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Young KL, Fisher V, Deng X, Brody JA, Graff M, Lim E, Lin BM, Xu H, Amin N, An P, Aslibekyan S, Fohner AE, Hidalgo B, Lenzini P, Kraaij R, Medina-Gomez C, Prokić I, Rivadeneira F, Sitlani C, Tao R, van Rooij J, Zhang D, Broome JG, Buth EJ, Heavner BD, Jain D, Smith AV, Barnes K, Boorgula MP, Chavan S, Darbar D, De Andrade M, Guo X, Haessler J, Irvin MR, Kalyani RR, Kardia SLR, Kooperberg C, Kim W, Mathias RA, McDonald ML, Mitchell BD, Peyser PA, Regan EA, Redline S, Reiner AP, Rich SS, Rotter JI, Smith JA, Weiss S, Wiggins KL, Yanek LR, Arnett D, Heard-Costa NL, Leal S, Lin D, McKnight B, Province M, van Duijn CM, North KE, Cupples LA, Liu CT. Whole-exome sequence analysis of anthropometric traits illustrates challenges in identifying effects of rare genetic variants. HGG ADVANCES 2023; 4:100163. [PMID: 36568030 PMCID: PMC9772568 DOI: 10.1016/j.xhgg.2022.100163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
Anthropometric traits, measuring body size and shape, are highly heritable and significant clinical risk factors for cardiometabolic disorders. These traits have been extensively studied in genome-wide association studies (GWASs), with hundreds of genome-wide significant loci identified. We performed a whole-exome sequence analysis of the genetics of height, body mass index (BMI) and waist/hip ratio (WHR). We meta-analyzed single-variant and gene-based associations of whole-exome sequence variation with height, BMI, and WHR in up to 22,004 individuals, and we assessed replication of our findings in up to 16,418 individuals from 10 independent cohorts from Trans-Omics for Precision Medicine (TOPMed). We identified four trait associations with single-nucleotide variants (SNVs; two for height and two for BMI) and replicated the LECT2 gene association with height. Our expression quantitative trait locus (eQTL) analysis within previously reported GWAS loci implicated CEP63 and RFT1 as potential functional genes for known height loci. We further assessed enrichment of SNVs, which were monogenic or syndromic variants within loci associated with our three traits. This led to the significant enrichment results for height, whereas we observed no Bonferroni-corrected significance for all SNVs. With a sample size of ∼20,000 whole-exome sequences in our discovery dataset, our findings demonstrate the importance of genomic sequencing in genetic association studies, yet they also illustrate the challenges in identifying effects of rare genetic variants.
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Affiliation(s)
- Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Virginia Fisher
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Xuan Deng
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Misa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Elise Lim
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Hanfei Xu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Ping An
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alison E Fohner
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA.,Institute for Public Health Genetics, University of Washington, Seattle, WA 98101, USA
| | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Petra Lenzini
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Ivana Prokić
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Colleen Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Di Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA.,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Erin J Buth
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Benjamin D Heavner
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen Barnes
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Tempus Labs, Chicago, IL 60654, USA
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Dawood Darbar
- Division of Cardiology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Mariza De Andrade
- Health Quantitative Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rita R Kalyani
- Division of Endocrinology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Merry-Lynn McDonald
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | | | - Susan Redline
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA.,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Scott Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kerri L Wiggins
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Donna Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | | | - Suzanne Leal
- Department of Neurology, Columbia University, New York City, NY, USA
| | - Danyu Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Michael Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
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3
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George DJ, Halabi S, Heath EI, Sartor AO, Sonpavde GP, Das D, Bitting RL, Berry W, Healy P, Anand M, Winters C, Riggan C, Kephart J, Wilder R, Shobe K, Rasmussen J, Milowsky MI, Fleming MT, Bearden J, Goodman M, Zhang T, Harrison MR, McNamara M, Zhang D, LaCroix BL, Kittles RA, Patierno BM, Sibley AB, Patierno SR, Owzar K, Hyslop T, Freedman JA, Armstrong AJ. A prospective trial of abiraterone acetate plus prednisone in Black and White men with metastatic castrate-resistant prostate cancer. Cancer 2021; 127:2954-2965. [PMID: 33951180 PMCID: PMC9527760 DOI: 10.1002/cncr.33589] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND Retrospective analyses of randomized trials suggest that Black men with metastatic castration-resistant prostate cancer (mCRPC) have longer survival than White men. The authors conducted a prospective study of abiraterone acetate plus prednisone to explore outcomes by race. METHODS This race-stratified, multicenter study estimated radiographic progression-free survival (rPFS) in Black and White men with mCRPC. Secondary end points included prostate-specific antigen (PSA) kinetics, overall survival (OS), and safety. Exploratory analysis included genome-wide genotyping to identify single nucleotide polymorphisms associated with progression in a model incorporating genetic ancestry. One hundred patients self-identified as White (n = 50) or Black (n = 50) were enrolled. Eligibility criteria were modified to facilitate the enrollment of individual Black patients. RESULTS The median rPFS for Black and White patients was 16.6 and 16.8 months, respectively; their times to PSA progression (TTP) were 16.6 and 11.5 months, respectively; and their OS was 35.9 and 35.7 months, respectively. Estimated rates of PSA decline by ≥50% in Black and White patients were 74% and 66%, respectively; and PSA declines to <0.2 ng/mL were 26% and 10%, respectively. Rates of grade 3 and 4 hypertension, hypokalemia, and hyperglycemia were higher in Black men. CONCLUSIONS Multicenter prospective studies by race are feasible in men with mCRPC but require less restrictive eligibility. Despite higher comorbidity rates, Black patients demonstrated rPFS and OS similar to those of White patients and trended toward greater TTP and PSA declines, consistent with retrospective reports. Importantly, Black men may have higher side-effect rates than White men. This exploratory genome-wide analysis of TTP identified a possible candidate marker of ancestry-dependent treatment outcomes.
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Affiliation(s)
- Daniel J. George
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, North Carolina
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Susan Halabi
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| | | | - A. Oliver Sartor
- Tulane Cancer Center, Tulane Health Sciences Center, New Orleans, Louisiana
| | - Guru P. Sonpavde
- Hematology and Oncology Division, Birmingham Veterans Affairs Medical Center, Birmingham, Alabama
| | - Devika Das
- Hematology and Oncology Division, Birmingham Veterans Affairs Medical Center, Birmingham, Alabama
| | - Rhonda L. Bitting
- Comprehensive Cancer Center, Wake Forest University, Winston Salem, North Carolina
| | - William Berry
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, North Carolina
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Patrick Healy
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Monika Anand
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Carol Winters
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Colleen Riggan
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Julie Kephart
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Rhonda Wilder
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Kellie Shobe
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Julia Rasmussen
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Matthew I. Milowsky
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | | | - Michael Goodman
- W.G. (Bill) Hefner VA Medical Center, Salisbury, North Carolina
| | - Tian Zhang
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, North Carolina
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Michael R. Harrison
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, North Carolina
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Megan McNamara
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, North Carolina
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Dadong Zhang
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina
| | - Bonnie L. LaCroix
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Rick A. Kittles
- Department of Population Sciences, Division of Health Equities, City of Hope National Medical Center, Duarte, California
| | - Brendon M. Patierno
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Alexander B. Sibley
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina
| | - Steven R. Patierno
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, North Carolina
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina
| | - Terry Hyslop
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| | - Jennifer A. Freedman
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, North Carolina
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
| | - Andrew J. Armstrong
- Department of Medicine, Division of Medical Oncology, Duke University, Durham, North Carolina
- Center for Prostate and Urologic Cancers, Duke Cancer Institute, Duke University, Durham, North Carolina
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6
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Guitton J, Bandet CL, Mariko ML, Tan-Chen S, Bourron O, Benomar Y, Hajduch E, Le Stunff H. Sphingosine-1-Phosphate Metabolism in the Regulation of Obesity/Type 2 Diabetes. Cells 2020; 9:E1682. [PMID: 32668665 PMCID: PMC7407406 DOI: 10.3390/cells9071682] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022] Open
Abstract
Obesity is a pathophysiological condition where excess free fatty acids (FFA) target and promote the dysfunctioning of insulin sensitive tissues and of pancreatic β cells. This leads to the dysregulation of glucose homeostasis, which culminates in the onset of type 2 diabetes (T2D). FFA, which accumulate in these tissues, are metabolized as lipid derivatives such as ceramide, and the ectopic accumulation of the latter has been shown to lead to lipotoxicity. Ceramide is an active lipid that inhibits the insulin signaling pathway as well as inducing pancreatic β cell death. In mammals, ceramide is a key lipid intermediate for sphingolipid metabolism as is sphingosine-1-phosphate (S1P). S1P levels have also been associated with the development of obesity and T2D. In this review, the current knowledge on S1P metabolism in regulating insulin signaling in pancreatic β cell fate and in the regulation of feeding by the hypothalamus in the context of obesity and T2D is summarized. It demonstrates that S1P can display opposite effects on insulin sensitive tissues and pancreatic β cells, which depends on its origin or its degradation pathway.
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Affiliation(s)
- Jeanne Guitton
- Institut des Neurosciences Paris-Saclay, Université Paris Saclay, CNRS UMR 9197, F-91190 Orsay, France; (J.G.); (M.L.M.); (Y.B.)
| | - Cecile L. Bandet
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France; (C.L.B.); (S.T.-C.); (O.B.); (E.H.)
- Institut Hospitalo-Universitaire ICAN, F-75013 Paris, France
| | - Mohamed L. Mariko
- Institut des Neurosciences Paris-Saclay, Université Paris Saclay, CNRS UMR 9197, F-91190 Orsay, France; (J.G.); (M.L.M.); (Y.B.)
| | - Sophie Tan-Chen
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France; (C.L.B.); (S.T.-C.); (O.B.); (E.H.)
- Institut Hospitalo-Universitaire ICAN, F-75013 Paris, France
| | - Olivier Bourron
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France; (C.L.B.); (S.T.-C.); (O.B.); (E.H.)
- Institut Hospitalo-Universitaire ICAN, F-75013 Paris, France
- Assistance Publique-Hôpitaux de Paris, Département de Diabétologie et Maladies métaboliques, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Yacir Benomar
- Institut des Neurosciences Paris-Saclay, Université Paris Saclay, CNRS UMR 9197, F-91190 Orsay, France; (J.G.); (M.L.M.); (Y.B.)
| | - Eric Hajduch
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France; (C.L.B.); (S.T.-C.); (O.B.); (E.H.)
- Institut Hospitalo-Universitaire ICAN, F-75013 Paris, France
| | - Hervé Le Stunff
- Institut des Neurosciences Paris-Saclay, Université Paris Saclay, CNRS UMR 9197, F-91190 Orsay, France; (J.G.); (M.L.M.); (Y.B.)
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