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Nagarajan P, Winkler TW, Bentley AR, Miller CL, Kraja AT, Schwander K, Lee S, Wang W, Brown MR, Morrison JL, Giri A, O’Connell JR, Bartz TM, de las Fuentes L, Gudmundsdottir V, Guo X, Harris SE, Huang Z, Kals M, Kho M, Lefevre C, Luan J, Lyytikäinen LP, Mangino M, Milaneschi Y, Palmer ND, Rao V, Rauramaa R, Shen B, Stadler S, Sun Q, Tang J, Thériault S, van der Graaf A, van der Most PJ, Wang Y, Weiss S, Westerman KE, Yang Q, Yasuharu T, Zhao W, Zhu W, Altschul D, Ansari MAY, Anugu P, Argoty-Pantoja AD, Arzt M, Aschard H, Attia JR, Bazzanno L, Breyer MA, Brody JA, Cade BE, Chen HH, Ida Chen YD, Chen Z, de Vries PS, Dimitrov LM, Do A, Du J, Dupont CT, Edwards TL, Evans MK, Faquih T, Felix SB, Fisher-Hoch SP, Floyd JS, Graff M, Gu C, Gu D, Hairston KG, Hanley AJ, Heid IM, Heikkinen S, Highland HM, Hood MM, Kähönen M, Karvonen-Gutierrez CA, Kawaguchi T, Kazuya S, Kelly TN, Komulainen P, Levy D, Lin HJ, Liu PY, Marques-Vidal P, McCormick JB, Mei H, Meigs JB, Menni C, Nam K, Nolte IM, Pacheco NL, Petty LE, Polikowsky HG, Province MA, Psaty BM, Raffield LM, Raitakari OT, Rich SS, Riha RL, Risch L, Risch M, Ruiz-Narvaez EA, Scott RJ, Sitlani CM, Smith JA, Sofer T, Teder-Laving M, Völker U, Vollenweider P, Wang G, van Dijk KW, Wilson OD, Xia R, Yao J, Young KL, Zhang R, Zhu X, Below JE, Böger CA, Conen D, Cox SR, Dörr M, Feitosa MF, Fox ER, Franceschini N, Gharib SA, Gudnason V, Harlow SD, He J, Holliday EG, Kutalik Z, Lakka TA, Lawlor DA, Lee S, Lehtimäki T, Li C, Liu CT, Mägi R, Matsuda F, Morrison AC, Penninx BWJH, Peyser PA, Rotter JI, Snieder H, Spector TD, Wagenknecht LE, Wareham NJ, Zonderman AB, North KE, Fornage M, Hung AM, Manning AK, Gauderman J, Chen H, Munroe PB, Rao DC, van Heemst D, Redline S, Noordam R, Wang H. A Large-Scale Genome-Wide Study of Gene-Sleep Duration Interactions for Blood Pressure in 811,405 Individuals from Diverse Populations. medRxiv 2024:2024.03.07.24303870. [PMID: 38496537 PMCID: PMC10942520 DOI: 10.1101/2024.03.07.24303870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Although both short and long sleep duration are associated with elevated hypertension risk, our understanding of their interplay with biological pathways governing blood pressure remains limited. To address this, we carried out genome-wide cross-population gene-by-short-sleep and long-sleep duration interaction analyses for three blood pressure traits (systolic, diastolic, and pulse pressure) in 811,405 individuals from diverse population groups. We discover 22 novel gene-sleep duration interaction loci for blood pressure, mapped to genes involved in neurological, thyroidal, bone metabolism, and hematopoietic pathways. Non-overlap between short sleep (12) and long sleep (10) interactions underscores the plausibility of distinct influences of both sleep duration extremes in cardiovascular health. With several of our loci reflecting specificity towards population background or sex, our discovery sheds light on the importance of embracing granularity when addressing heterogeneity entangled in gene-environment interactions, and in therapeutic design approaches for blood pressure management.
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Affiliation(s)
- Pavithra Nagarajan
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesvil le, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville ,VA, USA
| | - Aldi T Kraja
- University of Mississippi Medical Center, Jackson, MS, USA
| | - Karen Schwander
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Songmi Lee
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Wenyi Wang
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - John L Morrison
- Division of Biostatistics, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ayush Giri
- Division of Quantitative Sciences, Department of Obstetrics & Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626), Department of Veterans Affairs/ Nashville, TN, USA
| | - Jeffrey R O’Connell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lisa de las Fuentes
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine in St. Louis, MO, USA
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Valborg Gudmundsdottir
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, Department of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Sarah E Harris
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Zhijie Huang
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
| | - Mart Kals
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Minjung Kho
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Christophe Lefevre
- Department of Data Sciences, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Jian’an Luan
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center - Tampere, Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Massimo Mangino
- Department of Twin Research, King’s College London, London, UK
- National Heart & Lung Institute, Cardiovascular Genomics and Precision Medicine, Imperial College London, London, UK
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam UMC/Vrije universiteit, Amsterdam, Netherlands
- GGZ inGeest, Amsterdam, Netherlands
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Varun Rao
- Division of Nephrology, Department of Medicine, University of Illinois Chicago, Chicago, USA
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Botong Shen
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Stefan Stadler
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jingxian Tang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Sébastien Thériault
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec City, Qc, Canada
| | - Adriaan van der Graaf
- Statistical Genetics Group, Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Yujie Wang
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Kenneth E Westerman
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
| | - Qian Yang
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tabara Yasuharu
- Graduate School of Public Health, Shizuoka Graduate University of Public Health, Shizuoka, Japan
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Wei Zhao
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wanying Zhu
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Drew Altschul
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Md Abu Yusuf Ansari
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Pramod Anugu
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Anna D Argoty-Pantoja
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Michael Arzt
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
| | - Hugues Aschard
- Department of Computational Biology, F-75015 Paris, France Institut Pasteur, Université Paris Cité, Paris, France
- Department of Epidemiology, Harvard TH School of Public Health, Boston, MA, USA
| | - John R Attia
- School of Medicine and Public Health, College of Health Medicine and Wellbeing, University of Newcastle, New Lambton Heights, NSW, Australia
| | - Lydia Bazzanno
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
| | - Max A Breyer
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hung-hsin Chen
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Zekai Chen
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Latchezar M Dimitrov
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Anh Do
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Jiawen Du
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles T Dupont
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Todd L Edwards
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626), Department of Veterans Affairs/ Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, US A
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Tariq Faquih
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephan B Felix
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Cardiology, Pneumology, Infectious Diseases, Intensive Care Medicine, Department of Internal Medicine B, Un iversity Medicine Greifswald, Greifswald, Germany
| | - Susan P Fisher-Hoch
- School of Public Health, The University of Texas Health Science Center at Houston (UTHealth), Brownsville, TX, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Mariaelisa Graff
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles Gu
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Dongfeng Gu
- Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine, Southern University of Science an d Technology, Shenzhen, China
| | - Kristen G Hairston
- Department of Endocrinology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Anthony J Hanley
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Sami Heikkinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Kuopio
| | - Heather M Highland
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michelle M Hood
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Mika Kähönen
- Finnish Cardiovascular Research Center - Tampere, Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | | | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Setoh Kazuya
- Graduate School of Public Health, Shizuoka Graduate University of Public Health, Shizuoka, Japan
| | - Tanika N Kelly
- Division of Nephrology, Department of Medicine, University of Illinois Chicago, Chicago, USA
| | | | - Daniel Levy
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Henry J Lin
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Peter Y Liu
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Pedro Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Joseph B McCormick
- School of Public Health, The University of Texas Health Science Center at Houston (UTHealth), Brownsville, TX, USA
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - James B Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Cristina Menni
- Department of Twin Research, King’s College London, London, UK
| | - Kisung Nam
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Natasha L Pacheco
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Lauren E Petty
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hannah G Polikowsky
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, and Department of Clinical Physiology and Nuclear Medicine, University of Turku, and Turku University Hospital, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Renata L Riha
- Department of Sleep Medicine, The University of Edinburgh, Edinburgh, UK
| | - Lorenz Risch
- Faculty of Medical Sciences , Institute for Laboratory Medicine, Private University in the Principality of Liecht enstein, Vaduz, Liechtenstein
- Center of Laboratory Medicine, Institute of Clinical Chemistry, University of Bern and Inselspital, Bern, Switze rland
| | - Martin Risch
- Central Laboratory, Cantonal Hospital Graubünden, Chur, Switzerland
- Medical Laboratory, Dr. Risch Anstalt, Vaduz, Liechtenstein
| | | | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, College of Health Medicine and Wellbeing, University of Newcastle, New Lambton Heights, NSW, Australia
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- CardioVascular Institute (CVI), Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Maris Teder-Laving
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Guanchao Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Department of Internal Medicine, Division of Endocrinology, Leiden, Netherlands
| | - Otis D Wilson
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626), Department of Veterans Affairs/ Nashville, TN, USA
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rui Xia
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kristin L Young
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ruiyuan Zhang
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Nephrology and Rheumatology, Kliniken Südostbayern, Traunstein, Germany
- KfH Kidney Centre Traunstein, Traunstein, Germany
| | - David Conen
- Population Health Research Institute, Medicine, McMaster University, Hamilton, On, Canada
| | - Simon R Cox
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Marcus Dörr
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Cardiology, Pneumology, Infectious Diseases, Intensive Care Medicine, Department of Internal Medicine B, Un iversity Medicine Greifswald, Greifswald, Germany
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ervin R Fox
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Nora Franceschini
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sina A Gharib
- Pulmonary, Critical Care and Sleep Medicine, Medicine, University of Washington, Seattle, WA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, Department of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Sioban D Harlow
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
- Tulane University Translational Sciences Institute, New Orleans, LA , USA
| | - Elizabeth G Holliday
- School of Medicine and Public Health, College of Health Medicine and Wellbeing, University of Newcastle, New Lambton Heights, NSW, Australia
| | - Zoltan Kutalik
- Statistical Genetics Group, Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Kuopio
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center - Tampere, Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, US
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Brenda WJH Penninx
- Department of Psychiatry, Amsterdam UMC/Vrije universiteit, Amsterdam, Netherlands
- GGZ inGeest, Amsterdam, Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Tim D Spector
- Department of Twin Research, King’s College London, London, UK
| | - Lynne E Wagenknecht
- Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | | | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Kari E North
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | | | - Adriana M Hung
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626), Department of Veterans Affairs/ Nashville, TN, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alisa K Manning
- Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James Gauderman
- Division of Biostatistics, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Patricia B Munroe
- Clinical Pharmacology and Precision Medicine, Queen Mary University of London, London, UK
| | - Dabeeru C Rao
- Center for Biostatistics and Data Science, Institute for Informatics, Data Science, and Biostatistics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Lei den, Netherlands
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Lei den, Netherlands
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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Zamariolli M, Auwerx C, Sadler MC, van der Graaf A, Lepik K, Schoeler T, Moysés-Oliveira M, Dantas AG, Melaragno MI, Kutalik Z. Response to Bassett et al. Am J Hum Genet 2023; 110:1219-1220. [PMID: 37419093 PMCID: PMC10357494 DOI: 10.1016/j.ajhg.2023.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023] Open
Affiliation(s)
- Malú Zamariolli
- Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Chiara Auwerx
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | | | - Kaido Lepik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Tabea Schoeler
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | | | - Anelisa G Dantas
- Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland.
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3
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Zamariolli M, Auwerx C, Sadler MC, van der Graaf A, Lepik K, Schoeler T, Moysés-Oliveira M, Dantas AG, Melaragno MI, Kutalik Z. The impact of 22q11.2 copy-number variants on human traits in the general population. Am J Hum Genet 2023; 110:300-313. [PMID: 36706759 PMCID: PMC9943723 DOI: 10.1016/j.ajhg.2023.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
While extensively studied in clinical cohorts, the phenotypic consequences of 22q11.2 copy-number variants (CNVs) in the general population remain understudied. To address this gap, we performed a phenome-wide association scan in 405,324 unrelated UK Biobank (UKBB) participants by using CNV calls from genotyping array. We mapped 236 Human Phenotype Ontology terms linked to any of the 90 genes encompassed by the region to 170 UKBB traits and assessed the association between these traits and the copy-number state of 504 genotyping array probes in the region. We found significant associations for eight continuous and nine binary traits associated under different models (duplication-only, deletion-only, U-shape, and mirror models). The causal effect of the expression level of 22q11.2 genes on associated traits was assessed through transcriptome-wide Mendelian randomization (TWMR), revealing that increased expression of ARVCF increased BMI. Similarly, increased DGCR6 expression causally reduced mean platelet volume, in line with the corresponding CNV effect. Furthermore, cross-trait multivariable Mendelian randomization (MVMR) suggested a predominant role of genuine (horizontal) pleiotropy in the CNV region. Our findings show that within the general population, 22q11.2 CNVs are associated with traits previously linked to genes in the region, and duplications and deletions act upon traits in different fashions. We also showed that gain or loss of distinct segments within 22q11.2 may impact a trait under different association models. Our results have provided new insights to help further the understanding of the complex 22q11.2 region.
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Affiliation(s)
- Malú Zamariolli
- Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Chiara Auwerx
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | | | - Kaido Lepik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Tabea Schoeler
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | | | - Anelisa G Dantas
- Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland.
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4
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Rimbert A, Yeung MW, Dalila N, Thio CHL, Yu H, Loaiza N, Oldoni F, van der Graaf A, Wang S, Said MA, Blauw LL, Girardeau A, Bray L, Caillaud A, Bloks VW, Marrec M, Moulin P, Rensen PCN, van de Sluis B, Snieder H, Di Filippo M, van der Harst P, Tybjaerg-Hansen A, Zimmerman P, Cariou B, Kuivenhoven JA. Variants in the GPR146 Gene Are Associated With a Favorable Cardiometabolic Risk Profile. Arterioscler Thromb Vasc Biol 2022; 42:1262-1271. [PMID: 36047410 DOI: 10.1161/atvbaha.122.317514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND In mice, GPR146 (G-protein-coupled receptor 146) deficiency reduces plasma lipids and protects against atherosclerosis. Whether these findings translate to humans is unknown. METHODS Common and rare genetic variants in the GPR146 gene locus were used as research instruments in the UK Biobank. The Lifelines, The Copenhagen-City Heart Study, and a cohort of individuals with familial hypobetalipoproteinemia were used to find and study rare GPR146 variants. RESULTS In the UK Biobank, carriers of the common rs2362529-C allele present with lower low-density lipoprotein cholesterol, apo (apolipoprotein) B, high-density lipoprotein cholesterol, apoAI, CRP (C-reactive protein), and plasma liver enzymes compared with noncarriers. Carriers of the common rs1997243-G allele, associated with higher GPR146 expression, present with the exact opposite phenotype. The associations with plasma lipids of the above alleles are allele dose-dependent. Heterozygote carriers of a rare coding variant (p.Pro62Leu; n=2615), predicted to be damaging, show a stronger reductions in the above parameters compared with carriers of the common rs2362529-C allele. The p.Pro62Leu variant is furthermore shown to segregate with low low-density lipoprotein cholesterol in a family with familial hypobetalipoproteinemia. Compared with controls, carriers of the common rs2362529-C allele show a marginally reduced risk of coronary artery disease (P=0.03) concomitant with a small effect size on low-density lipoprotein cholesterol (average decrease of 2.24 mg/dL in homozygotes) of this variant. Finally, mendelian randomization analyses suggest a causal relationship between GPR146 gene expression and plasma lipid and liver enzyme levels. CONCLUSIONS This study shows that carriers of new genetic GPR146 variants have a beneficial cardiometabolic risk profile, but it remains to be shown whether genetic or pharmaceutical inhibition of GPR146 protects against atherosclerosis in humans.
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Affiliation(s)
- Antoine Rimbert
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, France (A.R., A.G., L.B., A.C., M.M., B.C.)
| | - Ming W Yeung
- Department of Cardiology (M.W.Y., S.W., M.S., P.v.d.H.), University Medical Center Groningen, University of Groningen, the Netherlands.,Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., P.v.d.H.)
| | - Nawar Dalila
- Section for Molecular Genetics, Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (N.D., A.T.-H.)
| | - Chris H L Thio
- Department of Epidemiology (C.H.L.T., S.W., H.S.), University Medical Center Groningen, University of Groningen, the Netherlands
| | - Haojie Yu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (H.Y.).,Precision Medicine Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (H.Y.)
| | - Natalia Loaiza
- Department of Pediatrics, Section Molecular Genetics (N.L., B.v.d.S., J.A.K.), University Medical Center Groningen, University of Groningen, the Netherlands
| | - Federico Oldoni
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas (F.O.)
| | - Adriaan van der Graaf
- Department of Genetics (A.v.d.G.), University Medical Center Groningen, University of Groningen, the Netherlands
| | - Siqi Wang
- Department of Cardiology (M.W.Y., S.W., M.S., P.v.d.H.), University Medical Center Groningen, University of Groningen, the Netherlands.,Department of Epidemiology (C.H.L.T., S.W., H.S.), University Medical Center Groningen, University of Groningen, the Netherlands
| | - M Abdullah Said
- Department of Cardiology (M.W.Y., S.W., M.S., P.v.d.H.), University Medical Center Groningen, University of Groningen, the Netherlands
| | - Lisanne L Blauw
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands (L.L.B., P.C.N.R.)
| | - Aurore Girardeau
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, France (A.R., A.G., L.B., A.C., M.M., B.C.)
| | - Lise Bray
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, France (A.R., A.G., L.B., A.C., M.M., B.C.)
| | - Amandine Caillaud
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, France (A.R., A.G., L.B., A.C., M.M., B.C.)
| | - Vincent W Bloks
- Sections of Molecular Metabolism and Nutrition, Department of Pediatrics (V.W.B.), University Medical Center Groningen, University of Groningen, the Netherlands
| | - Marie Marrec
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, France (A.R., A.G., L.B., A.C., M.M., B.C.)
| | - Philippe Moulin
- CarMen Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Pierre-Bénite, France (P.M., M.D.F.).,Hospices Civils de Lyon, Fédération d'endocrinologie, maladies métaboliques, diabète et nutrition, Hôpital Louis Pradel, Bron, France (P.M.)
| | - Patrick C N Rensen
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands (L.L.B., P.C.N.R.)
| | - Bart van de Sluis
- Department of Pediatrics, Section Molecular Genetics (N.L., B.v.d.S., J.A.K.), University Medical Center Groningen, University of Groningen, the Netherlands
| | - Harold Snieder
- Department of Epidemiology (C.H.L.T., S.W., H.S.), University Medical Center Groningen, University of Groningen, the Netherlands
| | - Mathilde Di Filippo
- CarMen Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, Pierre-Bénite, France (P.M., M.D.F.).,Hospices Civils de Lyon, UF Dyslipidémies Service de Biochimie et de Biologie Moléculaire Grand Est, Bron, France (M.D.F.)
| | - Pim van der Harst
- Department of Cardiology (M.W.Y., S.W., M.S., P.v.d.H.), University Medical Center Groningen, University of Groningen, the Netherlands.,Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, University of Utrecht, the Netherlands (M.W.Y., P.v.d.H.)
| | - Anne Tybjaerg-Hansen
- Section for Molecular Genetics, Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (N.D., A.T.-H.).,Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark (A.T.-H.).,The Copenhagen City Heart Study, Bispebjerg and Frederiksberg Hospital, Denmark (A.T.-H.)
| | | | - Bertrand Cariou
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, France (A.R., A.G., L.B., A.C., M.M., B.C.)
| | - Jan Albert Kuivenhoven
- Department of Pediatrics, Section Molecular Genetics (N.L., B.v.d.S., J.A.K.), University Medical Center Groningen, University of Groningen, the Netherlands
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5
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Lopera-Maya EA, Kurilshikov A, van der Graaf A, Hu S, Andreu-Sánchez S, Chen L, Vila AV, Gacesa R, Sinha T, Collij V, Klaassen MAY, Bolte LA, Gois MFB, Neerincx PBT, Swertz MA, Harmsen HJM, Wijmenga C, Fu J, Weersma RK, Zhernakova A, Sanna S. Author Correction: Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project. Nat Genet 2022; 54:1448. [PMID: 35879415 DOI: 10.1038/s41588-022-01164-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Esteban A Lopera-Maya
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marjiolein A Y Klaassen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Laura A Bolte
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pieter B T Neerincx
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | | | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. .,Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy.
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6
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Sanna S, Kurilshikov A, van der Graaf A, Fu J, Zhernakova A. Challenges and future directions for studying effects of host genetics on the gut microbiome. Nat Genet 2022; 54:100-106. [PMID: 35115688 DOI: 10.1038/s41588-021-00983-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/02/2021] [Indexed: 12/15/2022]
Abstract
The human gut microbiome is a complex ecosystem that is involved in its host's metabolism, immunity and health. Although interindividual variations in gut microbial composition are mainly driven by environmental factors, some gut microorganisms are heritable and thus can be influenced by host genetics. In the past 5 years, 12 microbial genome-wide association studies (mbGWAS) with >1,000 participants have been published, yet only a few genetic loci have been consistently confirmed across multiple studies. Here we discuss the state of the art for mbGWAS, focusing on current challenges such as the heterogeneity of microbiome measurements and power issues, and we elaborate on potential future directions for genetic analysis of the microbiome.
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Affiliation(s)
- Serena Sanna
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Monserrato, Cagliari, Italy.
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
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7
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Lopera-Maya EA, Kurilshikov A, van der Graaf A, Hu S, Andreu-Sánchez S, Chen L, Vila AV, Gacesa R, Sinha T, Collij V, Klaassen MAY, Bolte LA, Gois MFB, Neerincx PBT, Swertz MA, Harmsen HJM, Wijmenga C, Fu J, Weersma RK, Zhernakova A, Sanna S. Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project. Nat Genet 2022; 54:143-151. [PMID: 35115690 DOI: 10.1038/s41588-021-00992-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 11/19/2021] [Indexed: 02/07/2023]
Abstract
Host genetics are known to influence the gut microbiome, yet their role remains poorly understood. To robustly characterize these effects, we performed a genome-wide association study of 207 taxa and 205 pathways representing microbial composition and function in 7,738 participants of the Dutch Microbiome Project. Two robust, study-wide significant (P < 1.89 × 10-10) signals near the LCT and ABO genes were found to be associated with multiple microbial taxa and pathways and were replicated in two independent cohorts. The LCT locus associations seemed modulated by lactose intake, whereas those at ABO could be explained by participant secretor status determined by their FUT2 genotype. Twenty-two other loci showed suggestive evidence (P < 5 × 10-8) of association with microbial taxa and pathways. At a more lenient threshold, the number of loci we identified strongly correlated with trait heritability, suggesting that much larger sample sizes are needed to elucidate the remaining effects of host genetics on the gut microbiome.
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Affiliation(s)
- Esteban A Lopera-Maya
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marjiolein A Y Klaassen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Laura A Bolte
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pieter B T Neerincx
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy.
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8
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Zanoni P, Panteloglou G, Othman A, Haas JT, Meier R, Rimbert A, Futema M, Abou Khalil Y, Norrelykke SF, Rzepiela AJ, Stoma S, Stebler M, van Dijk F, Wijers M, Wolters JC, Dalila N, Huijkman NCA, Smit M, Gallo A, Carreau V, Philippi A, Rabès JP, Boileau C, Visentin M, Vonghia L, Weyler J, Francque S, Verrijken A, Verhaegen A, Van Gaal L, van der Graaf A, van Rosmalen BV, Robert J, Velagapudi S, Yalcinkaya M, Keel M, Radosavljevic S, Geier A, Tybjaerg-Hansen A, Varret M, Rohrer L, Humphries SE, Staels B, van de Sluis B, Kuivenhoven JA, von Eckardstein A. Posttranscriptional Regulation of the Human LDL Receptor by the U2-Spliceosome. Circ Res 2022; 130:80-95. [PMID: 34809444 DOI: 10.1161/circresaha.120.318141] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The LDLR (low-density lipoprotein receptor) in the liver is the major determinant of LDL-cholesterol levels in human plasma. The discovery of genes that regulate the activity of LDLR helps to identify pathomechanisms of hypercholesterolemia and novel therapeutic targets against atherosclerotic cardiovascular disease. METHODS We performed a genome-wide RNA interference screen for genes limiting the uptake of fluorescent LDL into Huh-7 hepatocarcinoma cells. Top hit genes were validated by in vitro experiments as well as analyses of data sets on gene expression and variants in human populations. RESULTS The knockdown of 54 genes significantly inhibited LDL uptake. Fifteen of them encode for components or interactors of the U2-spliceosome. Knocking down any one of 11 out of 15 genes resulted in the selective retention of intron 3 of LDLR. The translated LDLR fragment lacks 88% of the full length LDLR and is detectable neither in nontransfected cells nor in human plasma. The hepatic expression of the intron 3 retention transcript is increased in nonalcoholic fatty liver disease as well as after bariatric surgery. Its expression in blood cells correlates with LDL-cholesterol and age. Single nucleotide polymorphisms and 3 rare variants of one spliceosome gene, RBM25, are associated with LDL-cholesterol in the population and familial hypercholesterolemia, respectively. Compared with overexpression of wild-type RBM25, overexpression of the 3 rare RBM25 mutants in Huh-7 cells led to lower LDL uptake. CONCLUSIONS We identified a novel mechanism of posttranscriptional regulation of LDLR activity in humans and associations of genetic variants of RBM25 with LDL-cholesterol levels.
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Affiliation(s)
- Paolo Zanoni
- Institute for Clinical Chemistry, University and University Hospital Zurich, Switzerland (P.Z., G.P., J.R., S.V., M.Y., M.K., S.R., L.R., A.v.E.).,Now with Institute of Medical Genetics, University of Zurich, Switzerland (P.Z.).,Center for Integrative Human Physiology, University of Zurich, Switzerland (P.Z., G.P., S.V., M.Y., M.K., S.R., L.R., A.v.E.)
| | - Grigorios Panteloglou
- Institute for Clinical Chemistry, University and University Hospital Zurich, Switzerland (P.Z., G.P., J.R., S.V., M.Y., M.K., S.R., L.R., A.v.E.).,Center for Integrative Human Physiology, University of Zurich, Switzerland (P.Z., G.P., S.V., M.Y., M.K., S.R., L.R., A.v.E.)
| | - Alaa Othman
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland (A.O.)
| | - Joel T Haas
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011- EGID, France (J.T.H., B.S.)
| | - Roger Meier
- Scientific center for optical and electron microscopy (ScopeM), ETH Zurich, Switzerland (R.M., S.F.N., A.J.R., S.S., M. Stebler)
| | - Antoine Rimbert
- Department of Pediatrics, Section Molecular Genetics, University of Groningen, University Medical Center Groningen, the Netherlands (A.R., M.W., J.C.W., N.C.A.H., M. Smit, B.v.d.S., J.A.K.).,Now with Inserm UMR 1087/CNRS UMR 6291 IRS-UN, Nantes, France (A.R.)
| | - Marta Futema
- Cardiology Research Centre, Molecular and Clinical Sciences Research Institute, St George's, University of London, United Kingdom (M.F.)
| | - Yara Abou Khalil
- LVTS-INSERM UMRS 1148 and University of Paris, CHU Xavier Bichat, Paris, France (Y.A.K., J.-P.R., C.B., M. Varret).,Laboratory of Biochemistry and Molecular Therapeutics (LBTM), Faculty of Pharmacy and Pôle technologie Santé (PTS), Saint-Joseph University, Beirut, Lebanon (Y.A.K.)
| | - Simon F Norrelykke
- Scientific center for optical and electron microscopy (ScopeM), ETH Zurich, Switzerland (R.M., S.F.N., A.J.R., S.S., M. Stebler)
| | - Andrzej J Rzepiela
- Scientific center for optical and electron microscopy (ScopeM), ETH Zurich, Switzerland (R.M., S.F.N., A.J.R., S.S., M. Stebler)
| | - Szymon Stoma
- Scientific center for optical and electron microscopy (ScopeM), ETH Zurich, Switzerland (R.M., S.F.N., A.J.R., S.S., M. Stebler)
| | - Michael Stebler
- Scientific center for optical and electron microscopy (ScopeM), ETH Zurich, Switzerland (R.M., S.F.N., A.J.R., S.S., M. Stebler)
| | - Freerk van Dijk
- Department of Genetics, University of Groningen, University Medical Center Groningen, the Netherlands (F.v.D., A.v.d.G.)
| | - Melinde Wijers
- Department of Pediatrics, Section Molecular Genetics, University of Groningen, University Medical Center Groningen, the Netherlands (A.R., M.W., J.C.W., N.C.A.H., M. Smit, B.v.d.S., J.A.K.)
| | - Justina C Wolters
- Department of Pediatrics, Section Molecular Genetics, University of Groningen, University Medical Center Groningen, the Netherlands (A.R., M.W., J.C.W., N.C.A.H., M. Smit, B.v.d.S., J.A.K.)
| | - Nawar Dalila
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (N.D., A.T.-H.)
| | - Nicolette C A Huijkman
- Department of Pediatrics, Section Molecular Genetics, University of Groningen, University Medical Center Groningen, the Netherlands (A.R., M.W., J.C.W., N.C.A.H., M. Smit, B.v.d.S., J.A.K.)
| | - Marieke Smit
- Department of Pediatrics, Section Molecular Genetics, University of Groningen, University Medical Center Groningen, the Netherlands (A.R., M.W., J.C.W., N.C.A.H., M. Smit, B.v.d.S., J.A.K.)
| | - Antonio Gallo
- AP-HP, Endocrinology and Metabolism Department, Human Research Nutrition Center, Pitié-Salpêtrière Hospital, Paris, France (A. Gallo, V.C.)
| | - Valérie Carreau
- AP-HP, Endocrinology and Metabolism Department, Human Research Nutrition Center, Pitié-Salpêtrière Hospital, Paris, France (A. Gallo, V.C.)
| | - Anne Philippi
- Université de Paris, Faculté de Médecine Paris-Diderot, UMR-S958 Paris, France; Now with Université de Paris, Institut Cochin, INSERM U1016, CNRS UMR-8104, Paris, France (A.P.)
| | - Jean-Pierre Rabès
- LVTS-INSERM UMRS 1148 and University of Paris, CHU Xavier Bichat, Paris, France (Y.A.K., J.-P.R., C.B., M. Varret).,AP-HP, Université Paris-Saclay, Paris, France (J.-P.R.).,UFR Simone Veil des Sciences de la Santé, UVSQ, Montigny-Le-Bretonneux, France (J.-P.R.)
| | - Catherine Boileau
- LVTS-INSERM UMRS 1148 and University of Paris, CHU Xavier Bichat, Paris, France (Y.A.K., J.-P.R., C.B., M. Varret).,AP-HP, Genetics Department, CHU Xavier Bichat, Université de Paris, France (C.B.)
| | - Michele Visentin
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Switzerland (M. Visentin)
| | - Luisa Vonghia
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Edegem, Belgium (L.V., J.W., S.F.).,Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine, University of Antwerp, Belgium (L.V., J.W., S.F., A. Verrijken, A. Verhaegen, L.V.G.)
| | - Jonas Weyler
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Edegem, Belgium (L.V., J.W., S.F.)
| | - Sven Francque
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Edegem, Belgium (L.V., J.W., S.F.).,Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine, University of Antwerp, Belgium (L.V., J.W., S.F., A. Verrijken, A. Verhaegen, L.V.G.)
| | - An Verrijken
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine, University of Antwerp, Belgium (L.V., J.W., S.F., A. Verrijken, A. Verhaegen, L.V.G.).,Department of Endocrinology, Diabetology and Metabolism, Antwerp University Hospital, Edegem, Belgium (A. Verrijken, A. Verhaegen, L.V.G.)
| | - Ann Verhaegen
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine, University of Antwerp, Belgium (L.V., J.W., S.F., A. Verrijken, A. Verhaegen, L.V.G.).,Department of Endocrinology, Diabetology and Metabolism, Antwerp University Hospital, Edegem, Belgium (A. Verrijken, A. Verhaegen, L.V.G.)
| | - Luc Van Gaal
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine, University of Antwerp, Belgium (L.V., J.W., S.F., A. Verrijken, A. Verhaegen, L.V.G.).,Department of Endocrinology, Diabetology and Metabolism, Antwerp University Hospital, Edegem, Belgium (A. Verrijken, A. Verhaegen, L.V.G.)
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, the Netherlands (F.v.D., A.v.d.G.)
| | - Belle V van Rosmalen
- Department of Surgery, Academic Medical Center, University of Amsterdam, the Netherlands (B.V.v.R.)
| | - Jerome Robert
- Institute for Clinical Chemistry, University and University Hospital Zurich, Switzerland (P.Z., G.P., J.R., S.V., M.Y., M.K., S.R., L.R., A.v.E.)
| | - Srividya Velagapudi
- Institute for Clinical Chemistry, University and University Hospital Zurich, Switzerland (P.Z., G.P., J.R., S.V., M.Y., M.K., S.R., L.R., A.v.E.).,Center for Molecular Cardiology, University of Zurich, Switzerland (S.V.).,Center for Integrative Human Physiology, University of Zurich, Switzerland (P.Z., G.P., S.V., M.Y., M.K., S.R., L.R., A.v.E.)
| | - Mustafa Yalcinkaya
- Institute for Clinical Chemistry, University and University Hospital Zurich, Switzerland (P.Z., G.P., J.R., S.V., M.Y., M.K., S.R., L.R., A.v.E.).,Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (M.Y.).,Center for Integrative Human Physiology, University of Zurich, Switzerland (P.Z., G.P., S.V., M.Y., M.K., S.R., L.R., A.v.E.)
| | - Michaela Keel
- Institute for Clinical Chemistry, University and University Hospital Zurich, Switzerland (P.Z., G.P., J.R., S.V., M.Y., M.K., S.R., L.R., A.v.E.).,Center for Integrative Human Physiology, University of Zurich, Switzerland (P.Z., G.P., S.V., M.Y., M.K., S.R., L.R., A.v.E.)
| | - Silvija Radosavljevic
- Institute for Clinical Chemistry, University and University Hospital Zurich, Switzerland (P.Z., G.P., J.R., S.V., M.Y., M.K., S.R., L.R., A.v.E.).,Center for Integrative Human Physiology, University of Zurich, Switzerland (P.Z., G.P., S.V., M.Y., M.K., S.R., L.R., A.v.E.)
| | - Andreas Geier
- Division of Hepatology, Department of Medicine II, University Hospital Würzburg, Germany (A. Geier)
| | - Anne Tybjaerg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark (N.D., A.T.-H.)
| | - Mathilde Varret
- LVTS-INSERM UMRS 1148 and University of Paris, CHU Xavier Bichat, Paris, France (Y.A.K., J.-P.R., C.B., M. Varret)
| | - Lucia Rohrer
- Institute for Clinical Chemistry, University and University Hospital Zurich, Switzerland (P.Z., G.P., J.R., S.V., M.Y., M.K., S.R., L.R., A.v.E.).,Center for Integrative Human Physiology, University of Zurich, Switzerland (P.Z., G.P., S.V., M.Y., M.K., S.R., L.R., A.v.E.)
| | - Steve E Humphries
- Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, United Kingdom (S.E.H.)
| | - Bart Staels
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011- EGID, France (J.T.H., B.S.)
| | - Bart van de Sluis
- Department of Pediatrics, Section Molecular Genetics, University of Groningen, University Medical Center Groningen, the Netherlands (A.R., M.W., J.C.W., N.C.A.H., M. Smit, B.v.d.S., J.A.K.)
| | - Jan Albert Kuivenhoven
- Department of Pediatrics, Section Molecular Genetics, University of Groningen, University Medical Center Groningen, the Netherlands (A.R., M.W., J.C.W., N.C.A.H., M. Smit, B.v.d.S., J.A.K.)
| | - Arnold von Eckardstein
- Institute for Clinical Chemistry, University and University Hospital Zurich, Switzerland (P.Z., G.P., J.R., S.V., M.Y., M.K., S.R., L.R., A.v.E.).,Center for Integrative Human Physiology, University of Zurich, Switzerland (P.Z., G.P., S.V., M.Y., M.K., S.R., L.R., A.v.E.)
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9
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Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, Turpin W, Moon JY, Kim HN, Lüll K, Barkan E, Shah SA, Fornage M, Szopinska-Tokov J, Wallen ZD, Borisevich D, Agreus L, Andreasson A, Bang C, Bedrani L, Bell JT, Bisgaard H, Boehnke M, Boomsma DI, Burk RD, Claringbould A, Croitoru K, Davies GE, van Duijn CM, Duijts L, Falony G, Fu J, van der Graaf A, Hansen T, Homuth G, Hughes DA, Ijzerman RG, Jackson MA, Jaddoe VWV, Joossens M, Jørgensen T, Keszthelyi D, Knight R, Laakso M, Laudes M, Launer LJ, Lieb W, Lusis AJ, Masclee AAM, Moll HA, Mujagic Z, Qibin Q, Rothschild D, Shin H, Sørensen SJ, Steves CJ, Thorsen J, Timpson NJ, Tito RY, Vieira-Silva S, Völker U, Völzke H, Võsa U, Wade KH, Walter S, Watanabe K, Weiss S, Weiss FU, Weissbrod O, Westra HJ, Willemsen G, Payami H, Jonkers DMAE, Arias Vasquez A, de Geus EJC, Meyer KA, Stokholm J, Segal E, Org E, Wijmenga C, Kim HL, Kaplan RC, Spector TD, Uitterlinden AG, Rivadeneira F, Franke A, Lerch MM, Franke L, Sanna S, D'Amato M, Pedersen O, Paterson AD, Kraaij R, Raes J, Zhernakova A. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat Genet 2021; 53:156-165. [PMID: 33462485 PMCID: PMC8515199 DOI: 10.1038/s41588-020-00763-1] [Citation(s) in RCA: 541] [Impact Index Per Article: 180.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023]
Abstract
To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 × 10-8) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 × 10-20), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 × 10-10 < P < 5 × 10-8) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.
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Affiliation(s)
- Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Rodrigo Bacigalupe
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jun Wang
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ayse Demirkan
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Section of Statistical Multi-Omics, Department of Clinical & Experimental Medicine, School of Biosciences & Medicine, University of Surrey, Guildford, UK
| | - Caroline I Le Roy
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Juan Antonio Raygoza Garay
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Casey T Finnicum
- Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA
| | - Xingrong Liu
- Center for Molecular Medicine and Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Daria V Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg, Russia
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Williams Turpin
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Kreete Lüll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Elad Barkan
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shiraz A Shah
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Myriam Fornage
- Institute of Molecular Medicine McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joanna Szopinska-Tokov
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Zachary D Wallen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dmitrii Borisevich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Agreus
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Anna Andreasson
- Stress Research Institute, Stockholm University, Stockholm, Sweden
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Larbi Bedrani
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Hans Bisgaard
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Dorret I Boomsma
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Robert D Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kenneth Croitoru
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gareth E Davies
- Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Liesbeth Duijts
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gwen Falony
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Richard G Ijzerman
- Department of Endocrinology, Amsterdam University Medical Center, location VUMC, Amsterdam, the Netherlands
| | - Matthew A Jackson
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Vincent W V Jaddoe
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marie Joossens
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Torben Jørgensen
- Centre for Clinical Research and Prevention, Bispebjerg/Frederiksberg Hospital, Capital Region of Copenhagen and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Keszthelyi
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation and Department of Bioengeering, University of California, San Diego, La Jolla, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Matthias Laudes
- Department of Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Bethesda, MD, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Aldons J Lusis
- Departments of Microbiology, Immunology and Molecular Genetics, and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ad A M Masclee
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Henriette A Moll
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Zlatan Mujagic
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Qi Qibin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daphna Rothschild
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hocheol Shin
- Department of Family Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | | | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Raul Y Tito
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kaitlin H Wade
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Susanna Walter
- Department of Biomedical and Clinical Sciences, University of Linköping, Linköping, Sweden
- Department of Gastroenterology, County Council of Östergötland, Linköping, Sweden
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, the Netherlands
| | - Stefan Weiss
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Frank U Weiss
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Omer Weissbrod
- School of Public Health, Harvard University, Boston, MA, USA
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gonneke Willemsen
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daisy M A E Jonkers
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Alejandro Arias Vasquez
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Eco J C de Geus
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam UMC, Amsterdam, the Netherlands
| | - Katie A Meyer
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Jakob Stokholm
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Eran Segal
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elin Org
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hyung-Lae Kim
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Robert C Kaplan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Markus M Lerch
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Istituto di Ricerca Genetica e Biomedica, National Research Council, Monserrato, Italy
| | - Mauro D'Amato
- Center for Molecular Medicine and Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, San Sebastián, Spain
- Ikerbasque, Basque Science Foundation, Bilbao, Spain
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrew D Paterson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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10
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van der Graaf A, Zorro MM, Claringbould A, Võsa U, Aguirre-Gamboa R, Li C, Mooiweer J, Ricaño-Ponce I, Borek Z, Koning F, Kooy-Winkelaar Y, Sollid LM, Qiao SW, Kumar V, Li Y, Franke L, Withoff S, Wijmenga C, Sanna S, Jonkers I. Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFNγ Signaling in Celiac Disease. Front Genet 2021; 11:562434. [PMID: 33569077 PMCID: PMC7868554 DOI: 10.3389/fgene.2020.562434] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
Celiac disease (CeD) is a complex T cell-mediated enteropathy induced by gluten. Although genome-wide association studies have identified numerous genomic regions associated with CeD, it is difficult to accurately pinpoint which genes in these loci are most likely to cause CeD. We used four different in silico approaches-Mendelian randomization inverse variance weighting, COLOC, LD overlap, and DEPICT-to integrate information gathered from a large transcriptomics dataset. This identified 118 prioritized genes across 50 CeD-associated regions. Co-expression and pathway analysis of these genes indicated an association with adaptive and innate cytokine signaling and T cell activation pathways. Fifty-one of these genes are targets of known drug compounds or likely druggable genes, suggesting that our methods can be used to pinpoint potential therapeutic targets. In addition, we detected 172 gene combinations that were affected by our CeD-prioritized genes in trans. Notably, 41 of these trans-mediated genes appear to be under control of one master regulator, TRAF-type zinc finger domain containing 1 (TRAFD1), and were found to be involved in interferon (IFN)γ signaling and MHC I antigen processing/presentation. Finally, we performed in vitro experiments in a human monocytic cell line that validated the role of TRAFD1 as an immune regulator acting in trans. Our strategy confirmed the role of adaptive immunity in CeD and revealed a genetic link between CeD and IFNγ signaling as well as with MHC I antigen processing, both major players of immune activation and CeD pathogenesis.
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Affiliation(s)
- Adriaan van der Graaf
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Maria M. Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Annique Claringbould
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Urmo Võsa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Raúl Aguirre-Gamboa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Chan Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Joram Mooiweer
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Zuzanna Borek
- Deutsches Rheumaforschungszentrum Berlin (DRFZ), An Institute of the Leibniz Association, Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gastroenterology, Infectious Diseases and Rheumatology, Berlin, Germany
| | - Frits Koning
- Department of Immunology, Leiden University, Leiden, Netherlands
| | | | - Ludvig M. Sollid
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School, Hanover, Germany
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Istituto di Ricerca Genetica e Biomedica (IRGB) del Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Iris Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
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11
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Lopera Maya EA, van der Graaf A, Lanting P, van der Geest M, Fu J, Swertz M, Franke L, Wijmenga C, Deelen P, Zhernakova A, Sanna S. Lack of Association Between Genetic Variants at ACE2 and TMPRSS2 Genes Involved in SARS-CoV-2 Infection and Human Quantitative Phenotypes. Front Genet 2020; 11:613. [PMID: 32582302 PMCID: PMC7295011 DOI: 10.3389/fgene.2020.00613] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) shows a wide variation in expression and severity of symptoms, from very mild or no symptoms, to flu-like symptoms, and in more severe cases, to pneumonia, acute respiratory distress syndrome, and even death. Large differences in outcome have also been observed between males and females. The causes for this variability are likely to be multifactorial, and to include genetics. The SARS-CoV-2 virus responsible for the infection depends on two human genes: the human receptor angiotensin converting enzyme 2 (ACE2) for cell invasion, and the serine protease TMPRSS2 for S protein priming. Genetic variation in these two genes may thus modulate an individual's genetic predisposition to infection and virus clearance. While genetic data on COVID-19 patients is being gathered, we carried out a phenome-wide association scan (PheWAS) to investigate the role of these genes in other human phenotypes in the general population. We examined 178 quantitative phenotypes including cytokines and cardio-metabolic biomarkers, as well as usage of 58 medications in 36,339 volunteers from the Lifelines population cohort, in relation to 1,273 genetic variants located in or near ACE2 and TMPRSS2. While none reached our threshold for significance, we observed several interesting suggestive associations. For example, single nucleotide polymorphisms (SNPs) near the TMPRSS2 genes were associated with thrombocytes count (p = 1.8 × 10-5). SNPs within the ACE2 gene were associated with (1) the use of angiotensin II receptor blockers (ARBs) combination therapies (p = 5.7 × 10-4), an association that is significantly stronger in females (p dif f = 0.01), and (2) with the use of non-steroid anti-inflammatory and antirheumatic products (p = 5.5 × 10-4). While these associations need to be confirmed in larger sample sizes, they suggest that these variants could play a role in diseases such as thrombocytopenia, hypertension, and chronic inflammation that are often observed in the more severe COVID-19 cases. Further investigation of these genetic variants in the context of COVID-19 is thus promising for better understanding of disease variability. Full results are available at https://covid19research.nl.
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Affiliation(s)
- Esteban A. Lopera Maya
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Pauline Lanting
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Marije van der Geest
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Morris Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Genetics, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Institute for Genetics and Biomedical Research (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
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12
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Ricaño-Ponce I, Gutierrez-Achury J, Costa AF, Deelen P, Kurilshikov A, Zorro MM, Platteel M, van der Graaf A, Sanna S, Daffra O, Zhernakova A, Fu J, Trynka G, Smecuol E, Niveloni SI, Bai JC, Kumar V, Wijmenga C. Immunochip meta-analysis in European and Argentinian populations identifies two novel genetic loci associated with celiac disease. Eur J Hum Genet 2020; 28:313-323. [PMID: 31591516 PMCID: PMC7028987 DOI: 10.1038/s41431-019-0520-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/30/2022] Open
Abstract
Celiac disease (CeD) is a common immune-mediated disease of the small intestine that is triggered by exposure to dietary gluten. While the HLA locus plays a major role in disease susceptibility, 39 non-HLA loci were also identified in a study of 24,269 individuals. We now build on this earlier study by adding 4125 additional Caucasian samples including an Argentinian cohort. In doing so, we not only confirm the previous associations, we also identify two novel independent genome-wide significant associations at loci: 12p13.31 and 22q13.1. By applying a genomics approach and differential expression analysis in CeD intestinal biopsies, we prioritize potential causal genes at these novel loci, including LTBR, CYTH4, and RAC2. Nineteen prioritized causal genes are overlapping known drug targets. Pathway enrichment analysis and expression of these genes in CeD biopsies suggest that they have roles in regulating multiple pathways such as the tumor necrosis factor (TNF) mediated signaling pathway and positive regulation of I-κB kinase/NF-κB signaling.
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Affiliation(s)
- Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Javier Gutierrez-Achury
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Ana Florencia Costa
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Maria Magdalena Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Mathieu Platteel
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Oscar Daffra
- Gastroenterology Service, OSEP Mendoza, Mendoza, Argentina
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Gosia Trynka
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Edgardo Smecuol
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Sonia Isabel Niveloni
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Julio Cesar Bai
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA, Nijmegen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands.
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.
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13
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van Dam S, Võsa U, van der Graaf A, Franke L, de Magalhães JP. Gene co-expression analysis for functional classification and gene-disease predictions. Brief Bioinform 2018; 19:575-592. [PMID: 28077403 PMCID: PMC6054162 DOI: 10.1093/bib/bbw139] [Citation(s) in RCA: 409] [Impact Index Per Article: 68.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/01/2016] [Indexed: 01/06/2023] Open
Abstract
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes. Here, we introduce and guide researchers through a (differential) co-expression analysis. We provide an overview of methods and tools used to create and analyse co-expression networks constructed from gene expression data, and we explain how these can be used to identify genes with a regulatory role in disease. Furthermore, we discuss the integration of other data types with co-expression networks and offer future perspectives of co-expression analysis.
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Affiliation(s)
- Sipko van Dam
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
| | - Urmo Võsa
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
| | | | - Lude Franke
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
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