magnitude in former smokers and Hispanic participants. The MR study showed similar trends toward positive associations of genetically predicted downstream omega-3 fatty acids with FEV1 and FVC. Conclusions: The longitudinal and MR studies provide evidence supporting beneficial effects of higher levels of downstream omega-3 fatty acids, especially DHA, on lung health.
Collapse
Affiliation(s)
- Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | - Pallavi Balte
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health
| | - R Graham Barr
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - David R Jacobs
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, Minnesota
| | - Ravi Kalhan
- Departments of Medicine and Preventative Medicine, Northwestern Medicine, Chicago, Illinois
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health
| | - George O'Connor
- Pulmonary, Allergy, Sleep and Critical Care Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health
| | - Jungkyun Seo
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Alexis C Wood
- U.S. Department of Agriculture/Agricultural Research Service Children Nutrition Research Center, Houston, Texas
| | - Hanfei Xu
- Departments of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Jingwen Zhang
- Departments of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Sina A Gharib
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, Washington
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Kari North
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
| | - Lyn M Steffen
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Josée Dupuis
- U.S. Department of Agriculture/Agricultural Research Service Children Nutrition Research Center, Houston, Texas
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montréal, Québec, Canada
| | - Elizabeth Oelsner
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Dana B Hancock
- RTI International, Research Triangle Park, North Carolina; and
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York
| |
Collapse
|
17
|
Zhang Y, Zhao W, Liu K, Chen Z, Fei Q, Ahmad N, Yi M. The causal associations of altered inflammatory proteins with sleep duration, insomnia and daytime sleepiness. Sleep 2023; 46:zsad207. [PMID: 37535878 DOI: 10.1093/sleep/zsad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/27/2023] [Indexed: 08/05/2023] Open
Abstract
STUDY OBJECTIVES Growing evidence linked inflammation with sleep. This study aimed to evaluate the associations and causal effects of sleep traits including insomnia, excessive daytime sleepiness (EDS), and sleep duration (short: <7 h; normal: 7-9 h; long: ≥9 h), with levels of C-reactive protein (CRP), tumor necrosis factor-alpha (TNF-α), and interleukins. METHODS Standard procedures of quantitative analysis were applied to estimate the expression differences for each protein in compared groups. Then, a two-sample Mendelian randomization (MR) analysis was performed to explore their causal relationships with published genome-wide association study summary statistics. The inverse-variance weighted was used as the primary method, followed by several complementary approaches as sensitivity analyses. RESULTS A total of 44 publications with 51 879 participants were included in the quantitative analysis. Our results showed that the levels of CRP, interleukin-1β (IL-1β), IL-6, and TNF-α were higher from 0.36 to 0.58 (after standardization) in insomnia compared with controls, while there was no significant difference between participants with EDS and controls. Besides, there was a U/J-shaped expression of CRP and IL-6 with sleep durations. In MR analysis, the primary results demonstrated the causal effects of CRP on sleep duration (estimate: 0.017; 95% confidence intervals [CI], [0.003, 0.031]) and short sleep duration (estimate: -0.006; 95% CI, [-0.011, -0.001]). Also, IL-6 was found to be associated with long sleep duration (estimate: 0.006; 95% CI, [0.000, 0.013]). These results were consistent in sensitivity analyses. CONCLUSIONS There are high inflammatory profiles in insomnia and extremes of sleep duration. Meanwhile, elevated CRP and IL-6 have causal effects on longer sleep duration. Further studies can focus on related upstream and downstream mechanisms.
Collapse
Affiliation(s)
- Yuan Zhang
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wangcheng Zhao
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Kun Liu
- School of Life Sciences, Central South University, Changsha, China
| | - Ziliang Chen
- School of Life Sciences, Central South University, Changsha, China
| | - Quanming Fei
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Namra Ahmad
- School of Life Sciences, Central South University, Changsha, China
| | - Minhan Yi
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- School of Life Sciences, Central South University, Changsha, China
| |
Collapse
|
18
|
Xu C, Ganesh SK, Zhou X. mtPGS: Leverage multiple correlated traits for accurate polygenic score construction. Am J Hum Genet 2023; 110:1673-1689. [PMID: 37716346 PMCID: PMC10577082 DOI: 10.1016/j.ajhg.2023.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/18/2023] [Accepted: 08/27/2023] [Indexed: 09/18/2023] Open
Abstract
Accurate polygenic scores (PGSs) facilitate the genetic prediction of complex traits and aid in the development of personalized medicine. Here, we develop a statistical method called multi-trait assisted PGS (mtPGS), which can construct accurate PGSs for a target trait of interest by leveraging multiple traits relevant to the target trait. Specifically, mtPGS borrows SNP effect size similarity information between the target trait and its relevant traits to improve the effect size estimation on the target trait, thus achieving accurate PGSs. In the process, mtPGS flexibly models the shared genetic architecture between the target and the relevant traits to achieve robust performance, while explicitly accounting for the environmental covariance among them to accommodate different study designs with various sample overlap patterns. In addition, mtPGS uses only summary statistics as input and relies on a deterministic algorithm with several algebraic techniques for scalable computation. We evaluate the performance of mtPGS through comprehensive simulations and applications to 25 traits in the UK Biobank, where in the real data mtPGS achieves an average of 0.90%-52.91% accuracy gain compared to the state-of-the-art PGS methods. Overall, mtPGS represents an accurate, fast, and robust solution for PGS construction in biobank-scale datasets.
Collapse
Affiliation(s)
- Chang Xu
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Santhi K Ganesh
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
| |
Collapse
|
19
|
Hollmén M, Laaka A, Partanen JJ, Koskela J, Sutinen E, Kaarteenaho R, Ainola M, Myllärniemi M. KIF15 missense variant is associated with the early onset of idiopathic pulmonary fibrosis. Respir Res 2023; 24:240. [PMID: 37777755 PMCID: PMC10543873 DOI: 10.1186/s12931-023-02540-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/15/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) has an unknown aetiology and limited treatment options. A recent meta-analysis identified three novel causal variants in the TERT, SPDL1, and KIF15 genes. This observational study aimed to investigate whether the aforementioned variants cause clinical phenotypes in a well-characterised IPF cohort. METHODS The study consisted of 138 patients with IPF who were diagnosed and treated at the Helsinki University Hospital and genotyped in the FinnGen FinnIPF study. Data on > 25 clinical parameters were collected by two pulmonologists who were blinded to the genetic data for patients with TERT loss of function and missense variants, SPDL1 and KIF15 missense variants, and a MUC5B variant commonly present in patients with IPF, or no variants were separately analysed. RESULTS The KIF15 missense variant is associated with the early onset of the disease, leading to progression to early-age transplantation or death. In patients with the KIF15 variant, the median age at diagnosis was 54.0 years (36.5-69.5 years) compared with 72.0 years (65.8-75.3 years) in the other patients (P = 0.023). The proportion of KIF15 variant carriers was 9- or 3.6-fold higher in patients aged < 55 or 65 years, respectively. The variants for TERT and MUC5B had similar effects on the patient's clinical course, as previously described. No distinct phenotypes were observed in patients with the SPDL1 variant. CONCLUSIONS Our study indicated the potential of KIF15 to be used in the genetic diagnostics of IPF. Further studies are needed to elucidate the biological mechanisms of KIF15 in IPF.
Collapse
Affiliation(s)
- Maria Hollmén
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
| | - Atte Laaka
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
| | - Juulia J. Partanen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Jukka Koskela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Eva Sutinen
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
| | - Riitta Kaarteenaho
- Research Unit of Biomedicine and Internal Medicine, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Mari Ainola
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
| | - Marjukka Myllärniemi
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
| |
Collapse
|
20
|
Manning A, Sevilla-González M, Smith K, Wang N, Jensen A, Litkowski E, Kim H, DiCorpo D, Westerman K, Cui J, Liu CT, Yu C, McNeil J, Lacaze P, Chang KM, Tsao P, Phillips L, Goodarzi M, Sladek R, Rotter J, Dupuis J, Florez J, Merino J, Meigs J, Zhou J, Raghavan S, Udler M. Heterogeneous effects on type 2 diabetes and cardiovascular outcomes of genetic variants and traits associated with fasting insulin. RESEARCH SQUARE 2023:rs.3.rs-3317661. [PMID: 37790568 PMCID: PMC10543499 DOI: 10.21203/rs.3.rs-3317661/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Hyperinsulinemia is a complex and heterogeneous phenotype that characterizes molecular alterations that precede the development of type 2 diabetes (T2D). It results from a complex combination of molecular processes, including insulin secretion and insulin sensitivity, that differ between individuals. To better understand the physiology of hyperinsulinemia and ultimately T2D, we implemented a genetic approach grouping fasting insulin (FI)-associated genetic variants based on their molecular and phenotypic similarities. We identified seven distinctive genetic clusters representing different physiologic mechanisms leading to rising FI levels, ranging from clusters of variants with effects on increased FI, but without increased risk of T2D (non-diabetogenic hyperinsulinemia), to clusters of variants that increase FI and T2D risk with demonstrated strong effects on body fat distribution, liver, lipid, and inflammatory processes (diabetogenic hyperinsulinemia). We generated cluster-specific polygenic scores in 1,104,258 individuals from five multi-ancestry cohorts to show that the clusters differed in associations with cardiometabolic traits. Among clusters characterized by non-diabetogenic hyperinsulinemia, there was both increased and decreased risk of coronary artery disease despite the non-increased risk of T2D. Similarly, the clusters characterized by diabetogenic hyperinsulinemia were associated with an increased risk of T2D, yet had differing risks of cardiovascular conditions, including coronary artery disease, myocardial infarction, and stroke. The strongest cluster-T2D associations were observed with the same direction of effect in non-Hispanic Black, Hispanic, non-Hispanic White, and non-Hispanic East Asian populations. These genetic clusters provide important insights into granular metabolic processes underlying the physiology of hyperinsulinemia, notably highlighting specific processes that decouple increasing FI levels from T2D and cardiovascular risk. Our findings suggest that increasing FI levels are not invariably associated with adverse cardiometabolic outcomes.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kyong-Mi Chang
- The Corporal Michael J. Crescenz Veterans Affairs Medical Center and University of Pennsylvania Perelman School of Medicine
| | - Phil Tsao
- Stanford University School of Medicine
| | | | | | | | - Jerome Rotter
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
| | | | | | | | - James Meigs
- Department of Medicine, Harvard Medical School
| | | | | | | |
Collapse
|
21
|
Liu Z, Wang H, Yang Z, Lu Y, Zou C. Causal associations between type 1 diabetes mellitus and cardiovascular diseases: a Mendelian randomization study. Cardiovasc Diabetol 2023; 22:236. [PMID: 37659996 PMCID: PMC10475187 DOI: 10.1186/s12933-023-01974-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/25/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND The presence of type 1 diabetes mellitus (T1DM) has been demonstrated to pose an increased risk for developing cardiovascular diseases (CVDs). However, the causal relationships between T1DM and CVDs remain unclear due to the uncontrolled confounding factors and reverse causation bias of the observational studies. METHODS Summary statistics of T1DM and seven CVDs from the largest available genome-wide association studies (GWAS) of European ancestry and FinnGen biobank were extracted for the primary MR analysis, and the analysis was replicated using UK biobank (UKBB) for validation. Three complementary methods: inverse variance weighted (IVW), weighted median, and MR-Egger were used for the MR estimates. The potential pleiotropic effects were assessed by MR-Egger intercept and MR-PRESSO global test. Additionally, multivariable MR (MVMR) analysis was performed to examine whether T1DM has independent effects on CVDs with adjustment of potential confounding factors. Moreover, a two-step MR approach was used to assess the potential mediating effects of these factors on the causal effects between T1DM and CVDs. RESULTS Causal effects of T1DM on peripheral atherosclerosis (odds ratio [OR] = 1.06, 95% confidence interval [CI]: 1.02-1.10; p = 0.002)] and coronary atherosclerosis (OR = 1.03, 95% CI: 1.01-1.05; p = 0.001) were found. The results were less likely to be biased by the horizontal pleiotropic effects (both p values of MR-Egger intercept and MR-PRESSO Global test > 0.05). In the following MVMR analysis, we found the causal effects of T1DM on peripheral atherosclerosis and coronary atherosclerosis remain significant after adjusting for a series of potential confounding factors. Moreover, we found that hypertension partly mediated the causal effects of T1DM on peripheral atherosclerosis (proportion of mediation effect in total effect: 11.47%, 95% CI: 3.23-19.71%) and coronary atherosclerosis (16.84%, 95% CI: 5.35-28.33%). We didn't find significant causal relationships between T1DM and other CVDs, including heart failure (HF), coronary artery disease (CAD), atrial fibrillation (AF), myocardial infarction (MI) and stroke. For the reverse MR from CVD to T1DM, no significant causal relationships were identified. CONCLUSION This MR study provided evidence supporting the causal effect of T1DM on peripheral atherosclerosis and coronary atherosclerosis, with hypertension partly mediating this effect.
Collapse
Affiliation(s)
- Zirui Liu
- Department of Cardiology, First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou City, Jiangsu Province, China
| | - Haocheng Wang
- Department of Cardiology, First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou City, Jiangsu Province, China
| | - Zhengkai Yang
- Department of Cardiology, First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou City, Jiangsu Province, China
| | - Yu Lu
- Department of Cardiology, First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou City, Jiangsu Province, China
| | - Cao Zou
- Department of Cardiology, First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou City, Jiangsu Province, China.
| |
Collapse
|
22
|
Stevelink R, Campbell C, Chen S, Abou-Khalil B, Adesoji OM, Afawi Z, Amadori E, Anderson A, Anderson J, Andrade DM, Annesi G, Auce P, Avbersek A, Bahlo M, Baker MD, Balagura G, Balestrini S, Barba C, Barboza K, Bartolomei F, Bast T, Baum L, Baumgartner T, Baykan B, Bebek N, Becker AJ, Becker F, Bennett CA, Berghuis B, Berkovic SF, Beydoun A, Bianchini C, Bisulli F, Blatt I, Bobbili DR, Borggraefe I, Bosselmann C, Braatz V, Bradfield JP, Brockmann K, Brody LC, Buono RJ, Busch RM, Caglayan H, Campbell E, Canafoglia L, Canavati C, Cascino GD, Castellotti B, Catarino CB, Cavalleri GL, Cerrato F, Chassoux F, Cherny SS, Cheung CL, Chinthapalli K, Chou IJ, Chung SK, Churchhouse C, Clark PO, Cole AJ, Compston A, Coppola A, Cosico M, Cossette P, Craig JJ, Cusick C, Daly MJ, Davis LK, de Haan GJ, Delanty N, Depondt C, Derambure P, Devinsky O, Di Vito L, Dlugos DJ, Doccini V, Doherty CP, El-Naggar H, Elger CE, Ellis CA, Eriksson JG, Faucon A, Feng YCA, Ferguson L, Ferraro TN, Ferri L, Feucht M, Fitzgerald M, Fonferko-Shadrach B, Fortunato F, Franceschetti S, Franke A, French JA, Freri E, Gagliardi M, Gambardella A, Geller EB, Giangregorio T, Gjerstad L, Glauser T, Goldberg E, Goldman A, Granata T, Greenberg DA, Guerrini R, Gupta N, Haas KF, Hakonarson H, Hallmann K, Hassanin E, Hegde M, Heinzen EL, Helbig I, Hengsbach C, Heyne HO, Hirose S, Hirsch E, Hjalgrim H, Howrigan DP, Hucks D, Hung PC, Iacomino M, Imbach LL, Inoue Y, Ishii A, Jamnadas-Khoda J, Jehi L, Johnson MR, Kälviäinen R, Kamatani Y, Kanaan M, Kanai M, Kantanen AM, Kara B, Kariuki SM, Kasperavičiūte D, Kasteleijn-Nolst Trenite D, Kato M, Kegele J, Kesim Y, Khoueiry-Zgheib N, King C, Kirsch HE, Klein KM, Kluger G, Knake S, Knowlton RC, Koeleman BPC, Korczyn AD, Koupparis A, Kousiappa I, Krause R, Krenn M, Krestel H, Krey I, Kunz WS, Kurki MI, Kurlemann G, Kuzniecky R, Kwan P, Labate A, Lacey A, Lal D, Landoulsi Z, Lau YL, Lauxmann S, Leech SL, Lehesjoki AE, Lemke JR, Lerche H, Lesca G, Leu C, Lewin N, Lewis-Smith D, Li GHY, Li QS, Licchetta L, Lin KL, Lindhout D, Linnankivi T, Lopes-Cendes I, Lowenstein DH, Lui CHT, Madia F, Magnusson S, Marson AG, May P, McGraw CM, Mei D, Mills JL, Minardi R, Mirza N, Møller RS, Molloy AM, Montomoli M, Mostacci B, Muccioli L, Muhle H, Müller-Schlüter K, Najm IM, Nasreddine W, Neale BM, Neubauer B, Newton CRJC, Nöthen MM, Nothnagel M, Nürnberg P, O’Brien TJ, Okada Y, Ólafsson E, Oliver KL, Özkara C, Palotie A, Pangilinan F, Papacostas SS, Parrini E, Pato CN, Pato MT, Pendziwiat M, Petrovski S, Pickrell WO, Pinsky R, Pippucci T, Poduri A, Pondrelli F, Powell RHW, Privitera M, Rademacher A, Radtke R, Ragona F, Rau S, Rees MI, Regan BM, Reif PS, Rhelms S, Riva A, Rosenow F, Ryvlin P, Saarela A, Sadleir LG, Sander JW, Sander T, Scala M, Scattergood T, Schachter SC, Schankin CJ, Scheffer IE, Schmitz B, Schoch S, Schubert-Bast S, Schulze-Bonhage A, Scudieri P, Sham P, Sheidley BR, Shih JJ, Sills GJ, Sisodiya SM, Smith MC, Smith PE, Sonsma ACM, Speed D, Sperling MR, Stefansson H, Stefansson K, Steinhoff BJ, Stephani U, Stewart WC, Stipa C, Striano P, Stroink H, Strzelczyk A, Surges R, Suzuki T, Tan KM, Taneja RS, Tanteles GA, Taubøll E, Thio LL, Thomas GN, Thomas RH, Timonen O, Tinuper P, Todaro M, Topaloğlu P, Tozzi R, Tsai MH, Tumiene B, Turkdogan D, Unnsteinsdóttir U, Utkus A, Vaidiswaran P, Valton L, van Baalen A, Vetro A, Vining EPG, Visscher F, von Brauchitsch S, von Wrede R, Wagner RG, Weber YG, Weckhuysen S, Weisenberg J, Weller M, Widdess-Walsh P, Wolff M, Wolking S, Wu D, Yamakawa K, Yang W, Yapıcı Z, Yücesan E, Zagaglia S, Zahnert F, Zara F, Zhou W, Zimprich F, Zsurka G, Zulfiqar Ali Q. GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture. Nat Genet 2023; 55:1471-1482. [PMID: 37653029 PMCID: PMC10484785 DOI: 10.1038/s41588-023-01485-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Epilepsy is a highly heritable disorder affecting over 50 million people worldwide, of which about one-third are resistant to current treatments. Here we report a multi-ancestry genome-wide association study including 29,944 cases, stratified into three broad categories and seven subtypes of epilepsy, and 52,538 controls. We identify 26 genome-wide significant loci, 19 of which are specific to genetic generalized epilepsy (GGE). We implicate 29 likely causal genes underlying these 26 loci. SNP-based heritability analyses show that common variants explain between 39.6% and 90% of genetic risk for GGE and its subtypes. Subtype analysis revealed markedly different genetic architectures between focal and generalized epilepsies. Gene-set analyses of GGE signals implicate synaptic processes in both excitatory and inhibitory neurons in the brain. Prioritized candidate genes overlap with monogenic epilepsy genes and with targets of current antiseizure medications. Finally, we leverage our results to identify alternate drugs with predicted efficacy if repurposed for epilepsy treatment.
Collapse
|
23
|
Ding Y, Yang S, He M, Fan S, Tao X, Lu W. Lipid Metabolism Traits Mediate the Effect of Psoriasis on Myocardial Infarction Risk: A Two-Step Mendelian Randomization Study. Metabolites 2023; 13:976. [PMID: 37755256 PMCID: PMC10538214 DOI: 10.3390/metabo13090976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/28/2023] Open
Abstract
Mendelian randomization (MR) analysis was performed to explore the effect of psoriasis on lipid metabolism traits and myocardial infarction (MI) risk and to analyze the proportion of the mediatory effect of lipid metabolism traits. Publicly accessible summary-level data for psoriasis, lipid metabolism traits, and MI were provided by the genome-wide association studies (GWASs) of the FinnGen Biobank, UK Biobank, and CARDIoGRAMplusC4D, respectively. A two-sample MR was carried out to evaluate the association of psoriasis with lipid metabolism traits and MI. Furthermore, the current research focused on determining if the impact of psoriasis on MI is mediated by lipid metabolism traits. The outcomes of the random effect inverse-variance-weighted (IVW) technique indicated a substantial link between genetically predicted psoriasis and a higher risk of low-density lipoprotein (LDL) cholesterol (OR: 1.006, 95% CI: 1.005-1.007, p = 0.024), apolipoprotein B (OR: 1.018, 95% CI: 1.010-1.026, p = 0.015), lipoprotein A (OR: 1.006, 95% CI: 1.002-1.010, p = 0.039), and MI (OR: 1.066, 95% CI: 1.014-1.121, p = 0.012). The percentages of the mediatory effect of LDL cholesterol, apolipoprotein B, and lipoprotein A under psoriasis conditions on MI risk was 7.4%, 10.2%, and 4.1%, respectively. Psoriasis was causally linked to an elevated risk of lipid metabolism levels and MI. This study further demonstrated that LDL cholesterol, apolipoprotein B, and lipoprotein A mediated the effect of psoriasis on MI risk. And timely lipid-lowering treatment should be given to MI patients.
Collapse
Affiliation(s)
- Yang Ding
- Center for Plastic & Reconstructive Surgery, Department of Dermatology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital of Hangzhou Medical College, Hangzhou 310014, China; (Y.D.); (S.F.)
| | - Shengyi Yang
- Department of Infection Control, Second Afliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China;
| | - Mengjiao He
- Departments of Environmental Health, School of Public Health, Hangzhou Normal University, Hangzhou 310009, China;
| | - Shasha Fan
- Center for Plastic & Reconstructive Surgery, Department of Dermatology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital of Hangzhou Medical College, Hangzhou 310014, China; (Y.D.); (S.F.)
| | - Xiaohua Tao
- Center for Plastic & Reconstructive Surgery, Department of Dermatology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital of Hangzhou Medical College, Hangzhou 310014, China; (Y.D.); (S.F.)
| | - Wei Lu
- Center for Plastic & Reconstructive Surgery, Department of Dermatology, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital of Hangzhou Medical College, Hangzhou 310014, China; (Y.D.); (S.F.)
| |
Collapse
|
24
|
Shen JY, Xu L, Ding Y, Wu XY. Effect of vitamin supplementation on polycystic ovary syndrome and key pathways implicated in its development: A Mendelian randomization study. World J Clin Cases 2023; 11:5468-5478. [PMID: 37637683 PMCID: PMC10450375 DOI: 10.12998/wjcc.v11.i23.5468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Many epidemiologic investigations have explored the relationship between viatmins and polycystic ovary syndrome (PCOS). However, the effectiveness of vitamin, vitamin-like nutrient, or mineral supplementation in reducing the risk of PCOS remains a subject of debate. AIM To investigate the impact of plasma levels of vitamins A, B12, D, E, and K on PCOS and key pathways implicated in its development, namely, insulin resistance, hyperlipidemia, and obesity, through Mendelian randomization (MR) analysis. METHODS Single nucleotide polymorphisms associated with vitamin levels were selected from genome-wide association studies. The primary analysis was performed using the random-effects inverse-variance-weighted approach. Complementary analyses were conducted using the weighted median, MR-Egger, MR-robust adjusted profile score, and MR-PRESSO approaches. RESULTS The results provided suggestive evidence of a decreased risk of PCOS with genetically predicted higher levels of vitamin E (odds ratio [OR] = 0.118; 95% confidence interval [CI]: 0.071-0.226; P < 0.001) and vitamin B12 (OR = 0.753, 95%CI: 0.568-0.998, P = 0.048). An association was observed between vitamin E levels and insulin resistance (OR = 0.977, 95%CI: 0.976-0.978, P < 0.001). Additionally, genetically predicted higher concentrations of vitamins E, D, and A were suggested to be associated with a decreased risk of hyperlipidemia. Increased vitamins K and B12 levels were linked to a lower obesity risk (OR = 0.917, 95%CI: 0.848-0.992, P = 0.031). CONCLUSION The findings of this MR study suggest a causal relationship between increased vitamins A, D, E, K, and B12 levels and a reduced risk of PCOS or primary pathways implicated in its development.
Collapse
Affiliation(s)
- Jia-Yan Shen
- Department of Reproductive Medicine, Huzhou Maternity & Child Health Care Hospital, Huzhou 313000, Zhejiang Province, China
| | - Li Xu
- Department of Obstetrics and Gynecology, Huzhou Maternity & Child Health Care Hospital, Huzhou 313000, Zhejiang Province, China
| | - Yang Ding
- Department of Dermatology, Zhejiang Provincial People’s Hospital, Hangzhou 310014, Zhejiang Province, China
| | - Xiao-Yun Wu
- Department of Reproductive Medicine, Huzhou Maternity & Child Health Care Hospital, Huzhou 313000, Zhejiang Province, China
| |
Collapse
|
25
|
Yang S, Tan W, Wei B, Gu C, Li S, Wang S. Association between alcohol and urolithiasis: a mendelian randomization study. Urolithiasis 2023; 51:103. [PMID: 37581757 PMCID: PMC10427707 DOI: 10.1007/s00240-023-01472-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 08/16/2023]
Abstract
The causal relationship between alcohol and urolithiasis remains uncertain, despite previous observational studies reporting an association between the two. To determine the causality, we conducted a two-sample Mendelian randomization (MR) analysis. In this study, we aimed to investigate the causal relationship between alcohol and kidney stones using a two-sample MR approach. Two sets of genetic instruments were utilized in the analysis, both of which were derived from publicly available genetic summary data. The first set consisted of 73 single-nucleotide polymorphisms (SNPs) robustly linked to alcohol intake frequency (AIF) and the second set was comprised of 69 SNPs associated with alcohol consumption (AC). Our MR analysis was performed using several methods including the inverse-variance weighted (IVW) method, weighted median method, MR-Egger regression, MR Pleiotropy RESidual Sum and Outlier test. Our results from the MR analysis revealed a borderline significant association between AIF and the risk of urolithiasis. This was established through the use of the IVW method (OR (95% CI) = 1.29 (1.02, 1.65), p = 0.036) and the weighted median approach (OR (95% CI) = 1.44 (1.10, 1.89), p = 0.008). The MR-Egger model also yielded similar risk estimates (OR (95% CI) = 1.39 (0.66, 2.93), p = 0.386), although the relationship was not statistically significant. Sixty-eight SNPs were identified as having a substantial and independent link with AC. However, the IVW approach revealed no significant effect of AC on the risk of urolithiasis (OR (95% CI) = 0.74 (0.48, 1.14), p = 0.173). The MR analysis suggested a potential causal association between alcohol intake frequency and the risk of urolithiasis, but not alcohol consumption.
Collapse
Affiliation(s)
- Shijian Yang
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Wenyue Tan
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Baian Wei
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chiming Gu
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Siyi Li
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Shusheng Wang
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China.
| |
Collapse
|
26
|
Edwards TL, Greene CA, Piekos JA, Hellwege JN, Hampton G, Jasper EA, Velez Edwards DR. Challenges and Opportunities for Data Science in Women's Health. Annu Rev Biomed Data Sci 2023; 6:23-45. [PMID: 37040736 PMCID: PMC10877578 DOI: 10.1146/annurev-biodatasci-020722-105958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The intersection of women's health and data science is a field of research that has historically trailed other fields, but more recently it has gained momentum. This growth is being driven not only by new investigators who are moving into this area but also by the significant opportunities that have emerged in new methodologies, resources, and technologies in data science. Here, we describe some of the resources and methods being used by women's health researchers today to meet challenges in biomedical data science. We also describe the opportunities and limitations of applying these approaches to advance women's health outcomes and the future of the field, with emphasis on repurposing existing methodologies for women's health.
Collapse
Affiliation(s)
- Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Catherine A Greene
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jacqueline A Piekos
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jacklyn N Hellwege
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gabrielle Hampton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Elizabeth A Jasper
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Precision Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Digna R Velez Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
27
|
Trajanoska K, Bhérer C, Taliun D, Zhou S, Richards JB, Mooser V. From target discovery to clinical drug development with human genetics. Nature 2023; 620:737-745. [PMID: 37612393 DOI: 10.1038/s41586-023-06388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/29/2023] [Indexed: 08/25/2023]
Abstract
The substantial investments in human genetics and genomics made over the past three decades were anticipated to result in many innovative therapies. Here we investigate the extent to which these expectations have been met, excluding cancer treatments. In our search, we identified 40 germline genetic observations that led directly to new targets and subsequently to novel approved therapies for 36 rare and 4 common conditions. The median time between genetic target discovery and drug approval was 25 years. Most of the genetically driven therapies for rare diseases compensate for disease-causing loss-of-function mutations. The therapies approved for common conditions are all inhibitors designed to pharmacologically mimic the natural, disease-protective effects of rare loss-of-function variants. Large biobank-based genetic studies have the power to identify and validate a large number of new drug targets. Genetics can also assist in the clinical development phase of drugs-for example, by selecting individuals who are most likely to respond to investigational therapies. This approach to drug development requires investments into large, diverse cohorts of deeply phenotyped individuals with appropriate consent for genetically assisted trials. A robust framework that facilitates responsible, sustainable benefit sharing will be required to capture the full potential of human genetics and genomics and bring effective and safe innovative therapies to patients quickly.
Collapse
Affiliation(s)
- Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Claude Bhérer
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Daniel Taliun
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology and Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada.
| |
Collapse
|
28
|
Patel AP, Wang M, Ruan Y, Koyama S, Clarke SL, Yang X, Tcheandjieu C, Agrawal S, Fahed AC, Ellinor PT, Tsao PS, Sun YV, Cho K, Wilson PWF, Assimes TL, van Heel DA, Butterworth AS, Aragam KG, Natarajan P, Khera AV. A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease. Nat Med 2023; 29:1793-1803. [PMID: 37414900 PMCID: PMC10353935 DOI: 10.1038/s41591-023-02429-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/30/2023] [Indexed: 07/08/2023]
Abstract
Identification of individuals at highest risk of coronary artery disease (CAD)-ideally before onset-remains an important public health need. Prior studies have developed genome-wide polygenic scores to enable risk stratification, reflecting the substantial inherited component to CAD risk. Here we develop a new and significantly improved polygenic score for CAD, termed GPSMult, that incorporates genome-wide association data across five ancestries for CAD (>269,000 cases and >1,178,000 controls) and ten CAD risk factors. GPSMult strongly associated with prevalent CAD (odds ratio per standard deviation 2.14, 95% confidence interval 2.10-2.19, P < 0.001) in UK Biobank participants of European ancestry, identifying 20.0% of the population with 3-fold increased risk and conversely 13.9% with 3-fold decreased risk as compared with those in the middle quintile. GPSMult was also associated with incident CAD events (hazard ratio per standard deviation 1.73, 95% confidence interval 1.70-1.76, P < 0.001), identifying 3% of healthy individuals with risk of future CAD events equivalent to those with existing disease and significantly improving risk discrimination and reclassification. Across multiethnic, external validation datasets inclusive of 33,096, 124,467, 16,433 and 16,874 participants of African, European, Hispanic and South Asian ancestry, respectively, GPSMult demonstrated increased strength of associations across all ancestries and outperformed all available previously published CAD polygenic scores. These data contribute a new GPSMult for CAD to the field and provide a generalizable framework for how large-scale integration of genetic association data for CAD and related traits from diverse populations can meaningfully improve polygenic risk prediction.
Collapse
Affiliation(s)
- Aniruddh P Patel
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - 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.
| | - Yunfeng Ruan
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Satoshi Koyama
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Veteran Affairs Boston Healthcare System, Boston, MA, USA
| | - Shoa L Clarke
- Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Xiong Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | | | - Saaket Agrawal
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Akl C Fahed
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Philip S Tsao
- Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Yan V Sun
- Veteran Affairs Atlanta Healthcare System, Decatur, GA, USA
| | - Kelly Cho
- Veteran Affairs Boston Healthcare System, Boston, MA, USA
| | | | - Themistocles L Assimes
- Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, and Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Krishna G Aragam
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Pradeep Natarajan
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Amit V Khera
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Verve Therapeutics, Boston, MA, USA.
| |
Collapse
|
29
|
Ray D, Loomis SJ, Venkataraghavan S, Tin A, Yu B, Chatterjee N, Selvin E, Duggal P. Characterizing common and rare variations in non-traditional glycemic biomarkers using multivariate approaches on multi-ancestry ARIC study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.13.23289200. [PMID: 37398180 PMCID: PMC10312851 DOI: 10.1101/2023.06.13.23289200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Glycated hemoglobin, fasting glucose, glycated albumin, and fructosamine are biomarkers that reflect different aspects of the glycemic process. Genetic studies of these glycemic biomarkers can shed light on unknown aspects of type 2 diabetes genetics and biology. While there exists several GWAS of glycated hemoglobin and fasting glucose, very few GWAS have focused on glycated albumin or fructosamine. We performed a multi-phenotype GWAS of glycated albumin and fructosamine from 7,395 White and 2,016 Black participants in the Atherosclerosis Risk in Communities (ARIC) study on the common variants from genotyped/imputed data. We found 2 genome-wide significant loci, one mapping to known type 2 diabetes gene (ARAP1/STARD10, p = 2.8 × 10-8) and another mapping to a novel gene (UGT1A, p = 1.4 × 10-8) using multi-omics gene mapping strategies in diabetes-relevant tissues. We identified additional loci that were ancestry-specific (e.g., PRKCA from African ancestry individuals, p = 1.7 × 10-8) and sex-specific (TEX29 locus in males only, p = 3.0 × 10-8). Further, we implemented multi-phenotype gene-burden tests on whole-exome sequence data from 6,590 White and 2,309 Black ARIC participants. Eleven genes across different rare variant aggregation strategies were exome-wide significant only in multi-ancestry analysis. Four out of 11 genes had notable enrichment of rare predicted loss of function variants in African ancestry participants despite smaller sample size. Overall, 8 out of 15 loci/genes were implicated to influence these biomarkers via glycemic pathways. This study illustrates improved locus discovery and potential effector gene discovery by leveraging joint patterns of related biomarkers across entire allele frequency spectrum in multi-ancestry analyses. Most of the loci/genes we identified have not been previously implicated in studies of type 2 diabetes, and future investigation of the loci/genes potentially acting through glycemic pathways may help us better understand risk of developing type 2 diabetes.
Collapse
Affiliation(s)
- Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | | | - Sowmya Venkataraghavan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Adrienne Tin
- School of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Bing Yu
- Department of Epidemiology, UTHealth School of Public Health, Houston, TX
| | - Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Elizabeth Selvin
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
- Welch Center for Prevention, Epidemiology, & Clinical Research, Johns Hopkins University, Baltimore, MD
| | - Priya Duggal
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| |
Collapse
|
30
|
Gilbert E, Zurel H, MacMillan ME, Demiriz S, Mirhendi S, Merrigan M, O'Reilly S, Molloy AM, Brody LC, Bodmer W, Leach RA, Scott REM, Mugford G, Randhawa R, Stephens JC, Symington AL, Cavalleri GL, Phillips MS. The Newfoundland and Labrador mosaic founder population descends from an Irish and British diaspora from 300 years ago. Commun Biol 2023; 6:469. [PMID: 37117635 PMCID: PMC10147672 DOI: 10.1038/s42003-023-04844-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/28/2023] [Indexed: 04/30/2023] Open
Abstract
The founder population of Newfoundland and Labrador (NL) is a unique genetic resource, in part due to its geographic and cultural isolation, where historical records describe a migration of European settlers, primarily from Ireland and England, to NL in the 18th and 19th centuries. Whilst its historical isolation, and increased prevalence of certain monogenic disorders are well appreciated, details of the fine-scale genetic structure and ancestry of the population are lacking. Understanding the genetic origins and background of functional, disease causing, genetic variants would aid genetic mapping efforts in the Province. Here, we leverage dense genome-wide SNP data on 1,807 NL individuals to reveal fine-scale genetic structure in NL that is clustered around coastal communities and correlated with Christian denomination. We show that the majority of NL European ancestry can be traced back to the south-east and south-west of Ireland and England, respectively. We date a substantial population size bottleneck approximately 10-15 generations ago in NL, associated with increased haplotype sharing and autozygosity. Our results reveal insights into the population history of NL and demonstrate evidence of a population conducive to further genetic studies and biomarker discovery.
Collapse
Affiliation(s)
- Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland.
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Heather Zurel
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | | | - Sedat Demiriz
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Sadra Mirhendi
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | | | | | - Anne M Molloy
- School of Medicine, Trinity College, Dublin, Ireland
| | - Lawrence C Brody
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Walter Bodmer
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Richard A Leach
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Roderick E M Scott
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Gerald Mugford
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Ranjit Randhawa
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | | | - Alison L Symington
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Michael S Phillips
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| |
Collapse
|
31
|
Lähteenvuo M, Ahola-Olli A, Suokas K, Holm M, Misiewicz Z, Jukuri T, Männynsalo T, Wegelius A, Haaki W, Kajanne R, Kyttälä A, Tuulio-Henriksson A, Lahdensuo K, Häkkinen K, Hietala J, Paunio T, Niemi-Pynttäri J, Kieseppä T, Veijola J, Lönnqvist J, Isometsä E, Kampman O, Tiihonen J, Hyman S, Neale B, Daly M, Suvisaari J, Palotie A. Cohort profile: SUPER-Finland - the Finnish study for hereditary mechanisms of psychotic disorders. BMJ Open 2023; 13:e070710. [PMID: 37045567 PMCID: PMC10106053 DOI: 10.1136/bmjopen-2022-070710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
PURPOSE SUPER-Finland is a large Finnish collection of psychosis cases. This cohort also represents the Finnish contribution to the Stanley Global Neuropsychiatric Genetics Initiative, which seeks to diversify genetic sample collection to include Asian, Latin American and African populations in addition to known population isolates, such as Finland. PARTICIPANTS 10 474 individuals aged 18 years or older were recruited throughout the country. The subjects have been genotyped with a genome-wide genotyping chip and exome sequenced. A subset of 897 individuals selected from known population sub-isolates were selected for whole-genome sequencing. Recruitment was done between November 2015 and December 2018. FINDINGS TO DATE 5757 (55.2%) had a diagnosis of schizophrenia, 944 (9.1%) schizoaffective disorder, 1612 (15.5%) type I or type II bipolar disorder, 532 (5.1 %) psychotic depression, 1047 (10.0%) other psychosis and for 530 (5.1%) self-reported psychosis at recruitment could not be confirmed from register data. Mean duration of schizophrenia was 22.0 years at the time of the recruitment. By the end of the year 2018, 204 of the recruited individuals had died. The most common cause of death was cardiovascular disease (n=61) followed by neoplasms (n=40). Ten subjects had psychiatric morbidity as the primary cause of death. FUTURE PLANS Compare the effects of common variants, rare variants and copy number variations (CNVs) on severity of psychotic illness. In addition, we aim to track longitudinal course of illness based on nation-wide register data to estimate how phenotypic and genetic differences alter it.
Collapse
Affiliation(s)
- Markku Lähteenvuo
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Ari Ahola-Olli
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kimmo Suokas
- Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Minna Holm
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Zuzanna Misiewicz
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tuomas Jukuri
- Department of Psychiatry, Oulu University Hospital, Oulu, Finland
| | - Teemu Männynsalo
- Psychiatric and Substance Abuse Services, City of Helsinki, Helsinki, Finland
| | - Asko Wegelius
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
- Department of Mental Health and Substance Abuse Services, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Willehard Haaki
- Department of Psychiatry, University of Turku, Turku, Finland
- Department of Psychiatry, TYKS Turku University Hospital, Turku, Finland
| | - Risto Kajanne
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Aija Kyttälä
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Kaisla Lahdensuo
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Mehiläinen Oy, Helsinki, Finland
| | - Katja Häkkinen
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
| | - Jarmo Hietala
- Department of Psychiatry, University of Turku, Turku, Finland
- Department of Psychiatry, TYKS Turku University Hospital, Turku, Finland
| | - Tiina Paunio
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
- SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Tuula Kieseppä
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
| | - Juha Veijola
- Research Unit of Clinical Neuroscience, Department of Psychiatry, University of Oulu, Oulu, Finland
- Medical Research Centre Oulu, University Hospital of Oulu and University of Oulu, Oulu, Finland
| | - Jouko Lönnqvist
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
| | - Erkki Isometsä
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
| | - Olli Kampman
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Psychiatry, The Pirkanmaa Wellbeing Services County, Tampere, Finland
- Department of Clinical Sciences, Psychiatry, Umeå University, Umeå, Sweden
- Department of Clinical Medicine (Psychiatry), Faculty of Medicine, University of Turku, Turku, Finland
- Department of Psychiatry, The Wellbeing Services County of Ostrobothnia, Vaasa, Finland
| | - Jari Tiihonen
- Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Center for Psychiatry Research, Stockholm City Council, Stockholm, Sweden
| | - Steven Hyman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Benjamin Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mark Daly
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| |
Collapse
|
32
|
Wang G, Bond TA, Warrington NM, Evans DM. Birth weight and cardiometabolic risk factors: a discordant twin study in the UK Biobank. J Dev Orig Health Dis 2023; 14:242-248. [PMID: 36193707 PMCID: PMC7615918 DOI: 10.1017/s2040174422000538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
One of the longstanding debates in life-course epidemiology is whether an adverse intrauterine environment, often proxied by birth weight, causally increases the future risk of cardiometabolic disease. The use of a discordant twin study design, which controls for the influence of shared genetic and environmental confounding factors, may be useful to investigate whether this relationship is causal. We conducted a discordant twin study of 120 monozygotic (MZ) and 148 dizygotic (DZ) twin pairs from the UK Biobank to explore the potential causal relationships between birth weight and a broad spectrum of later-life cardiometabolic risk factors. We used a linear mixed model to investigate the association between birth weight and later-life cardiometabolic risk factors for twins, allowing for both within-pair differences and between-pair differences in birth weight. Of primary interest is the within-pair association between differences in birth weight and cardiometabolic risk factors, which could reflect an intrauterine effect on later-life risk factors. We found no strong evidence of association in MZ twins between the within-pair differences in birth weight and most cardiometabolic risk factors in later life, except for nominal associations with C-reactive protein and insulin-like growth factor 1. However, these associations were not replicated in DZ twin pairs. Our study provided no strong evidence for intrauterine effects on later-life cardiometabolic risk factors, which is consistent with previous large-scale studies of singletons testing the potential causal relationship. It does not support the hypothesis that adverse intrauterine environments increase the risk of cardiometabolic disease in later life.
Collapse
Affiliation(s)
- Geng Wang
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Tom A Bond
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
| | - Nicole M Warrington
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - David M Evans
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Australia
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK
| |
Collapse
|
33
|
Jurrjens AW, Seldin MM, Giles C, Meikle PJ, Drew BG, Calkin AC. The potential of integrating human and mouse discovery platforms to advance our understanding of cardiometabolic diseases. eLife 2023; 12:e86139. [PMID: 37000167 PMCID: PMC10065800 DOI: 10.7554/elife.86139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Cardiometabolic diseases encompass a range of interrelated conditions that arise from underlying metabolic perturbations precipitated by genetic, environmental, and lifestyle factors. While obesity, dyslipidaemia, smoking, and insulin resistance are major risk factors for cardiometabolic diseases, individuals still present in the absence of such traditional risk factors, making it difficult to determine those at greatest risk of disease. Thus, it is crucial to elucidate the genetic, environmental, and molecular underpinnings to better understand, diagnose, and treat cardiometabolic diseases. Much of this information can be garnered using systems genetics, which takes population-based approaches to investigate how genetic variance contributes to complex traits. Despite the important advances made by human genome-wide association studies (GWAS) in this space, corroboration of these findings has been hampered by limitations including the inability to control environmental influence, limited access to pertinent metabolic tissues, and often, poor classification of diseases or phenotypes. A complementary approach to human GWAS is the utilisation of model systems such as genetically diverse mouse panels to study natural genetic and phenotypic variation in a controlled environment. Here, we review mouse genetic reference panels and the opportunities they provide for the study of cardiometabolic diseases and related traits. We discuss how the post-GWAS era has prompted a shift in focus from discovery of novel genetic variants to understanding gene function. Finally, we highlight key advantages and challenges of integrating complementary genetic and multi-omics data from human and mouse populations to advance biological discovery.
Collapse
Affiliation(s)
- Aaron W Jurrjens
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, United States
| | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
- Baker Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, Australia
| | - Brian G Drew
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
| | - Anna C Calkin
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Central Clinical School, Monash University, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
| |
Collapse
|
34
|
Chen XH, Liu HQ, Nie Q, Wang H, Xiang T. Causal relationship between type 1 diabetes mellitus and six high-frequency infectious diseases: A two-sample mendelian randomization study. Front Endocrinol (Lausanne) 2023; 14:1135726. [PMID: 37065754 PMCID: PMC10102543 DOI: 10.3389/fendo.2023.1135726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Purpose Type 1 diabetes mellitus (T1DM) is associated with different types of infections; however, studies on the causal relationship between T1DM and infectious diseases are lacking. Therefore, our study aimed to explore the causalities between T1DM and six high-frequency infections using a Mendelian randomization (MR) approach. Methods Two-sample MR studies were conducted to explore the causalities between T1DM and six high-frequency infections: sepsis, acute lower respiratory infections (ALRIs), intestinal infections (IIs), infections of the genitourinary tract (GUTIs) in pregnancy, infections of the skin and subcutaneous tissues (SSTIs), and urinary tract infections (UTIs). Data on summary statistics for T1DM and infections were obtained from the European Bioinformatics Institute database, the United Kingdom Biobank, FinnGen biobank, and Medical Research Council Integrative Epidemiology Unit. All data obtained for summary statistics were from European countries. The inverse-variance weighted (IVW) method was employed as the main analysis. Considering the multiple comparisons, statistical significance was set at p< 0.008. If univariate MR analyses found a significant causal association, multivariable MR (MVMR) analyses were performed to adjust body mass index (BMI) and glycated hemoglobin (HbA1c). MVMR-IVW was performed as the primary analysis, and the least absolute shrinkage and selection operator (LASSO) regression and MVMR-Robust were performed as complementary analyses. Results MR analysis showed that susceptibility to IIs increased in patients with T1DM by 6.09% using the IVW-fixed method [odds ratio (OR)=1.0609; 95% confidence interval (CI): 1.0281-1.0947, p=0.0002]. Results were still significant after multiple testing. Sensitivity analyses did not show any significant horizontal pleiotropy or heterogeneity. After adjusting for BMI and HbA1c, MVMR-IVW (OR=1.0942; 95% CI: 1.0666-1.1224, p<0.0001) showed significant outcomes that were consistent with those of LASSO regression and MVMR-Robust. However, no significant causal relationship was found between T1DM and sepsis susceptibility, ALRI susceptibility, GUTI susceptibility in pregnancy, SSTI susceptibility, and UTI susceptibility. Conclusions Our MR analysis genetically predicted increased susceptibility to IIs in T1DM. However, no causality between T1DM and sepsis, ALRIs, GUTIs in pregnancy, SSTIs, or UTIs was found. Larger epidemiological and metagenomic studies are required to further investigate the observed associations between the susceptibility of certain infectious diseases with T1DM.
Collapse
Affiliation(s)
- Xiao-Hong Chen
- Emergency Department, The Affiliated Hospital of Southwest Jiaotong University, The Third People’s Hospital of Chengdu, Chengdu, Sichuan, China
| | - Hong-Qiong Liu
- Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Qiong Nie
- Department of Geriatrics, The Affiliated Hospital of Southwest Jiaotong University, The Third People’s Hospital of Chengdu, Chengdu, Sichuan, China
| | - Han Wang
- Department of Cardiology, The Affiliated Hospital of Southwest Jiaotong University, The Third People’s Hospital of Chengdu, Chengdu, Sichuan, China
| | - Tao Xiang
- Emergency Department, The Affiliated Hospital of Southwest Jiaotong University, The Third People’s Hospital of Chengdu, Chengdu, Sichuan, China
| |
Collapse
|
35
|
Kim H, Westerman KE, Smith K, Chiou J, Cole JB, Majarian T, von Grotthuss M, Kwak SH, Kim J, Mercader JM, Florez JC, Gaulton K, Manning AK, Udler MS. High-throughput genetic clustering of type 2 diabetes loci reveals heterogeneous mechanistic pathways of metabolic disease. Diabetologia 2023; 66:495-507. [PMID: 36538063 PMCID: PMC10108373 DOI: 10.1007/s00125-022-05848-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/28/2022] [Indexed: 12/24/2022]
Abstract
AIMS/HYPOTHESIS Type 2 diabetes is highly polygenic and influenced by multiple biological pathways. Rapid expansion in the number of type 2 diabetes loci can be leveraged to identify such pathways. METHODS We developed a high-throughput pipeline to enable clustering of type 2 diabetes loci based on variant-trait associations. Our pipeline extracted summary statistics from genome-wide association studies (GWAS) for type 2 diabetes and related traits to generate a matrix of 323 variants × 64 trait associations and applied Bayesian non-negative matrix factorisation (bNMF) to identify genetic components of type 2 diabetes. Epigenomic enrichment analysis was performed in 28 cell types and single pancreatic cells. We generated cluster-specific polygenic scores and performed regression analysis in an independent cohort (N=25,419) to assess for clinical relevance. RESULTS We identified ten clusters of genetic loci, recapturing the five from our prior analysis as well as novel clusters related to beta cell dysfunction, pronounced insulin secretion, and levels of alkaline phosphatase, lipoprotein A and sex hormone-binding globulin. Four clusters related to mechanisms of insulin deficiency, five to insulin resistance and one had an unclear mechanism. The clusters displayed tissue-specific epigenomic enrichment, notably with the two beta cell clusters differentially enriched in functional and stressed pancreatic beta cell states. Additionally, cluster-specific polygenic scores were differentially associated with patient clinical characteristics and outcomes. The pipeline was applied to coronary artery disease and chronic kidney disease, identifying multiple overlapping clusters with type 2 diabetes. CONCLUSIONS/INTERPRETATION Our approach stratifies type 2 diabetes loci into physiologically interpretable genetic clusters associated with distinct tissues and clinical outcomes. The pipeline allows for efficient updating as additional GWAS become available and can be readily applied to other conditions, facilitating clinical translation of GWAS findings. Software to perform this clustering pipeline is freely available.
Collapse
Affiliation(s)
- Hyunkyung Kim
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kenneth E Westerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Kirk Smith
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joshua Chiou
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Joanne B Cole
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Marcin von Grotthuss
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Takeda Pharmaceuticals, Cambridge, MA, USA
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- GlaxoSmithKline, Cambridge, MA, USA
| | - Josep M Mercader
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jose C Florez
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kyle Gaulton
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Alisa K Manning
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Miriam S Udler
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
36
|
Melton HJ, Zhang Z, Wu C. SUMMIT-FA: A new resource for improved transcriptome imputation using functional annotations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.02.23285208. [PMID: 36798253 PMCID: PMC9934719 DOI: 10.1101/2023.02.02.23285208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transcriptome-wide association studies (TWAS) integrate gene expression prediction models and genome-wide association studies (GWAS) to identify gene-trait associations. The power of TWAS is determined by the sample size of GWAS and the accuracy of the expression prediction model. Here, we present a new method, the Summary-level Unified Method for Modeling Integrated Transcriptome using Functional Annotations (SUMMIT-FA), that improves the accuracy of gene expression prediction by leveraging functional annotation resources and a large expression quantitative trait loci (eQTL) summary-level dataset. We build gene expression prediction models using SUMMIT-FA with a comprehensive functional database MACIE and the eQTL summary-level data from the eQTLGen consortium. By applying the resulting models to GWASs for 24 complex traits and exploring it through a simulation study, we show that SUMMIT-FA improves the accuracy of gene expression prediction models in whole blood, identifies significantly more gene-trait associations, and improves predictive power for identifying "silver standard" genes compared to several benchmark methods.
Collapse
Affiliation(s)
- Hunter J. Melton
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Zichen Zhang
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
37
|
Carss KJ, Deaton AM, Del Rio-Espinola A, Diogo D, Fielden M, Kulkarni DA, Moggs J, Newham P, Nelson MR, Sistare FD, Ward LD, Yuan J. Using human genetics to improve safety assessment of therapeutics. Nat Rev Drug Discov 2023; 22:145-162. [PMID: 36261593 DOI: 10.1038/s41573-022-00561-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2022] [Indexed: 02/07/2023]
Abstract
Human genetics research has discovered thousands of proteins associated with complex and rare diseases. Genome-wide association studies (GWAS) and studies of Mendelian disease have resulted in an increased understanding of the role of gene function and regulation in human conditions. Although the application of human genetics has been explored primarily as a method to identify potential drug targets and support their relevance to disease in humans, there is increasing interest in using genetic data to identify potential safety liabilities of modulating a given target. Human genetic variants can be used as a model to anticipate the effect of lifelong modulation of therapeutic targets and identify the potential risk for on-target adverse events. This approach is particularly useful for non-clinical safety evaluation of novel therapeutics that lack pharmacologically relevant animal models and can contribute to the intrinsic safety profile of a drug target. This Review illustrates applications of human genetics to safety studies during drug discovery and development, including assessing the potential for on- and off-target associated adverse events, carcinogenicity risk assessment, and guiding translational safety study designs and monitoring strategies. A summary of available human genetic resources and recommended best practices is provided. The challenges and future perspectives of translating human genetic information to identify risks for potential drug effects in preclinical and clinical development are discussed.
Collapse
Affiliation(s)
| | - Aimee M Deaton
- Amgen, Cambridge, MA, USA.,Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Alberto Del Rio-Espinola
- Novartis Institutes for BioMedical Research, Basel, Switzerland.,GentiBio Inc., Cambridge, MA, USA
| | | | - Mark Fielden
- Amgen, Thousand Oaks, MA, USA.,Kate Therapeutics, San Diego, CA, USA
| | | | - Jonathan Moggs
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | - Frank D Sistare
- Merck & Co., West Point, PA, USA.,315 Meadowmont Ln, Chapel Hill, NC, USA
| | - Lucas D Ward
- Amgen, Cambridge, MA, USA. .,Alnylam Pharmaceuticals, Cambridge, MA, USA.
| | - Jing Yuan
- Amgen, Cambridge, MA, USA.,Pfizer, Cambridge, MA, USA
| |
Collapse
|
38
|
Patchen BK, Balte P, Bartz TM, Barr RG, Fornage M, Graff M, Jacobs DR, Kalhan R, Lemaitre RN, O'Connor G, Psaty B, Seo J, Tsai MY, Wood AC, Xu H, Zhang J, Gharib SA, Manichaikul A, North K, Steffen LM, Dupuis J, Oelsner E, Hancock DB, Cassano PA. Investigating associations of omega-3 fatty acids, lung function decline, and airway obstruction. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.18.23284671. [PMID: 36711663 PMCID: PMC9882557 DOI: 10.1101/2023.01.18.23284671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Rationale Inflammation contributes to lung function decline and the development of chronic obstructive pulmonary disease. Omega-3 fatty acids have anti-inflammatory properties and may benefit lung health. Objectives Investigate associations of omega-3 fatty acids with lung function decline and incident airway obstruction in adults of diverse races/ethnicities from general population cohorts. Methods Complementary study designs: (1) longitudinal study of plasma phospholipid omega-3 fatty acids and repeated FEV 1 and FVC measures in the National Heart, Lung, and Blood Institute Pooled Cohorts Study, and (2) two-sample Mendelian Randomization (MR) study of genetically predicted omega-3 fatty acids and lung function parameters. Measurements and Main Results The longitudinal study found that higher omega-3 fatty acid concentrations were associated with attenuated lung function decline in 15,063 participants, with the largest effect sizes for docosahexaenoic acid (DHA). One standard deviation higher DHA was associated with an attenuation of 1.8 mL/year for FEV 1 (95% confidence interval [CI] 1.3-2.2) and 2.4 mL/year for FVC (95% CI 1.9-3.0). One standard deviation higher DHA was also associated with a 9% lower incidence of spirometry-defined airway obstruction (95% CI 0.86-0.97). DHA associations persisted across sexes, smoking histories, and Black, white and Hispanic participants, with the largest magnitude associations in former smokers and Hispanics. The MR study showed positive associations of genetically predicted omega-3 fatty acids with FEV 1 and FVC, with statistically significant findings across multiple MR methods. Conclusions The longitudinal and MR studies provide evidence supporting beneficial effects of higher circulating omega-3 fatty acids, especially DHA, on lung health.
Collapse
Affiliation(s)
- Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Palavi Balte
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, Health Systems and Population Health, University of Washington, Seattle, WA
| | - R Graham Barr
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, TX
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - David R Jacobs
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, Health Systems and Population Health, University of Washington, Seattle, WA
| | | | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, Health Systems and Population Health, University of Washington, Seattle, WA
| | - Jungkyun Seo
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Houston, TX
| | - Hanfei Xu
- Boston University School of Public Health, Boston, MA
| | - Jingwen Zhang
- Boston University School of Public Health, Boston, MA
| | - Sina A Gharib
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Kari North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - Lyn M Steffen
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN
| | - Josée Dupuis
- Boston University School of Public Health, Boston, MA
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montréal, Québec
| | - Elizabeth Oelsner
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | | | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY
| |
Collapse
|
39
|
Noerman S, Virtanen JK, Lehtonen M, Brunius C, Hanhineva K. Serum metabolites associated with wholegrain consumption using nontargeted metabolic profiling: a discovery and reproducibility study. Eur J Nutr 2023; 62:713-726. [PMID: 36198920 PMCID: PMC9941277 DOI: 10.1007/s00394-022-03010-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE To identify fasting serum metabolites associated with WG intake in a free-living population adjusted for potential confounders. METHODS We selected fasting serum samples at baseline from a subset (n = 364) of the prospective population-based Kuopio Ischaemic Heart Disease Risk Factor Study (KIHD) cohort. The samples were analyzed using nontargeted metabolomics with liquid chromatography coupled with mass spectrometry (LC-MS). Association with WG intake was investigated using both random forest followed by linear regression adjusted for age, BMI, smoking, physical activity, energy and alcohol consumption, and partial Spearman correlation adjusted for the same covariates. Features selected by any of these models were shortlisted for annotation. We then checked if we could replicate the findings in an independent subset from the same cohort (n = 200). RESULTS Direct associations were observed between WG intake and pipecolic acid betaine, tetradecanedioic acid, four glucuronidated alkylresorcinols (ARs), and an unknown metabolite both in discovery and replication cohorts. The associations remained significant (FDR<0.05) even after adjustment for the confounders in both cohorts. Sinapyl alcohol was positively correlated with WG intake in both cohorts after adjustment for the confounders but not in linear models in the replication cohort. Some microbial metabolites, such as indolepropionic acid, were positively correlated with WG intake in the discovery cohort, but the correlations were not replicated in the replication cohort. CONCLUSIONS The identified associations between WG intake and the seven metabolites after adjusting for confounders in both discovery and replication cohorts suggest the potential of these metabolites as robust biomarkers of WG consumption.
Collapse
Affiliation(s)
- Stefania Noerman
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.
| | - Jyrki K. Virtanen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Marko Lehtonen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Carl Brunius
- Present Address: Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Kati Hanhineva
- Department of Life Technologies, Food Chemistry and Food Development Unit, University of Turku, Turku, Finland. .,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland.
| |
Collapse
|
40
|
Fauman EB, Keppo S, Cerioli N, Vyas R, Kurki M, Daly M, Reeve MP. LAVAA: a lightweight association viewer across ailments. BIOINFORMATICS ADVANCES 2023; 3:vbad018. [PMID: 36908397 PMCID: PMC9998102 DOI: 10.1093/bioadv/vbad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/06/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
Motivation Biobank scale genetic associations results over thousands of traits can be difficult to visualize and navigate. Results We have created LAVAA, a visualization web-application to generate genetic volcano plots for simultaneously considering the P-value, effect size, case counts, trait class and fine-mapping posterior probability at a single-nucleotide polymorphism (SNP) across a range of traits from a large set of genome-wide association study. We find that user interaction with association results in LAVAA can enrich and enhance the biological interpretation of individual loci. Availability and implementation LAVAA is available as a stand-alone web service (https://geneviz.aalto.fi/LAVAA/) and will be available in future releases of the finngen.fi website starting with release 10 in late 2023.
Collapse
Affiliation(s)
- Eric B Fauman
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - Stella Keppo
- Visual Communication Design, Aalto University, Espoo 02150, Finland
| | - Nicola Cerioli
- Visual Communication Design, Aalto University, Espoo 02150, Finland
| | - Rupesh Vyas
- Visual Communication Design, Aalto University, Espoo 02150, Finland
| | - Mitja Kurki
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00014, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mark Daly
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00014, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary Pat Reeve
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
41
|
Kiiskinen T, Helkkula P, Krebs K, Karjalainen J, Saarentaus E, Mars N, Lehisto A, Zhou W, Cordioli M, Jukarainen S, Rämö JT, Mehtonen J, Veerapen K, Räsänen M, Ruotsalainen S, Maasha M, Niiranen T, Tuomi T, Salomaa V, Kurki M, Pirinen M, Palotie A, Daly M, Ganna A, Havulinna AS, Milani L, Ripatti S. Genetic predictors of lifelong medication-use patterns in cardiometabolic diseases. Nat Med 2023; 29:209-218. [PMID: 36653479 PMCID: PMC9873570 DOI: 10.1038/s41591-022-02122-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/08/2022] [Indexed: 01/19/2023]
Abstract
Little is known about the genetic determinants of medication use in preventing cardiometabolic diseases. Using the Finnish nationwide drug purchase registry with follow-up since 1995, we performed genome-wide association analyses of longitudinal patterns of medication use in hyperlipidemia, hypertension and type 2 diabetes in up to 193,933 individuals (55% women) in the FinnGen study. In meta-analyses of up to 567,671 individuals combining FinnGen with the Estonian Biobank and the UK Biobank, we discovered 333 independent loci (P < 5 × 10-9) associated with medication use. Fine-mapping revealed 494 95% credible sets associated with the total number of medication purchases, changes in medication combinations or treatment discontinuation, including 46 credible sets in 40 loci not associated with the underlying treatment targets. The polygenic risk scores (PRS) for cardiometabolic risk factors were strongly associated with the medication-use behavior. A medication-use enhanced multitrait PRS for coronary artery disease matched the performance of a risk factor-based multitrait coronary artery disease PRS in an independent sample (UK Biobank, n = 343,676). In summary, we demonstrate medication-based strategies for identifying cardiometabolic risk loci and provide genome-wide tools for preventing cardiovascular diseases.
Collapse
Affiliation(s)
- Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Pyry Helkkula
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Kristi Krebs
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Arto Lehisto
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Wei Zhou
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mattia Cordioli
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sakari Jukarainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Joel T Rämö
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Juha Mehtonen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Kumar Veerapen
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Markus Räsänen
- Wihuri Research Institute, University of Helsinki, Helsinki, Finland
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mutaamba Maasha
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Internal Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Research Programs Unit, Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
- Lund University Diabetes Center, Malmo, Sweden
- Folkhälsan Research Centre, Helsinki, Finland
- Department of Endocrinology, Helsinki University Hospital, Helsinki, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Mitja Kurki
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mark Daly
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Lund University Diabetes Center, Malmo, Sweden.
| |
Collapse
|
42
|
Heyne HO, Karjalainen J, Karczewski KJ, Lemmelä SM, Zhou W, Havulinna AS, Kurki M, Rehm HL, Palotie A, Daly MJ. Mono- and biallelic variant effects on disease at biobank scale. Nature 2023; 613:519-525. [PMID: 36653560 PMCID: PMC9849130 DOI: 10.1038/s41586-022-05420-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/06/2022] [Indexed: 01/20/2023]
Abstract
Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics1. Population bottleneck events, such as those that occurred in the history of the Finnish population, enrich some homozygous variants to higher frequencies, which facilitates the identification of variants that cause diseases with recessive inheritance2,3. Here we examine the homozygous and heterozygous effects of 44,370 coding variants on 2,444 disease phenotypes using data from the nationwide electronic health records of 176,899 Finnish individuals. We find associations for homozygous genotypes across a broad spectrum of phenotypes, including known associations with retinal dystrophy and novel associations with adult-onset cataract and female infertility. Of the recessive disease associations that we identify, 13 out of 20 would have been missed by the additive model that is typically used in genome-wide association studies. We use these results to find many known Mendelian variants whose inheritance cannot be adequately described by a conventional definition of dominant or recessive. In particular, we find variants that are known to cause diseases with recessive inheritance with significant heterozygous phenotypic effects. Similarly, we find presumed benign variants with disease effects. Our results show how biobanks, particularly in founder populations, can broaden our understanding of complex dosage effects of Mendelian variants on disease.
Collapse
Affiliation(s)
- H O Heyne
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland. .,Digital Health Center, Hasso Plattner Institute for Digital Engineering, University of Potsdam, Potsdam, Germany. .,Hasso Plattner Institute for Digital Health at Mount Sinai, 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. .,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - J Karjalainen
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - K J Karczewski
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - S M Lemmelä
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare, Helsinki, Finland
| | - W Zhou
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - A S Havulinna
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Finnish Institute for Health and Welfare, Helsinki, Finland
| | - M Kurki
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - H L Rehm
- Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - A Palotie
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - M J Daly
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland. .,Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. .,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
43
|
Severe COVID-19 May Impact Hepatic Fibrosis /Hepatic Stellate Cells Activation as Indicated by a Pathway and Population Genetic Study. Genes (Basel) 2022; 14:genes14010022. [PMID: 36672763 PMCID: PMC9858736 DOI: 10.3390/genes14010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 09/22/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
Coronavirus disease 19 (COVID-19) has affected over 112 million people and killed more than 2.5 million worldwide. When the pandemic was declared, Spain and Italy accounted for 29% of the total COVID-19 related deaths in Europe, while most infected patients did not present severe illness. We hypothesised that shared genomic characteristics, distinct from the rest of Europe, could be a contributor factor to a poor prognosis in these two populations. To identify pathways related to COVID-19 severity, we shortlisted 437 candidate genes associated with host viral intake and immune evasion from SARS-like viruses. From these, 21 were associated specifically with clinically aggressive COVID-19. To determine the potential mechanism of viral infections, we performed signalling pathway analysis with either the full list (n = 437) or the subset group (n = 21) of genes. Four pathways were significantly associated with the full gene list (Caveolar-mediated Endocytosis and the MSP-RON Signalling) or with the aggressive gene list (Hepatic Fibrosis/Hepatic Stellate Cell (HSC) Activation and the Communication between Innate and Adaptive Immune Cells). Single nucleotide polymorphisms (SNPs) from the ±1 Mb window of all genes related to these four pathways were retrieved from the dbSNP database. We then performed Principal Component analysis for these SNPs in individuals from the 1000 Genomes of European ancestry. Only the Hepatic Fibrosis/HSC Activation pathway showed population-specific segregation. The Spanish and Italian populations clustered together and away from the rest of the European ancestries, with the first segregating further from the rest. Additional in silico analysis identified potential genetic markers and clinically actionable therapeutic targets in this pathway, that may explain the severe disease.
Collapse
|
44
|
Lazareva TE, Barbitoff YA, Changalidis AI, Tkachenko AA, Maksiutenko EM, Nasykhova YA, Glotov AS. Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. J Pers Med 2022; 12:jpm12122040. [PMID: 36556260 PMCID: PMC9783756 DOI: 10.3390/jpm12122040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, great advances have been made in the field of collection, storage, and analysis of biological samples. Large collections of samples, biobanks, have been established in many countries. Biobanks typically collect large amounts of biological samples and associated clinical information; the largest collections include over a million samples. In this review, we summarize the main directions in which biobanks aid medical genetics and genomic research, from providing reference allele frequency information to allowing large-scale cross-ancestry meta-analyses. The largest biobanks greatly vary in the size of the collection, and the amount of available phenotype and genotype data. Nevertheless, all of them are extensively used in genomics, providing a rich resource for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome. Recently, multiple research efforts were based on trans-biobank data integration, which increases sample size and allows for the identification of robust genetic associations. We provide prominent examples of such data integration and discuss important caveats which have to be taken into account in trans-biobank research.
Collapse
Affiliation(s)
- Tatyana E. Lazareva
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Yury A. Barbitoff
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
| | - Anton I. Changalidis
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Faculty of Software Engineering and Computer Systems, ITMO University, 197101 St. Petersburg, Russia
| | - Alexander A. Tkachenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Evgeniia M. Maksiutenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Yulia A. Nasykhova
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Andrey S. Glotov
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
| |
Collapse
|
45
|
Maj C, Staerk C, Borisov O, Klinkhammer H, Wai Yeung M, Krawitz P, Mayr A. Statistical learning for sparser fine-mapped polygenic models: The prediction of LDL-cholesterol. Genet Epidemiol 2022; 46:589-603. [PMID: 35938382 DOI: 10.1002/gepi.22495] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022]
Abstract
Polygenic risk scores quantify the individual genetic predisposition regarding a particular trait. We propose and illustrate the application of existing statistical learning methods to derive sparser models for genome-wide data with a polygenic signal. Our approach is based on three consecutive steps. First, potentially informative loci are identified by a marginal screening approach. Then, fine-mapping is independently applied for blocks of variants in linkage disequilibrium, where informative variants are retrieved by using variable selection methods including boosting with probing and stochastic searches with the Adaptive Subspace method. Finally, joint prediction models with the selected variants are derived using statistical boosting. In contrast to alternative approaches relying on univariate summary statistics from genome-wide association studies, our three-step approach enables to select and fit multivariable regression models on large-scale genotype data. Based on UK Biobank data, we develop prediction models for LDL-cholesterol as a continuous trait. Additionally, we consider a recent scalable algorithm for the Lasso. Results show that statistical learning approaches based on fine-mapping of genetic signals result in a competitive prediction performance compared to classical polygenic risk approaches, while yielding sparser risk models.
Collapse
Affiliation(s)
- Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Christian Staerk
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| | - Ming Wai Yeung
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
- Department of Cardiology, University of Groningen, Groningen, The Netherlands
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University Bonn, Bonn, Germany
| |
Collapse
|
46
|
Tang Q, Yang Q, Yu X, Liu Y, Tong Z, Li B, Chen Y, Yu EY, Li W. Association of demographic and clinical factors with risk of acute pancreatitis: An exposure-wide Mendelian randomization study. Mol Genet Genomic Med 2022; 11:e2091. [PMID: 36345251 PMCID: PMC9834139 DOI: 10.1002/mgg3.2091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 05/27/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The incidence of acute pancreatitis (AP) is increasing over years, which brings enormous economy and health burden. However, the aetiologies of AP and underlying mechanisms are still unclear. Here, we performed a two-sample Mendelian randomization (MR) analysis to investigate the associations between all reported possible risk factors and AP using publicly available genome-wide association study summary statistics. METHODS A series of quality control steps were taken in our analysis to select eligible instrumental single nucleotide polymorphisms which were strongly associated with exposures. To make the conclusions more robust and reliable, we utilized several analytical methods (inverse-variance weighting, MR-PRESSO method, weighted median, MR-Egger regression) that are based on different assumptions of two-sample MR analysis. The MR-Egger intercept test, radial regression and leave-one-out sensitivity analysis were performed to evaluate the horizontal pleiotropy, heterogeneities, and stability of these genetic variants on each exposure. A two-step MR method was applied to explore mediators in significant associations. RESULTS Genetic predisposition to cholelithiasis (effect estimate: 17.30, 95% CI: 12.25-22.36, p = 1.95 E-11), body mass index (0.32, 95% CI: 0.13-0.51, p < 0.001), body fat percentage (0.57, 95% CI: 0.31-0.83, p = 1.31 E-05), trunk fat percentage (0.36, 95% CI: 0.14-0.59, p < 0.005), ever smoked (1.61, 95% CI: 0.45-2.77, p = 0.007), and limbs fat percentage (0.55, 95% CI: 0.41-0.69, p < 0.001) were associated with an increased risk of AP. In addition, whole-body fat-free mass (-0.32, 95% CI: -0.55 to -0.10, p = 0.004) was associated with a decrease risk of AP. CONCLUSION Genetic predisposition to cholelithiasis, obesity and smoking could be causally associated with an increased risk of AP, and whole body fat-free mass could be associated with a decreased risk of AP.
Collapse
Affiliation(s)
- Qiu‐Yi Tang
- Medical School of Southeast UniversityNanjingChina
| | - Qi Yang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care MedicineJinling HospitalNanjingChina
| | | | - Yu‐Xiu Liu
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care MedicineJinling HospitalNanjingChina
| | - Zhi‐Hui Tong
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care MedicineJinling HospitalNanjingChina
| | - Bai‐Qiang Li
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care MedicineJinling HospitalNanjingChina
| | - Ya‐Ting Chen
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology & Biostatistics, School of Public HealthSoutheast UniversityNanjingChina
| | - Evan Yi‐Wen Yu
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology & Biostatistics, School of Public HealthSoutheast UniversityNanjingChina,CAPHRI Care and Public Health Research Institute, School of Nutrition and Translational Research in MetabolismMaastricht UniversityMaastrichtthe Netherlands
| | - Wei‐Qin Li
- Medical School of Southeast UniversityNanjingChina,Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care MedicineJinling HospitalNanjingChina
| |
Collapse
|
47
|
SUMMIT: An integrative approach for better transcriptomic data imputation improves causal gene identification. Nat Commun 2022; 13:6336. [PMID: 36284135 PMCID: PMC9593997 DOI: 10.1038/s41467-022-34016-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 10/11/2022] [Indexed: 12/25/2022] Open
Abstract
Genes with moderate to low expression heritability may explain a large proportion of complex trait etiology, but such genes cannot be sufficiently captured in conventional transcriptome-wide association studies (TWASs), partly due to the relatively small available reference datasets for developing expression genetic prediction models to capture the moderate to low genetically regulated components of gene expression. Here, we introduce a method, the Summary-level Unified Method for Modeling Integrated Transcriptome (SUMMIT), to improve the expression prediction model accuracy and the power of TWAS by using a large expression quantitative trait loci (eQTL) summary-level dataset. We apply SUMMIT to the eQTL summary-level data provided by the eQTLGen consortium. Through simulation studies and analyses of genome-wide association study summary statistics for 24 complex traits, we show that SUMMIT improves the accuracy of expression prediction in blood, successfully builds expression prediction models for genes with low expression heritability, and achieves higher statistical power than several benchmark methods. Finally, we conduct a case study of COVID-19 severity with SUMMIT and identify 11 likely causal genes associated with COVID-19 severity.
Collapse
|
48
|
Hyppönen E, Vimaleswaran KS, Zhou A. Genetic Determinants of 25-Hydroxyvitamin D Concentrations and Their Relevance to Public Health. Nutrients 2022; 14:4408. [PMID: 36297091 PMCID: PMC9606877 DOI: 10.3390/nu14204408] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Twin studies suggest a considerable genetic contribution to the variability in 25-hydroxyvitamin D (25(OH)D) concentrations, reporting heritability estimates up to 80% in some studies. While genome-wide association studies (GWAS) suggest notably lower rates (13−16%), they have identified many independent variants that associate with serum 25(OH)D concentrations. These discoveries have provided some novel insight into the metabolic pathway, and in this review we outline findings from GWAS studies to date with a particular focus on 35 variants which have provided replicating evidence for an association with 25(OH)D across independent large-scale analyses. Some of the 25(OH)D associating variants are linked directly to the vitamin D metabolic pathway, while others may reflect differences in storage capacity, lipid metabolism, and pathways reflecting skin properties. By constructing a genetic score including these 25(OH)D associated variants we show that genetic differences in 25(OH)D concentrations persist across the seasons, and the odds of having low concentrations (<50 nmol/L) are about halved for individuals in the highest 20% of vitamin D genetic score compared to the lowest quintile, an impact which may have notable influences on retaining adequate levels. We also discuss recent studies on personalized approaches to vitamin D supplementation and show how Mendelian randomization studies can help inform public health strategies to reduce adverse health impacts of vitamin D deficiency.
Collapse
Affiliation(s)
- Elina Hyppönen
- Australian Centre for Precision Health, Clinical and Health Sciences, University of South Australia, Adelaide, SA 5001, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Karani S. Vimaleswaran
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6DZ, UK
- The Institute for Food, Nutrition and Health (IFNH), University of Reading, Reading RG6 6DZ, UK
| | - Ang Zhou
- Australian Centre for Precision Health, Clinical and Health Sciences, University of South Australia, Adelaide, SA 5001, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| |
Collapse
|
49
|
Sang J, Zhang T, Kim J, Li M, Pesatori AC, Consonni D, Song L, Liu J, Zhao W, Hoang PH, Campbell DS, Feng J, D'Arcy ME, Synnott N, Chen Y, Wu Z, Zhu B, Yang XR, Brown KM, Choi J, Shi J, Landi MT. Rare germline deleterious variants increase susceptibility for lung cancer. Hum Mol Genet 2022; 31:3558-3565. [PMID: 35717579 PMCID: PMC9558843 DOI: 10.1093/hmg/ddac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Although multiple common susceptibility loci for lung cancer (LC) have been identified by genome-wide association studies, they can explain only a small portion of heritability. The etiological contribution of rare deleterious variants (RDVs) to LC risk is not fully characterized and may account for part of the missing heritability. Here, we sequenced the whole exomes of 2777 participants from the Environment and Genetics in Lung cancer Etiology study, a homogenous population including 1461 LC cases and 1316 controls. In single-variant analyses, we identified a new RDV, rs77187983 [EHBP1, odds ratio (OR) = 3.13, 95% confidence interval (CI) = 1.34-7.30, P = 0.008] and replicated two previously reported RDVs, rs11571833 (BRCA2, OR = 2.18; 95% CI = 1.25-3.81, P = 0.006) and rs752672077 (MPZL2, OR = 3.70, 95% CI = 1.04-13.15, P = 0.044). In gene-based analyses, we confirmed BRCA2 (P = 0.007) and ATM (P = 0.014) associations with LC risk and identified TRIB3 (P = 0.009), involved in maintaining genome stability and DNA repair, as a new candidate susceptibility gene. Furthermore, cases were enriched with RDVs in homologous recombination repair [carrier frequency (CF) = 22.9% versus 19.5%, P = 0.017] and Fanconi anemia (CF = 12.5% versus 10.2%, P = 0.036) pathways. Our results were not significant after multiple testing corrections but were enriched in cases versus controls from large scale public biobank resources, including The Cancer Genome Atlas, FinnGen and UK Biobank. Our study identifies novel candidate genes and highlights the importance of RDVs in DNA repair-related genes for LC susceptibility. These findings improve our understanding of LC heritability and may contribute to the development of risk stratification and prevention strategies.
Collapse
Affiliation(s)
- Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mengying Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angela C Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Dario Consonni
- Epidemiology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Lei Song
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phuc H Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - James Feng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Monica E D'Arcy
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naoise Synnott
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yingxi Chen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zeni Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
50
|
Hale AT, He J, Jones J. Multinational Genome-Wide Association Study and Functional Genomics Analysis Implicates Decreased SIRT3 Expression Underlying Intracranial Aneurysm Risk. Neurosurgery 2022; 91:625-632. [PMID: 35838494 DOI: 10.1227/neu.0000000000002082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The genetic mechanisms regulating intracranial aneurysm (IA) formation and rupture are largely unknown. To identify germline-genetic risk factors for IA, we perform a multinational genome-wide association study (GWAS) of individuals from the United Kingdom, Finland, and Japan. OBJECTIVE To identify a shared, multinational genetic basis of IA. METHODS Using GWAS summary statistics from UK Biobank, FinnGen, and Biobank Japan, we perform a meta-analysis of IA, containing ruptured and unruptured IA cases. Logistic regression was used to identify IA-associated single-nucleotide polymorphisms. Effect size was calculated using the coefficient r , estimating the contribution of the single-nucleotide polymorphism to the genetic variance of the trait. Genome-wide significance was set at 5.0 × 10 -8 . Expression quantitative trait loci mapping and functional genomics approaches were used to infer mechanistic consequences of implicated variants. RESULTS Our cohort contained 155 154 individuals (3132 IA cases and 152 022 controls). We identified 4 genetic loci reaching genome-wide: rs73392700 ( SIRT3 , effect size = 0.28, P = 4.3 × 10 -12 ), rs58721068 ( EDNRA , effect size = -0.20, P = 4.8 × 10 -12 ), rs4977574 ( AL359922.1 , effect size = 0.18, P = 7.9 × 10 -12 ), and rs11105337 ( ATP2B1 , effect size = -0.15, P = 3.4 × 10 -8 ). Expression quantitative trait loci mapping suggests that rs73392700 has a large effect size on SIRT3 gene expression in arterial and muscle, but not neurological, tissues. Functional genomics analysis suggests that rs73392700 causes decreased SIRT3 gene expression. CONCLUSION We perform a multinational GWAS of IA and identify 4 genetic risk loci, including 2 novel IA risk loci ( SIRT3 and AL359922.1 ). Identification of high-risk genetic loci across ancestries will enable population-genetic screening approaches to identify patients with IA.
Collapse
Affiliation(s)
- Andrew T Hale
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jing He
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jesse Jones
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| |
Collapse
|