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Sterenborg RBTM, Steinbrenner I, Li Y, Bujnis MN, Naito T, Marouli E, Galesloot TE, Babajide O, Andreasen L, Astrup A, Åsvold BO, Bandinelli S, Beekman M, Beilby JP, Bork-Jensen J, Boutin T, Brody JA, Brown SJ, Brumpton B, Campbell PJ, Cappola AR, Ceresini G, Chaker L, Chasman DI, Concas MP, Coutinho de Almeida R, Cross SM, Cucca F, Deary IJ, Kjaergaard AD, Echouffo Tcheugui JB, Ellervik C, Eriksson JG, Ferrucci L, Freudenberg J, Fuchsberger C, Gieger C, Giulianini F, Gögele M, Graham SE, Grarup N, Gunjača I, Hansen T, Harding BN, Harris SE, Haunsø S, Hayward C, Hui J, Ittermann T, Jukema JW, Kajantie E, Kanters JK, Kårhus LL, Kiemeney LALM, Kloppenburg M, Kühnel B, Lahti J, Langenberg C, Lapauw B, Leese G, Li S, Liewald DCM, Linneberg A, Lominchar JVT, Luan J, Martin NG, Matana A, Meima ME, Meitinger T, Meulenbelt I, Mitchell BD, Møllehave LT, Mora S, Naitza S, Nauck M, Netea-Maier RT, Noordam R, Nursyifa C, Okada Y, Onano S, Papadopoulou A, Palmer CNA, Pattaro C, Pedersen O, Peters A, Pietzner M, Polašek O, Pramstaller PP, Psaty BM, Punda A, Ray D, Redmond P, Richards JB, Ridker PM, Russ TC, Ryan KA, Olesen MS, Schultheiss UT, Selvin E, Siddiqui MK, Sidore C, Slagboom PE, Sørensen TIA, Soto-Pedre E, Spector TD, Spedicati B, Srinivasan S, Starr JM, Stott DJ, Tanaka T, Torlak V, Trompet S, Tuhkanen J, Uitterlinden AG, van den Akker EB, van den Eynde T, van der Klauw MM, van Heemst D, Verroken C, Visser WE, Vojinovic D, Völzke H, Waldenberger M, Walsh JP, Wareham NJ, Weiss S, Willer CJ, Wilson SG, Wolffenbuttel BHR, Wouters HJCM, Wright MJ, Yang Q, Zemunik T, Zhou W, Zhu G, Zöllner S, Smit JWA, Peeters RP, Köttgen A, Teumer A, Medici M. Multi-trait analysis characterizes the genetics of thyroid function and identifies causal associations with clinical implications. Nat Commun 2024; 15:888. [PMID: 38291025 PMCID: PMC10828500 DOI: 10.1038/s41467-024-44701-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024] Open
Abstract
To date only a fraction of the genetic footprint of thyroid function has been clarified. We report a genome-wide association study meta-analysis of thyroid function in up to 271,040 individuals of European ancestry, including reference range thyrotropin (TSH), free thyroxine (FT4), free and total triiodothyronine (T3), proxies for metabolism (T3/FT4 ratio) as well as dichotomized high and low TSH levels. We revealed 259 independent significant associations for TSH (61% novel), 85 for FT4 (67% novel), and 62 novel signals for the T3 related traits. The loci explained 14.1%, 6.0%, 9.5% and 1.1% of the total variation in TSH, FT4, total T3 and free T3 concentrations, respectively. Genetic correlations indicate that TSH associated loci reflect the thyroid function determined by free T3, whereas the FT4 associations represent the thyroid hormone metabolism. Polygenic risk score and Mendelian randomization analyses showed the effects of genetically determined variation in thyroid function on various clinical outcomes, including cardiovascular risk factors and diseases, autoimmune diseases, and cancer. In conclusion, our results improve the understanding of thyroid hormone physiology and highlight the pleiotropic effects of thyroid function on various diseases.
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Affiliation(s)
- Rosalie B T M Sterenborg
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Eirini Marouli
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Digital Environment Research Institute, Queen Mary University of London, London, UK
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Oladapo Babajide
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Laura Andreasen
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arne Astrup
- Department of Obesity and Nutritional Sciences, The Novo Nordisk Foundation, Hellerup, Denmark
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | | | - Marian Beekman
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - John P Beilby
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thibaud Boutin
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Suzanne J Brown
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
| | - Ben Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, 7600, Norway
| | - Purdey J Campbell
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
| | - Anne R Cappola
- Division of Endocrinology, Diabetes, and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
| | - Graziano Ceresini
- Oncological Endocrinology, University of Parma, Parma, Italy
- Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Layal Chaker
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, USA
- Harvard Medical School, Boston, USA
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Rodrigo Coutinho de Almeida
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Simone M Cross
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042, Monserrato (CA), Italy
- Università di Sassari, Dipartimento di Scienze Biomediche, V.le San Pietro, 07100, Sassari (SS), Italy
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, EH8 9JZ, Edinburgh, United Kingdom
| | - Alisa Devedzic Kjaergaard
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Palle Juul-Jensens Blvd. 11, Entrance A, 8200, Aarhus, Denmark
| | - Justin B Echouffo Tcheugui
- Division of Endocrinology, Diabetes, and Metabolism, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Christina Ellervik
- Harvard Medical School, Boston, USA
- Faculty of Medical Science, Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Clinical Biochemistry, Zealand University Hospital, Køge, Denmark
| | - Johan G Eriksson
- Department of General Practice and Primary health Care, University of Helsinki, Helsinki, Finland
- National University Singapore, Yong Loo Lin School of Medicine, Department of Obstetrics and Gynecology, Singapore, Singapore
| | - Luigi Ferrucci
- Longitudinal Study Section, National Institute on Aging, Baltimore, MD, USA
| | | | - Christian Fuchsberger
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, USA
| | - Martin Gögele
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Sarah E Graham
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivana Gunjača
- Department of Medical Biology, University of Split, School of Medicine, Split, Croatia
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Barbara N Harding
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Barcelona Institute for Global Health, Barcelona, Spain
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, EH8 9JZ, Edinburgh, United Kingdom
| | - Stig Haunsø
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Jennie Hui
- Pathwest Laboratory Medicine WA, Nedlands, WA, 6009, Australia
- School of Population and Global Health, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Till Ittermann
- Institute for Community Medicine, University Medicine Greifswald, 17475, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | - Eero Kajantie
- Finnish Institute for Health and Welfare, Population Health Unit, Helsinki and Oulu, Oulu, Finland
- Clinical Medicine Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jørgen K Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center of Physiological Research, University of California San Francisco, San Francisco, USA
| | - Line L Kårhus
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Lambertus A L M Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margreet Kloppenburg
- Departments of Rheumatology and Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Brigitte Kühnel
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Bruno Lapauw
- Department of Endocrinology, Ghent University Hospital, C. Heymanslaan 10, 9000, Ghent, Belgium
| | | | - Shuo Li
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - David C M Liewald
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, EH8 9JZ, Edinburgh, United Kingdom
| | - Allan Linneberg
- Center of Physiological Research, University of California San Francisco, San Francisco, USA
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesus V T Lominchar
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | | | - Antonela Matana
- Department of Medical Biology, University of Split, School of Medicine, Split, Croatia
| | - Marcel E Meima
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Thomas Meitinger
- Institute for Human Genetics, Technical University of Munich, Munich, Germany
| | - Ingrid Meulenbelt
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Braxton D Mitchell
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition, Baltimore, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, 21201, USA
| | - Line T Møllehave
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Samia Mora
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, USA
- Harvard Medical School, Boston, USA
| | - Silvia Naitza
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042, Monserrato (CA), Italy
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Romana T Netea-Maier
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Casia Nursyifa
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Japan
| | - Stefano Onano
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042, Monserrato (CA), Italy
| | - Areti Papadopoulou
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Colin N A Palmer
- Division of Population Health Genomics, School of Medicine, University of Dundee, DD19SY, Dundee, UK
| | - Cristian Pattaro
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Metabolic Research, Herlev-Gentofte University Hospital, Copenhagen, Denmark
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maik Pietzner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Ozren Polašek
- Department of Public Health, University of Split, School of Medicine, Split, Croatia
- Algebra University College, Zagreb, Croatia
| | - Peter P Pramstaller
- Institute for Biomedicine (affiliated with the University of Lübeck), Eurac Research, Bolzano, Italy
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Ante Punda
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - Debashree Ray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Paul Redmond
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, EH8 9JZ, Edinburgh, United Kingdom
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, USA
- Harvard Medical School, Boston, USA
| | - Tom C Russ
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, EH8 9JZ, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathleen A Ryan
- University of Maryland School of Medicine, Division of Endocrinology, Diabetes and Nutrition, Baltimore, USA
| | - Morten Salling Olesen
- Laboratory for Molecular Cardiology, Department of Cardiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Medicine IV - Nephrology and Primary Care, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Moneeza K Siddiqui
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042, Monserrato (CA), Italy
| | - P Eline Slagboom
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Enrique Soto-Pedre
- Division of Population Health Genomics, School of Medicine, University of Dundee, DD19SY, Dundee, UK
| | - Tim D Spector
- The Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Campus, Lambeth Palace Road, London, SE1 7EH, UK
| | - Beatrice Spedicati
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Sundararajan Srinivasan
- Division of Population Health Genomics, School of Medicine, University of Dundee, DD19SY, Dundee, UK
| | - John M Starr
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Toshiko Tanaka
- Longitudinal Study Section, National Institute on Aging, Baltimore, MD, USA
| | - Vesela Torlak
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Johanna Tuhkanen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Erik B van den Akker
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands
| | - Tibbert van den Eynde
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Melanie M van der Klauw
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Charlotte Verroken
- Department of Endocrinology, Ghent University Hospital, C. Heymanslaan 10, 9000, Ghent, Belgium
| | - W Edward Visser
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dina Vojinovic
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, 17475, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Stefan Weiss
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Cristen J Willer
- Department of Internal Medicine, Cardiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Scott G Wilson
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- The Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Campus, Lambeth Palace Road, London, SE1 7EH, UK
| | - Bruce H R Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hanneke J C M Wouters
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Qiong Yang
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Tatijana Zemunik
- Department of Medical Biology, University of Split, School of Medicine, Split, Croatia
- Department of Nuclear Medicine, University Hospital Split, Split, Croatia
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gu Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Johannes W A Smit
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robin P Peeters
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475, Greifswald, Germany.
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany.
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland.
| | - Marco Medici
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, Nijmegen, The Netherlands.
- Academic Center for Thyroid Diseases, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
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Austin TR, Fink HA, Jalal DI, Törnqvist AE, Buzkova P, Barzilay JI, Lu T, Carbone L, Gabrielsen ME, Grahnemo L, Hveem K, Jonasson C, Kizer JR, Langhammer A, Mukamal KJ, Gerszten RE, Nethander M, Psaty BM, Robbins JA, Sun YV, Skogholt AH, Åsvold BO, Valderrabano RJ, Zheng J, Richards JB, Coward E, Ohlsson C. Large-scale circulating proteome association study (CPAS) meta-analysis identifies circulating proteins and pathways predicting incident hip fractures. J Bone Miner Res 2024; 39:zjad011. [PMID: 38477735 DOI: 10.1093/jbmr/zjad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/09/2023] [Accepted: 11/23/2023] [Indexed: 03/14/2024]
Abstract
Hip fractures are associated with significant disability, high cost, and mortality. However, the exact biological mechanisms underlying susceptibility to hip fractures remain incompletely understood. In an exploratory search of the underlying biology as reflected through the circulating proteome, we performed a comprehensive Circulating Proteome Association Study (CPAS) meta-analysis for incident hip fractures. Analyses included 6430 subjects from two prospective cohort studies (Cardiovascular Health Study and Trøndelag Health Study) with circulating proteomics data (aptamer-based 5 K SomaScan version 4.0 assay; 4979 aptamers). Associations between circulating protein levels and incident hip fractures were estimated for each cohort using age and sex-adjusted Cox regression models. Participants experienced 643 incident hip fractures. Compared with the individual studies, inverse-variance weighted meta-analyses yielded more statistically significant associations, identifying 23 aptamers associated with incident hip fractures (conservative Bonferroni correction 0.05/4979, P < 1.0 × 10-5). The aptamers most strongly associated with hip fracture risk corresponded to two proteins of the growth hormone/insulin growth factor system (GHR and IGFBP2), as well as GDF15 and EGFR. High levels of several inflammation-related proteins (CD14, CXCL12, MMP12, ITIH3) were also associated with increased hip fracture risk. Ingenuity pathway analysis identified reduced LXR/RXR activation and increased acute phase response signaling to be overrepresented among those proteins associated with increased hip fracture risk. These analyses identified several circulating proteins and pathways consistently associated with incident hip fractures. These findings underscore the usefulness of the meta-analytic approach for comprehensive CPAS in a similar manner as has previously been observed for large-scale human genetic studies. Future studies should investigate the underlying biology of these potential novel drug targets.
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Affiliation(s)
- Thomas R Austin
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, United States
| | - Howard A Fink
- Geriatric Research Education and Clinical Center, VA Health Care System, Minneapolis, MN, 56401, United States
| | - Diana I Jalal
- Division of Nephrology, Department of Internal Medicine, Carver College of Medicine, Iowa City, IA, 52242, United States
- Iowa City VA Medical Center, Iowa City, IA, 52246, United States
| | - Anna E Törnqvist
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Petra Buzkova
- Department of Biostatistics, University of Washington, Seattle, WA, 98115, United States
| | - Joshua I Barzilay
- Division of Endocrinology, Kaiser Permanente of Georgia, Atlanta, GA, 30339, United States
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, H3G 0B1, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, H3Y 2W4, Canada
| | - Laura Carbone
- Charlie Norwood VAMC, Augusta, GA, 30901, United States
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, United States
| | - Maiken E Gabrielsen
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Louise Grahnemo
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
| | - Kristian Hveem
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- HUNT Research Centre, NTNU, 7600, Levanger, Norway
| | - Christian Jonasson
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Jorge R Kizer
- Cardiology Section, San Francisco VA Health Care System, San Francisco, CA, 94121, United States
- Department of Medicine, Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, United States
| | - Arnulf Langhammer
- HUNT Research Centre, NTNU, 7600, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, 7600, Levanger, Norway
| | - Kenneth J Mukamal
- Department of Medicine, Beth Israel Deaconess Medical Center, Brookline, MA, 2446, United States
| | - Robert E Gerszten
- Department of Medicine, Beth Israel Deaconess Medical Center, Brookline, MA, 2446, United States
| | - Maria Nethander
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
- Bioinformatics and Data Center, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, United States
- Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, 98195, United States
| | - John A Robbins
- Department of Medicine, University of California, Davis, CA, 95817, United States
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, United States
| | - Anne Heidi Skogholt
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Bjørn Olav Åsvold
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, 7491, Trondheim, Norway
| | - Rodrigo J Valderrabano
- Research Program in Men's Health, Aging and Metabolism, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 2130, United States
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai, 200025, China
- Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai National Clinical Research Center for Metabolic Diseases, Shanghai Digital Medicine Innovation Center, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai, 200025, China
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Bristol, BS8 2BN, United Kingdom
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, H3Y 2W4, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada
- Department of Twin Research, King's College London, London, SE1 7EH, United Kingdom
| | - Eivind Coward
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, 413 45, Gothenburg, Sweden
- Department of Drug Treatment, Region Västra Götaland, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
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3
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Lu T, Forgetta V, Zhou S, Richards JB, Greenwood CM. Identifying Rare Genetic Determinants for Improved Polygenic Risk Prediction of Bone Mineral Density and Fracture Risk. J Bone Miner Res 2023; 38:1771-1781. [PMID: 37830501 DOI: 10.1002/jbmr.4920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 09/13/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023]
Abstract
Osteoporosis and fractures severely impact the elderly population. Polygenic risk scores for bone mineral density have demonstrated potential clinical utility. However, the value of rare genetic determinants in risk prediction has not been assessed. With whole-exome sequencing data from 436,824 UK Biobank participants, we assigned White British ancestry individuals into a training data set (n = 317,434) and a test data set (n = 74,825). In the training data set, we developed a common variant-based polygenic risk score for heel ultrasound speed of sound (SOS). Next, we performed burden testing to identify genes harboring rare determinants of bone mineral density, targeting influential rare variants with predicted high deleteriousness. We constructed a genetic risk score, called ggSOS, to incorporate influential rare variants in significant gene burden masks into the common variant-based polygenic risk score. We assessed the predictive performance of ggSOS in the White British test data set, as well as in populations of non-White British European (n = 18,885), African (n = 7165), East Asian (n = 2236), South Asian (n = 9829), and other admixed (n = 1481) ancestries. Twelve genes in pivotal regulatory pathways of bone homeostasis harbored influential rare variants associated with SOS (p < 5.5 × 10-7 ), including AHNAK, BMP5, CYP19A1, FAM20A, FBXW5, KDM5B, KREMEN1, LGR4, LRP5, SMAD6, SOST, and WNT1. Among 4013 (5.4%) individuals in the test data set carrying these variants, a one standard deviation decrease in ggSOS was associated with 1.35-fold (95% confidence interval [CI] 1.16-1.57) increased hazard of major osteoporotic fracture. However, compared with a common variant-based polygenic risk score (C-index = 0.641), ggSOS had only marginally improved prediction accuracy in identifying at-risk individuals (C-index = 0.644), with overlapping confidence intervals. Similarly, ggSOS did not demonstrate substantially improved predictive performance in non-European ancestry populations. In summary, modeling the effects of rare genetic determinants may assist polygenic prediction of fracture risk among carriers of influential rare variants. Nonetheless, improved clinical utility is not guaranteed for population-level risk screening. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
| | | | - Sirui Zhou
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- 5 Prime Sciences Inc., Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Celia Mt Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
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4
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Lu T, Nakanishi T, Yoshiji S, Butler-Laporte G, Greenwood CMT, Richards JB. Dose-dependent Association of Alcohol Consumption With Obesity and Type 2 Diabetes: Mendelian Randomization Analyses. J Clin Endocrinol Metab 2023; 108:3320-3329. [PMID: 37368847 DOI: 10.1210/clinem/dgad324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Indexed: 06/29/2023]
Abstract
CONTEXT Effects of modest alcohol consumption remain controversial. Mendelian randomization (MR) can help to mitigate biases due to confounding and reverse causation in observational studies, and evaluate the potential causal role of alcohol consumption. OBJECTIVE This work aimed to evaluate dose-dependent effect of alcohol consumption on obesity and type 2 diabetes. METHODS Assessing 408 540 participants of European ancestry in the UK Biobank, we first tested the association between self-reported alcohol intake frequency and 10 anthropometric measurements, obesity, and type 2 diabetes. We then conducted MR analyses both in the overall population and in subpopulations stratified by alcohol intake frequency. RESULTS Among individuals having more than 14 drinks per week, a 1-drink-per-week increase in genetically predicted alcohol intake frequency was associated with a 0.36-kg increase in fat mass (SD = 0.03 kg), a 1.08-fold increased odds of obesity (95% CI, 1.06-1.10), and a 1.10-fold increased odds of type 2 diabetes (95% CI, 1.06-1.13). These associations were stronger in women than in men. Furthermore, no evidence was found supporting the association between genetically increased alcohol intake frequency and improved health outcomes among individuals having 7 or fewer drinks per week, as MR estimates largely overlapped with the null. These results withstood multiple sensitivity analyses assessing the validity of MR assumptions. CONCLUSION As opposed to observational associations, MR results suggest there may not be protective effects of modest alcohol consumption on obesity traits and type 2 diabetes. Heavy alcohol consumption could lead to increased measures of obesity as well as increased risk of type 2 diabetes.
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, M5S 1A1, Canada
- 5 Prime Sciences Inc, Montréal, Québec, H3Y 2W4, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0G4, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
- Japan Society for Promotion of Science, Tokyo, 102-0083, Japan
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0G4, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
- Japan Society for Promotion of Science, Tokyo, 102-0083, Japan
| | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, H3A 04, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0G4, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, H3A 04, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, H3A 0G4, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
- 5 Prime Sciences Inc, Montréal, Québec, H3Y 2W4, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0G4, Canada
- Department of Twin Research, King's College London, London, WC2R 2LS, UK
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5
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Butler-Laporte G, Farjoun J, Nakanishi T, Lu T, Abner E, Chen Y, Hultström M, Metspalu A, Milani L, Mägi R, Nelis M, Hudjashov G, Yoshiji S, Ilboudo Y, Liang KYH, Su CY, Willet JDS, Esko T, Zhou S, Forgetta V, Taliun D, Richards JB. HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases. Commun Biol 2023; 6:1113. [PMID: 37923823 PMCID: PMC10624861 DOI: 10.1038/s42003-023-05496-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
The human leukocyte antigen (HLA) region on chromosome 6 is strongly associated with many immune-mediated and infection-related diseases. Due to its highly polymorphic nature and complex linkage disequilibrium patterns, traditional genetic association studies of single nucleotide polymorphisms do not perform well in this region. Instead, the field has adopted the assessment of the association of HLA alleles (i.e., entire HLA gene haplotypes) with disease. Often based on genotyping arrays, these association studies impute HLA alleles, decreasing accuracy and thus statistical power for rare alleles and in non-European ancestries. Here, we use whole-exome sequencing (WES) from 454,824 UK Biobank (UKB) participants to directly call HLA alleles using the HLA-HD algorithm. We show this method is more accurate than imputing HLA alleles and harness the improved statistical power to identify 360 associations for 11 auto-immune phenotypes (at least 129 likely novel), leading to better insights into the specific coding polymorphisms that underlie these diseases. We show that HLA alleles with synonymous variants, often overlooked in HLA studies, can significantly influence these phenotypes. Lastly, we show that HLA sequencing may improve polygenic risk scores accuracy across ancestries. These findings allow better characterization of the role of the HLA region in human disease.
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Affiliation(s)
- Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada.
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada.
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Joseph Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Tianyuan Lu
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | - Erik Abner
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Michael Hultström
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mari Nelis
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Georgi Hudjashov
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Satoshi Yoshiji
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Yann Ilboudo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Kevin Y H Liang
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Julian D S Willet
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | - Daniel Taliun
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- Department of Twin Research, King's College London, London, UK
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
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6
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Nethander M, Movérare-Skrtic S, Kämpe A, Coward E, Reimann E, Grahnemo L, Borbély É, Helyes Z, Funck-Brentano T, Cohen-Solal M, Tuukkanen J, Koskela A, Wu J, Li L, Lu T, Gabrielsen ME, Mägi R, Hoff M, Lerner UH, Henning P, Ullum H, Erikstrup C, Brunak S, Langhammer A, Tuomi T, Oddsson A, Stefansson K, Pettersson-Kymmer U, Ostrowski SR, Pedersen OBV, Styrkarsdottir U, Mäkitie O, Hveem K, Richards JB, Ohlsson C. An atlas of genetic determinants of forearm fracture. Nat Genet 2023; 55:1820-1830. [PMID: 37919453 PMCID: PMC10632131 DOI: 10.1038/s41588-023-01527-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 09/13/2023] [Indexed: 11/04/2023]
Abstract
Osteoporotic fracture is among the most common and costly of diseases. While reasonably heritable, its genetic determinants have remained elusive. Forearm fractures are the most common clinically recognized osteoporotic fractures with a relatively high heritability. To establish an atlas of the genetic determinants of forearm fractures, we performed genome-wide association analyses including 100,026 forearm fracture cases. We identified 43 loci, including 26 new fracture loci. Although most fracture loci associated with bone mineral density, we also identified loci that primarily regulate bone quality parameters. Functional studies of one such locus, at TAC4, revealed that Tac4-/- mice have reduced mechanical bone strength. The strongest forearm fracture signal, at WNT16, displayed remarkable bone-site-specificity with no association with hip fractures. Tall stature and low body mass index were identified as new causal risk factors for fractures. The insights from this atlas may improve fracture prediction and enable therapeutic development to prevent fractures.
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Grants
- Wellcome Trust
- IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)
- Novo Nordisk Fonden (Novo Nordisk Foundation)
- Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)
- the Swedish state under the agreement between the Swedish government and the county councils, the ALF-agreement (ALFGBG-720331 and ALFGBG-965235)
- the Hungarian Brain research Program 3.0, Hungarian National Research, Development and Innovation Office (OTKA K- 138046, OTKA FK-137951, TKP2021-EGA-16), New National Excellence Program of the Ministry for Innovation and Technology (ÚNKP-22-5-PTE-1447), János Bolyai János Scholarship (BO/00496/21/5) of the Hungarian Academy of Sciences, Eotvos Lorad Research Network, National Laboratory for Drug Research and Development.
- Vetenskapsrådet (Swedish Research Council)
- Svenska Läkaresällskapet (Swedish Society of Medicine)
- Kempestiftelserna (Kempe Foundations)
- the Swedish Sports Research Council (87/06) the Medical Faculty of Umeå University (ALFVLL:968:22-2005, ALFVLL: 937-2006, ALFVLL:223:11-2007, ALFVLL:78151-2009) the county council of Västerbotten (Spjutspetsanslag VLL:159:33-2007)
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Affiliation(s)
- Maria Nethander
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sofia Movérare-Skrtic
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Kämpe
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Eivind Coward
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ene Reimann
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Louise Grahnemo
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Éva Borbély
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- National Laboratory for Drug Research and Development, Budapest, Hungary
- Eotvos Lorand Research Network, Chronic Pain Research Group, University of Pécs, Pécs, Hungary
| | - Thomas Funck-Brentano
- BIOSCAR UMRS 1132, Université Paris Diderot, Sorbonne Paris Cité, INSERM, Paris, France
| | - Martine Cohen-Solal
- BIOSCAR UMRS 1132, Université Paris Diderot, Sorbonne Paris Cité, INSERM, Paris, France
| | - Juha Tuukkanen
- Department of Anatomy and Cell Biology, Faculty of Medicine, Institute of Cancer Research and Translational Medicine, University of Oulu, Oulu, Finland
| | - Antti Koskela
- Department of Anatomy and Cell Biology, Faculty of Medicine, Institute of Cancer Research and Translational Medicine, University of Oulu, Oulu, Finland
| | - Jianyao Wu
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lei Li
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mari Hoff
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Rheumatology, St Olavs Hospital, Trondheim, Norway
| | - Ulf H Lerner
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Petra Henning
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
- Department of Endocrinology, Abdominal Center, Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Kari Stefansson
- deCODE genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Sisse Rye Ostrowski
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen Hospital Biobank Unit, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Ole Birger Vesterager Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Koege, Denmark
| | | | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Children's Hospital and Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, and Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Drug Treatment, Gothenburg, Sweden.
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7
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Nakanishi T, Willett J, Farjoun Y, Allen RJ, Guillen-Guio B, Adra D, Zhou S, Richards JB. Alternative splicing in lung influences COVID-19 severity and respiratory diseases. Nat Commun 2023; 14:6198. [PMID: 37794074 PMCID: PMC10550956 DOI: 10.1038/s41467-023-41912-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Alternative splicing generates functional diversity in isoforms, impacting immune response to infection. Here, we evaluate the causal role of alternative splicing in COVID-19 severity and susceptibility by applying two-sample Mendelian randomization to cis-splicing quantitative trait loci and the results from COVID-19 Host Genetics Initiative. We identify that alternative splicing in lung, rather than total expression of OAS1, ATP11A, DPP9 and NPNT, is associated with COVID-19 severity. MUC1 and PMF1 splicing is associated with COVID-19 susceptibility. Colocalization analyses support a shared genetic mechanism between COVID-19 severity with idiopathic pulmonary fibrosis at the ATP11A and DPP9 loci, and with chronic obstructive lung diseases at the NPNT locus. Last, we show that ATP11A, DPP9, NPNT, and MUC1 are highly expressed in lung alveolar epithelial cells, both in COVID-19 uninfected and infected samples. These findings clarify the importance of alternative splicing in lung for COVID-19 and respiratory diseases, providing isoform-based targets for drug discovery.
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Affiliation(s)
- Tomoko Nakanishi
- Department of Human Genetics, McGill University, Montréal, QC, Canada.
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada.
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan.
| | - Julian Willett
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Yossi Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Five Prime Sciences Inc, Montréal, QC, Canada
| | - Richard J Allen
- Department of Population Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Darin Adra
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada.
- Five Prime Sciences Inc, Montréal, QC, Canada.
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal, QC, Canada.
- Department of Twin Research, King's College London, London, UK.
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8
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Mullin BH, Zhu K, Brown SJ, Mullin S, Dudbridge F, Pavlos NJ, Richards JB, Grundberg E, Bell JT, Zeggini E, Walsh JP, Xu J, Wilson SG. Leveraging osteoclast genetic regulatory data to identify genes with a role in osteoarthritis. Genetics 2023; 225:iyad150. [PMID: 37579195 PMCID: PMC10550309 DOI: 10.1093/genetics/iyad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023] Open
Abstract
There has been a growing interest in the role of the subchondral bone and its resident osteoclasts in the progression of osteoarthritis (OA). A recent genome-wide association study (GWAS) identified 100 independent association signals for OA traits. Most of these signals are led by noncoding variants, suggesting that genetic regulatory effects may drive many of the associations. We have generated a unique human osteoclast-like cell-specific expression quantitative trait locus (eQTL) resource for studying the genetics of bone disease. Considering the potential role of osteoclasts in the pathogenesis of OA, we performed an integrative analysis of this dataset with the recently published OA GWAS results. Summary data-based Mendelian randomization (SMR) and colocalization analyses identified 38 genes with a potential role in OA, including some that have been implicated in Mendelian diseases with joint/skeletal abnormalities, such as BICRA, EIF6, CHST3, and FBN2. Several OA GWAS signals demonstrated colocalization with more than one eQTL peak, including at 19q13.32 (hip OA with BCAM, PRKD2, and BICRA eQTL). We also identified a number of eQTL signals colocalizing with more than one OA trait, including FAM53A, GCAT, HMGN1, MGAT4A, RRP7BP, and TRIOBP. An SMR analysis identified 3 loci with evidence of pleiotropic effects on OA-risk and gene expression: LINC01481, CPNE1, and EIF6. Both CPNE1 and EIF6 are located at 20q11.22, a locus harboring 2 other strong OA candidate genes, GDF5 and UQCC1, suggesting the presence of an OA-risk gene cluster. In summary, we have used our osteoclast-specific eQTL dataset to identify genes potentially involved with the pathogenesis of OA.
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Affiliation(s)
- Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Kun Zhu
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Crawley, WA 6009, Australia
| | - Suzanne J Brown
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Shelby Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Frank Dudbridge
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Nathan J Pavlos
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - J Brent Richards
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
- Department of Medicine, Human Genetics, Epidemiology, and Biostatistics, Jewish General Hospital, McGill University, Montreal H3A 0G4, Canada
| | - Elin Grundberg
- Genomic Medicine Center, Children’s Mercy Kansas City, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Eleftheria Zeggini
- Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Translational Genomics, Neuherberg 85764, Germany
- TUM School of Medicine, Technical University of Munich (TUM) and Klinikum Rechts der Isar, Munich 81675, Germany
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Crawley, WA 6009, Australia
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen 518055, China
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
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9
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Willett JDS, Lu T, Nakanishi T, Yoshiji S, Butler-Laporte G, Zhou S, Farjoun Y, Richards JB. Colocalization of expression transcripts with COVID-19 outcomes is rare across cell states, cell types and organs. Hum Genet 2023; 142:1461-1476. [PMID: 37640912 PMCID: PMC10511363 DOI: 10.1007/s00439-023-02590-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 06/30/2023] [Indexed: 08/31/2023]
Abstract
Identifying causal genes at GWAS loci can help pinpoint targets for therapeutic interventions. Expression studies can disentangle such loci but signals from expression quantitative trait loci (eQTLs) often fail to colocalize-which means that the genetic control of measured expression is not shared with the genetic control of disease risk. This may be because gene expression is measured in the wrong cell type, physiological state, or organ. We tested whether Mendelian randomization (MR) could identify genes at loci influencing COVID-19 outcomes and whether the colocalization of genetic control of expression and COVID-19 outcomes was influenced by cell type, cell stimulation, and organ. We conducted MR of cis-eQTLs from single cell (scRNA-seq) and bulk RNA sequencing. We then tested variables that could influence colocalization, including cell type, cell stimulation, RNA sequencing modality, organ, symptoms of COVID-19, and SARS-CoV-2 status among individuals with symptoms of COVID-19. The outcomes used to test colocalization were COVID-19 severity and susceptibility as assessed in the Host Genetics Initiative release 7. Most transcripts identified using MR did not colocalize when tested across cell types, cell state and in different organs. Most that did colocalize likely represented false positives due to linkage disequilibrium. In general, colocalization was highly variable and at times inconsistent for the same transcript across cell type, cell stimulation and organ. While we identified factors that influenced colocalization for select transcripts, identifying 33 that mediate COVID-19 outcomes, our study suggests that colocalization of expression with COVID-19 outcomes is partially due to noisy signals even after following quality control and sensitivity testing. These findings illustrate the present difficulty of linking expression transcripts to disease outcomes and the need for skepticism when observing eQTL MR results, even accounting for cell types, stimulation state and different organs.
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Affiliation(s)
- Julian Daniel Sunday Willett
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, QC, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Tianyuan Lu
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, QC, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Tomoko Nakanishi
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, Kyoto-McGill International Collaborative Program in Genomic Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Satoshi Yoshiji
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, Kyoto-McGill International Collaborative Program in Genomic Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Guillaume Butler-Laporte
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
| | - Sirui Zhou
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- McGill University, Montreal, QC, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - Yossi Farjoun
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada
- Genome Centre, McGill University, Montreal, QC, Canada
| | - J Brent Richards
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Ste Catherine, Pavillon H-413, Montréal, Québec, H3T 1E2, Canada.
- McGill University, Montreal, QC, Canada.
- Genome Centre, McGill University, Montreal, QC, Canada.
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal, QC, Canada.
- Department of Twin Research, King's College London, London, UK.
- Five Prime Sciences Inc, Montréal, Québec, Canada.
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10
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Butler-Laporte G, Farjoun Y, Chen Y, Hultström M, Liang KYH, Nakanishi T, Su CY, Yoshiji S, Forgetta V, Richards JB. Increasing serum iron levels and their role in the risk of infectious diseases: a Mendelian randomization approach. Int J Epidemiol 2023; 52:1163-1174. [PMID: 36773317 PMCID: PMC10396421 DOI: 10.1093/ije/dyad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 02/02/2023] [Indexed: 02/13/2023] Open
Abstract
OBJECTIVES Increased iron stores have been associated with elevated risks of different infectious diseases, suggesting that iron supplementation may increase the risk of infections. However, these associations may be biased by confounding or reverse causation. This is important, since up to 19% of the population takes iron supplementation. We used Mendelian randomization (MR) to bypass these biases and estimate the causal effect of iron on infections. METHODS As instrumental variables, we used genetic variants associated with iron biomarkers in two genome-wide association studies (GWASs) of European ancestry participants. For outcomes, we used GWAS results from the UK Biobank, FinnGen, the COVID-19 Host Genetics Initiative or 23andMe, for seven infection phenotypes: 'any infections', combined, COVID-19 hospitalization, candidiasis, pneumonia, sepsis, skin and soft tissue infection (SSTI) and urinary tract infection (UTI). RESULTS Most of our analyses showed increasing iron (measured by its biomarkers) was associated with only modest changes in the odds of infectious outcomes, with all 95% odds ratios confidence intervals within the 0.88 to 1.26 range. However, for the three predominantly bacterial infections (sepsis, SSTI, UTI), at least one analysis showed a nominally elevated risk with increased iron stores (P <0.05). CONCLUSION Using MR, we did not observe an increase in risk of most infectious diseases with increases in iron stores. However for bacterial infections, higher iron stores may increase odds of infections. Hence, using genetic variation in iron pathways as a proxy for iron supplementation, iron supplements are likely safe on a population level, but we should continue the current practice of conservative iron supplementation during bacterial infections or in those at high risk of developing them.
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Affiliation(s)
- Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
| | - Yossi Farjoun
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Michael Hultström
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Kevin Y H Liang
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Chen-Yang Su
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Department of Twin Research, King’s College London, London, UK
- 5 Prime Sciences Inc., Montreal, QC, Canada
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11
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Zhou S, Sosina OA, Bovijn J, Laurent L, Sharma V, Akbari P, Forgetta V, Jiang L, Kosmicki JA, Banerjee N, Morris JA, Oerton E, Jones M, LeBlanc MG, Idone V, Overton JD, Reid JG, Cantor M, Abecasis GR, Goltzman D, Greenwood CMT, Langenberg C, Baras A, Economides AN, Ferreira MAR, Hatsell S, Ohlsson C, Richards JB, Lotta LA. Converging evidence from exome sequencing and common variants implicates target genes for osteoporosis. Nat Genet 2023; 55:1277-1287. [PMID: 37558884 DOI: 10.1038/s41588-023-01444-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/09/2023] [Indexed: 08/11/2023]
Abstract
In this study, we leveraged the combined evidence of rare coding variants and common alleles to identify therapeutic targets for osteoporosis. We undertook a large-scale multiancestry exome-wide association study for estimated bone mineral density, which showed that the burden of rare coding alleles in 19 genes was associated with estimated bone mineral density (P < 3.6 × 10-7). These genes were highly enriched for a set of known causal genes for osteoporosis (65-fold; P = 2.5 × 10-5). Exome-wide significant genes had 96-fold increased odds of being the top ranked effector gene at a given GWAS locus (P = 1.8 × 10-10). By integrating proteomics Mendelian randomization evidence, we prioritized CD109 (cluster of differentiation 109) as a gene for which heterozygous loss of function is associated with higher bone density. CRISPR-Cas9 editing of CD109 in SaOS-2 osteoblast-like cell lines showed that partial CD109 knockdown led to increased mineralization. This study demonstrates that the convergence of common and rare variants, proteomics and CRISPR can highlight new bone biology to guide therapeutic development.
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Affiliation(s)
- Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Olukayode A Sosina
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Jonas Bovijn
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Vasundhara Sharma
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Parsa Akbari
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Five Prime Sciences Inc, Montréal, Québec, Canada
| | - Lai Jiang
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Jack A Kosmicki
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Nilanjana Banerjee
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | | | - Erin Oerton
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Marcus Jones
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Michelle G LeBlanc
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | | | - John D Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Jeffrey G Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Michael Cantor
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Goncalo R Abecasis
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - David Goltzman
- Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Celia M T Greenwood
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health, Charité University Medicine Berlin, Berlin, Germany
| | - Aris Baras
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Aris N Economides
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Manuel A R Ferreira
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | | | - Claes Ohlsson
- Centre of Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada.
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.
- Five Prime Sciences Inc, Montréal, Québec, Canada.
- Department of Twin Research, King's College London, London, UK.
| | - Luca A Lotta
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
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12
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Trajanoska K, Bhérer C, Taliun D, Zhou S, Richards JB, Mooser V. From target discovery to clinical drug development with human genetics. Nature 2023; 620:737-745. [PMID: 37612393 DOI: 10.1038/s41586-023-06388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/29/2023] [Indexed: 08/25/2023]
Abstract
The substantial investments in human genetics and genomics made over the past three decades were anticipated to result in many innovative therapies. Here we investigate the extent to which these expectations have been met, excluding cancer treatments. In our search, we identified 40 germline genetic observations that led directly to new targets and subsequently to novel approved therapies for 36 rare and 4 common conditions. The median time between genetic target discovery and drug approval was 25 years. Most of the genetically driven therapies for rare diseases compensate for disease-causing loss-of-function mutations. The therapies approved for common conditions are all inhibitors designed to pharmacologically mimic the natural, disease-protective effects of rare loss-of-function variants. Large biobank-based genetic studies have the power to identify and validate a large number of new drug targets. Genetics can also assist in the clinical development phase of drugs-for example, by selecting individuals who are most likely to respond to investigational therapies. This approach to drug development requires investments into large, diverse cohorts of deeply phenotyped individuals with appropriate consent for genetically assisted trials. A robust framework that facilitates responsible, sustainable benefit sharing will be required to capture the full potential of human genetics and genomics and bring effective and safe innovative therapies to patients quickly.
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Affiliation(s)
- Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Claude Bhérer
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Daniel Taliun
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology and Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada.
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13
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Han X, Lains I, Li J, Li J, Chen Y, Yu B, Qi Q, Boerwinkle E, Kaplan R, Thyagarajan B, Daviglus M, Joslin CE, Cai J, Guasch-Ferré M, Tobias DK, Rimm E, Ascherio A, Costenbader K, Karlson E, Mucci L, Eliassen AH, Zeleznik O, Miller J, Vavvas DG, Kim IK, Silva R, Miller J, Hu F, Willett W, Lasky-Su J, Kraft P, Richards JB, MacGregor S, Husain D, Liang L. Integrating genetics and metabolomics from multi-ethnic and multi-fluid data reveals putative mechanisms for age-related macular degeneration. Cell Rep Med 2023; 4:101085. [PMID: 37348500 PMCID: PMC10394104 DOI: 10.1016/j.xcrm.2023.101085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/22/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness in older adults. Investigating shared genetic components between metabolites and AMD can enhance our understanding of its pathogenesis. We conduct metabolite genome-wide association studies (mGWASs) using multi-ethnic genetic and metabolomic data from up to 28,000 participants. With bidirectional Mendelian randomization analysis involving 16,144 advanced AMD cases and 17,832 controls, we identify 108 putatively causal relationships between plasma metabolites and advanced AMD. These metabolites are enriched in glycerophospholipid metabolism, lysophospholipid, triradylcglycerol, and long chain polyunsaturated fatty acid pathways. Bayesian genetic colocalization analysis and a customized metabolome-wide association approach prioritize putative causal AMD-associated metabolites. We find limited evidence linking urine metabolites to AMD risk. Our study emphasizes the contribution of plasma metabolites, particularly lipid-related pathways and genes, to AMD risk and uncovers numerous putative causal associations between metabolites and AMD risk.
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Affiliation(s)
- Xikun Han
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Ines Lains
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Jun Li
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jinglun Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada; Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA; Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis, MN, USA
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Charlotte E Joslin
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marta Guasch-Ferré
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Deirdre K Tobias
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric Rimm
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alberto Ascherio
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Karen Costenbader
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth Karlson
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorelei Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - A Heather Eliassen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Oana Zeleznik
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - John Miller
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Demetrios G Vavvas
- Retina Service, Ines and Fredrick Yeatts Retinal Research Laboratory, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Ivana K Kim
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Rufino Silva
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal; University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal; Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
| | - Joan Miller
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Frank Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Walter Willett
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jessica Lasky-Su
- Systems Genetics and Genomics Unit, Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada; Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal, QC, Canada; Department of Twin Research, King's College London, London, UK; Five Prime Sciences Inc, Montréal, QC, Canada
| | - Stuart MacGregor
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Deeba Husain
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA.
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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14
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Medina-Gomez C, Mullin BH, Chesi A, Prijatelj V, Kemp JP, Shochat-Carvalho C, Trajanoska K, Wang C, Joro R, Evans TE, Schraut KE, Li-Gao R, Ahluwalia TS, Zillikens MC, Zhu K, Mook-Kanamori DO, Evans DS, Nethander M, Knol MJ, Thorleifsson G, Prokic I, Zemel B, Broer L, McGuigan FE, van Schoor NM, Reppe S, Pawlak MA, Ralston SH, van der Velde N, Lorentzon M, Stefansson K, Adams HHH, Wilson SG, Ikram MA, Walsh JP, Lakka TA, Gautvik KM, Wilson JF, Orwoll ES, van Duijn CM, Bønnelykke K, Uitterlinden AG, Styrkársdóttir U, Akesson KE, Spector TD, Tobias JH, Ohlsson C, Felix JF, Bisgaard H, Grant SFA, Richards JB, Evans DM, van der Eerden B, van de Peppel J, Ackert-Bicknell C, Karasik D, Kague E, Rivadeneira F. Bone mineral density loci specific to the skull portray potential pleiotropic effects on craniosynostosis. Commun Biol 2023; 6:691. [PMID: 37402774 PMCID: PMC10319806 DOI: 10.1038/s42003-023-04869-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 04/25/2023] [Indexed: 07/06/2023] Open
Abstract
Skull bone mineral density (SK-BMD) provides a suitable trait for the discovery of key genes in bone biology, particularly to intramembranous ossification, not captured at other skeletal sites. We perform a genome-wide association meta-analysis (n ~ 43,800) of SK-BMD, identifying 59 loci, collectively explaining 12.5% of the trait variance. Association signals cluster within gene-sets involved in skeletal development and osteoporosis. Among the four novel loci (ZIC1, PRKAR1A, AZIN1/ATP6V1C1, GLRX3), there are factors implicated in intramembranous ossification and as we show, inherent to craniosynostosis processes. Functional follow-up in zebrafish confirms the importance of ZIC1 on cranial suture patterning. Likewise, we observe abnormal cranial bone initiation that culminates in ectopic sutures and reduced BMD in mosaic atp6v1c1 knockouts. Mosaic prkar1a knockouts present asymmetric bone growth and, conversely, elevated BMD. In light of this evidence linking SK-BMD loci to craniofacial abnormalities, our study provides new insight into the pathophysiology, diagnosis and treatment of skeletal diseases.
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Grants
- UL1 TR000128 NCATS NIH HHS
- U01 AG042124 NIA NIH HHS
- U01 AG042145 NIA NIH HHS
- U01 AG042168 NIA NIH HHS
- U01 AG042140 NIA NIH HHS
- U24 AG051129 NIA NIH HHS
- R01 AR051124 NIAMS NIH HHS
- U01 AG027810 NIA NIH HHS
- U01 AR066160 NIAMS NIH HHS
- MC_UU_00007/10 Medical Research Council
- R01 HD058886 NICHD NIH HHS
- RC2 AR058973 NIAMS NIH HHS
- Wellcome Trust
- M01 RR000240 NCRR NIH HHS
- U01 AG042143 NIA NIH HHS
- UL1 RR026314 NCRR NIH HHS
- U01 AG042139 NIA NIH HHS
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- European Cooperation in Science and Technology (COST)
- Wellcome Trust (Wellcome)
- Department of Health | National Health and Medical Research Council (NHMRC)
- U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)
- ZonMw (Netherlands Organisation for Health Research and Development)
- EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- Vetenskapsrådet (Swedish Research Council)
- U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
- Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
- NCHA (Netherlands Consortium Healthy Ageing) Leiden/ Rotterdam; Dutch Ministry of Economic Affairs, Agriculture and Innovation (project KB-15-004-003); the Research Institute for Diseases in the Elderly [Netherlands] (014-93-015; RIDE2)
- Clinical and Translational Research Center (5-MO1-RR-000240 and UL1 RR-026314); U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) GrantRecipient="Au50"
- European Commission FP6 STRP grant number 018947 (LSHG-CT-2006-01947); Netherlands Organization for Scientific Research and the Russian Foundation for Basic Research (NWO-RFBR 047.017.043); Netherlands Brain Foundation (project number F2013(1)-28) GrantRecipient="Au40"
- Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710) GrantRecipient="Au28"
- Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710) GrantRecipient="Au38"
- The Pawsey Supercomputing Centre (with Funding from the Australian Government and the Government of Western Australia; PG 16/0162, PG 17/director2025) GrantRecipient="Au45”
- European Commission (EC)
- U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS);NIH Roadmap for Medical Research [USA]: U01 AG027810, U01 AG042124, U01 AG042139, U01 AG042140, U01 AG042143, U01 AG042145, U01 AG042168, U01 AR066160, and UL1 TR000128 GrantRecipient="Au39”
- Versus Arthritis [USA] 21937 GrantRecipient="Au57”
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Affiliation(s)
- Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
| | - Alessandra Chesi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Vid Prijatelj
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - John P Kemp
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, 4102, Australia
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | | | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Carol Wang
- School of Women's and Infants' Health, University of Western Australia, Crawley, WA, 6009, Australia
| | - Raimo Joro
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, 70211, Finland
| | - Tavia E Evans
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX, Scotland
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH8 9AG, Scotland
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
- Steno Diabetes Center Copenhagen, Herlev, 2820, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Kun Zhu
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Maria Nethander
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Maria J Knol
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - Ivana Prokic
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Babette Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of GI, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Fiona E McGuigan
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Malmö, Sweden
| | - Natasja M van Schoor
- Department of Epidemiology and Data Science, Amsterdam UMC, 1081 HV, Amsterdam, The Netherlands
| | - Sjur Reppe
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0372, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, 0372, Oslo, Norway
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, 0456, Oslo, Norway
| | - Mikolaj A Pawlak
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Neurology, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Stuart H Ralston
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Nathalie van der Velde
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Geriatric Medicine, Amsterdam Public Health Research Institute, Amsterdam UMC, 1105 AZ, Amsterdam, The Netherlands
| | - Mattias Lorentzon
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia
| | | | - Hieab H H Adams
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Latin American Brain Health (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
| | - Timo A Lakka
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, 70211, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, 70100, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Kaare M Gautvik
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, 0456, Oslo, Norway
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Eric S Orwoll
- Department of Public Health & Preventive Medicine, Oregon Health & Science University, Portland, OR, OR97239, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - Kristina E Akesson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Malmö, Sweden
- Department of Orthopedics Malmö, Skåne University Hospital, S-21428, Malmö, Sweden
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jonathan H Tobias
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Bristol, BS10 5NB, UK
| | - Claes Ohlsson
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Region Västra Götaland, SE-413 45, Gothenburg, Sweden
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - J Brent Richards
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
- Lady Davis Institute, Jewish General Hospital, Montreal, H3T 1E2, QC, Canada
| | - David M Evans
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, 4102, Australia
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
- Marcus Institute for Aging Research, Hebrew SeniorLife, Roslindale, MA, 02131, USA
| | - Erika Kague
- The School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Fernando Rivadeneira
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands.
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15
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Butler-Laporte G, Auckland K, Noor Z, Kabir M, Alam M, Carstensen T, Wojcik GL, Chong AY, Pomilla C, Noble JA, McDevitt SL, Smits G, Wareing S, van der Klis FRM, Jeffery K, Kirkpatrick BD, Sirima S, Madhi S, Elliott A, Richards JB, Hill AVS, Duggal P, Sandhu MS, Haque R, Petri WA, Mentzer AJ. Targeting hepatitis B vaccine escape using immunogenetics in Bangladeshi infants. medRxiv 2023:2023.06.26.23291885. [PMID: 37425840 PMCID: PMC10327284 DOI: 10.1101/2023.06.26.23291885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Hepatitis B virus (HBV) vaccine escape mutants (VEM) are increasingly described, threatening progress in control of this virus worldwide. Here we studied the relationship between host genetic variation, vaccine immunogenicity and viral sequences implicating VEM emergence. In a cohort of 1,096 Bangladeshi children, we identified human leukocyte antigen (HLA) variants associated with response vaccine antigens. Using an HLA imputation panel with 9,448 south Asian individuals DPB1*04:01 was associated with higher HBV antibody responses (p=4.5×10-30). The underlying mechanism is a result of higher affinity binding of HBV surface antigen epitopes to DPB1*04:01 dimers. This is likely a result of evolutionary pressure at the HBV surface antigen 'a-determinant' segment incurring VEM specific to HBV. Prioritizing pre-S isoform HBV vaccines may tackle the rise of HBV vaccine evasion.
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Affiliation(s)
- Guillaume Butler-Laporte
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Division of Infectious Diseases, McGill University Health Centre, Montréal, Québec, Canada
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Zannatun Noor
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mamun Kabir
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Masud Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tommy Carstensen
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
- Queen Mary University of London, London, United Kingdom
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Amanda Y Chong
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Cristina Pomilla
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton, United Kingdom
| | - Janelle A Noble
- Children’s Hospital Oakland Research Institute, Oakland, California, USA
- Department of Pediatrics, University of California, San Francisco, California, USA
| | | | - Gaby Smits
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Susan Wareing
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | - Fiona RM van der Klis
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Katie Jeffery
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | - Beth D Kirkpatrick
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, University of Vermont College of Medicine, Vermont, USA
| | - Sodiomon Sirima
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248 Ouagadougou, Burkina Faso
| | - Shabir Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alison Elliott
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
| | - Adrian VS Hill
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Manjinder S Sandhu
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, United Kingdom
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - William A Petri
- Department of Medicine, Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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16
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Su CY, Zhou S, Gonzalez-Kozlova E, Butler-Laporte G, Brunet-Ratnasingham E, Nakanishi T, Jeon W, Morrison DR, Laurent L, Afilalo J, Afilalo M, Henry D, Chen Y, Carrasco-Zanini J, Farjoun Y, Pietzner M, Kimchi N, Afrasiabi Z, Rezk N, Bouab M, Petitjean L, Guzman C, Xue X, Tselios C, Vulesevic B, Adeleye O, Abdullah T, Almamlouk N, Moussa Y, DeLuca C, Duggan N, Schurr E, Brassard N, Durand M, Del Valle DM, Thompson R, Cedillo MA, Schadt E, Nie K, Simons NW, Mouskas K, Zaki N, Patel M, Xie H, Harris J, Marvin R, Cheng E, Tuballes K, Argueta K, Scott I, Greenwood CMT, Paterson C, Hinterberg MA, Langenberg C, Forgetta V, Pineau J, Mooser V, Marron T, Beckmann ND, Kim-Schulze S, Charney AW, Gnjatic S, Kaufmann DE, Merad M, Richards JB. Circulating proteins to predict COVID-19 severity. Sci Rep 2023; 13:6236. [PMID: 37069249 PMCID: PMC10107586 DOI: 10.1038/s41598-023-31850-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict COVID-19 severity in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different COVID-19 severity were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of COVID-19 severity. Further research is needed to understand how to incorporate protein measurement into clinical care.
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Affiliation(s)
- Chen-Yang Su
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Computer Science, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Graduate School of Medicine, McGill International Collaborative School in Genomic Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Wonseok Jeon
- Department of Computer Science, McGill University, Montréal, QC, Canada
| | - David R Morrison
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Laetitia Laurent
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Jonathan Afilalo
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marc Afilalo
- Department of Emergency Medicine, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Danielle Henry
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Julia Carrasco-Zanini
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yossi Farjoun
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Maik Pietzner
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nofar Kimchi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Zaman Afrasiabi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Nardin Rezk
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Meriem Bouab
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Louis Petitjean
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Charlotte Guzman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Xiaoqing Xue
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Chris Tselios
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Branka Vulesevic
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Olumide Adeleye
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Tala Abdullah
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Noor Almamlouk
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Yara Moussa
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Chantal DeLuca
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Naomi Duggan
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Nathalie Brassard
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montreal, QC, Canada
| | - Madeleine Durand
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montreal, QC, Canada
| | - Diane Marie Del Valle
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Thompson
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mario A Cedillo
- Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicole W Simons
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Konstantinos Mouskas
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicolas Zaki
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hui Xie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jocelyn Harris
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Marvin
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Argueta
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ieisha Scott
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | | | | | - Claudia Langenberg
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada
| | - Joelle Pineau
- Department of Computer Science, McGill University, Montréal, QC, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Thomas Marron
- Immunotherapy and Phase 1 Trials, Mount Sinai Hospital, New York, NY, USA
| | - Noam D Beckmann
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de L'Université de Montréal, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Division of Infectious Diseases, Department of Medicine, University Hospital of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Pavilion H-413, 3755 Côte-Ste-Catherine Montréal, Montreal, QC, H3T 1E2, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Department of Twin Research, King's College London, London, UK.
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17
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Liang KYH, Farjoun Y, Forgetta V, Chen Y, Yoshiji S, Lu T, Richards JB. Predicting ExWAS findings from GWAS data: a shorter path to causal genes. Hum Genet 2023; 142:749-758. [PMID: 37009933 DOI: 10.1007/s00439-023-02548-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/22/2023] [Indexed: 04/04/2023]
Abstract
GWAS has identified thousands of loci associated with disease, yet the causal genes within these loci remain largely unknown. Identifying these causal genes would enable deeper understanding of the disease and assist in genetics-based drug development. Exome-wide association studies (ExWAS) are more expensive but can pinpoint causal genes offering high-yield drug targets, yet suffer from a high false-negative rate. Several algorithms have been developed to prioritize genes at GWAS loci, such as the Effector Index (Ei), Locus-2-Gene (L2G), Polygenic Prioritization score (PoPs), and Activity-by-Contact score (ABC) and it is not known if these algorithms can predict ExWAS findings from GWAS data. However, if this were the case, thousands of associated GWAS loci could potentially be resolved to causal genes. Here, we quantified the performance of these algorithms by evaluating their ability to identify ExWAS significant genes for nine traits. We found that Ei, L2G, and PoPs can identify ExWAS significant genes with high areas under the precision recall curve (Ei: 0.52, L2G: 0.37, PoPs: 0.18, ABC: 0.14). Furthermore, we found that for every unit increase in the normalized scores, there was an associated 1.3-4.6-fold increase in the odds of a gene reaching exome-wide significance (Ei: 4.6, L2G: 2.5, PoPs: 2.1, ABC: 1.3). Overall, we found that Ei, L2G, and PoPs can anticipate ExWAS findings from widely available GWAS results. These techniques are therefore promising when well-powered ExWAS data are not readily available and can be used to anticipate ExWAS findings, allowing for prioritization of genes at GWAS loci.
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Affiliation(s)
- Kevin Y H Liang
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, QC, H3A 0G4, Canada
| | - Yossi Farjoun
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada
- 5 Prime Sciences Incorporated, Montréal, Canada
- Broad Institute, Cambridge, MA, 02142, USA
- Fulcrum Genomics LLC, Boulder, CO, 80302, USA
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada
- 5 Prime Sciences Incorporated, Montréal, Canada
| | - Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0G4, Canada
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0G4, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, QC, H3A 0G4, Canada
- 5 Prime Sciences Incorporated, Montréal, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, H3T 1E2, Canada.
- Quantitative Life Sciences Program, McGill University, Montréal, QC, H3A 0G4, Canada.
- Department of Human Genetics, McGill University, Montréal, QC, H3A 0G4, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, H3A 0G4, Canada.
- Department of Medicine, McGill University, Montréal, QC, H3A 0G4, Canada.
- Department of Twin Research, King's College London, London, UK.
- 5 Prime Sciences Incorporated, Montréal, Canada.
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18
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Nadkarni G, Paranjpe I, Jayaraman P, Su CY, Zhou S, Chen S, Valle DD, Thompson R, Kenigsberg E, Zhao S, Jaladanki S, Chaudhary K, Ascolillo S, Vaid A, Gonzalez-Kozlova E, Kumar A, Paranjpe M, O'Hagan R, Kamat S, Gulamali F, Kauffman J, Xie H, Harris J, Patel M, Argueta K, Batchelor C, Nie K, Dellepiane S, Scott L, Levin M, He J, Suárez-Fariñas M, Coca S, Chan L, Azeloglu E, Schadt E, Beckmann N, Gnjatic S, Merad M, Kim-Schulze S, Richards JB, Glicksberg B, Charney A. Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection. Res Sq 2023:rs.3.rs-2379226. [PMID: 36993735 PMCID: PMC10055503 DOI: 10.21203/rs.3.rs-2379226/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Background Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Methods Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261). Results We demonstrate that COVID-AKI is associated with increased markers of tubular injury ( NGAL ) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2 , trefoil factor 3 , transmembrane emp24 domain-containing protein 10 , and cystatin-C indicating tubular dysfunction and injury. Conclusions Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.
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19
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Yoshiji S, Butler-Laporte G, Lu T, Willett JDS, Su CY, Nakanishi T, Morrison DR, Chen Y, Liang K, Hultström M, Ilboudo Y, Afrasiabi Z, Lan S, Duggan N, DeLuca C, Vaezi M, Tselios C, Xue X, Bouab M, Shi F, Laurent L, Münter HM, Afilalo M, Afilalo J, Mooser V, Timpson NJ, Zeberg H, Zhou S, Forgetta V, Farjoun Y, Richards JB. Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity. Nat Metab 2023; 5:248-264. [PMID: 36805566 PMCID: PMC9940690 DOI: 10.1038/s42255-023-00742-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/10/2023] [Indexed: 02/22/2023]
Abstract
Obesity is a major risk factor for Coronavirus disease (COVID-19) severity; however, the mechanisms underlying this relationship are not fully understood. As obesity influences the plasma proteome, we sought to identify circulating proteins mediating the effects of obesity on COVID-19 severity in humans. Here, we screened 4,907 plasma proteins to identify proteins influenced by body mass index using Mendelian randomization. This yielded 1,216 proteins, whose effect on COVID-19 severity was assessed, again using Mendelian randomization. We found that an s.d. increase in nephronectin (NPNT) was associated with increased odds of critically ill COVID-19 (OR = 1.71, P = 1.63 × 10-10). The effect was driven by an NPNT splice isoform. Mediation analyses supported NPNT as a mediator. In single-cell RNA-sequencing, NPNT was expressed in alveolar cells and fibroblasts of the lung in individuals who died of COVID-19. Finally, decreasing body fat mass and increasing fat-free mass were found to lower NPNT levels. These findings provide actionable insights into how obesity influences COVID-19 severity.
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Grants
- C18281/A29019 Cancer Research UK
- 365825 CIHR
- 409511 CIHR
- 100558 CIHR
- 169303 CIHR
- The Richards research group is supported by the Canadian Institutes of Health Research (CIHR: 365825, 409511, 100558, 169303), the McGill Interdisciplinary Initiative in Infection and Immunity (MI4), the Lady Davis Institute of the Jewish General Hospital, the Jewish General Hospital Foundation, the Canadian Foundation for Innovation, the NIH Foundation, Cancer Research UK, Genome Québec, the Public Health Agency of Canada, McGill University, Cancer Research UK [grant number C18281/A29019] and the Fonds de Recherche Québec Santé (FRQS). J.B.R. is supported by an FRQS Mérite Clinical Research Scholarship. Support from Calcul Québec and Compute Canada is acknowledged. TwinsUK is funded by the Welcome Trust, Medical Research Council, European Union, the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London. S.Y. is supported by the Japan Society for the Promotion of Science. T.L. has been supported by a Vanier Canada Graduate Scholarship, an FRQS doctoral training fellowship, and a McGill University Faculty of Medicine Studentship. These funding agencies mentioned above had no role in the design, implementation, or interpretation of this study.
- MEXT | Japan Society for the Promotion of Science (JSPS)
- Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)
- Fonds de Recherche du Québec-Société et Culture (FRQSC)
- Cancer Research UK (CRUK)
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Affiliation(s)
- Satoshi Yoshiji
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - Tianyuan Lu
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Quebec, Canada
- 5 Prime Sciences, Montréal, Quebec, Canada
| | - Julian Daniel Sunday Willett
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Quebec, Canada
| | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Computer Science, McGill University, Montréal, Quebec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - David R Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Kevin Liang
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, Quebec, Canada
| | - Michael Hultström
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Yann Ilboudo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Zaman Afrasiabi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Shanshan Lan
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Naomi Duggan
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Chantal DeLuca
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Mitra Vaezi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Chris Tselios
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Xiaoqing Xue
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Meriem Bouab
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Fangyi Shi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | | | - Marc Afilalo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Emergency Medicine, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Jonathan Afilalo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
- Division of Cardiology, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- McGill Genome Centre, McGill University, Montréal, Quebec, Canada
| | | | - Hugo Zeberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- McGill Genome Centre, McGill University, Montréal, Quebec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
- 5 Prime Sciences, Montréal, Quebec, Canada
| | - Yossi Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada.
- 5 Prime Sciences, Montréal, Quebec, Canada.
- Department of Twin Research, King's College London, London, UK.
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20
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Lu T, Forgetta V, Greenwood CMT, Zhou S, Richards JB. Circulating Proteins Influencing Psychiatric Disease: A Mendelian Randomization Study. Biol Psychiatry 2023; 93:82-91. [PMID: 36280454 DOI: 10.1016/j.biopsych.2022.08.015] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND There is a pressing need for novel drug targets for psychiatric disorders. Circulating proteins are potential candidates because they are relatively easy to measure and modulate and play important roles in signaling. METHODS We performed two-sample Mendelian randomization analyses to estimate the associations between circulating protein abundances and risk of 10 psychiatric disorders. Genetic variants associated with 1611 circulating protein abundances identified in 6 large-scale proteomic studies were used as genetic instruments. Effects of the circulating proteins on psychiatric disorders were estimated by Wald ratio or inverse variance-weighted ratio tests. Horizontal pleiotropy, colocalization, and protein-altering effects were examined to validate the assumptions of Mendelian randomization. RESULTS Nine circulating protein-to-disease associations withstood multiple sensitivity analyses. Among them, 2 circulating proteins had associations replicated in 3 proteomic studies. A 1 standard deviation increase in the genetically predicted circulating TIMP4 level was associated with a reduced risk of anorexia nervosa (minimum odds ratio [OR] = 0.83; 95% CI, 0.76-0.91) and bipolar disorder (minimum OR = 0.88; 95% CI, 0.82-0.94). A 1 standard deviation increase in the genetically predicted circulating ESAM level was associated with an increased risk of schizophrenia (maximum OR = 1.32; 95% CI, 1.22-1.43). In addition, 58 suggestive protein-to-disease associations warrant validation with observational or experimental evidence. For instance, a 1 standard deviation increase in the ERLEC1-201-to-ERLEC1-202 splice variant ratio was associated with a reduced risk of schizophrenia (OR = 0.94; 95% CI, 0.90-0.97). CONCLUSIONS Prioritized circulating proteins appear to influence the risk of psychiatric disease and may be explored as intervention targets.
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada; Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom.
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21
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Butler-Laporte G, Richards JB. Mendelian randomisation and vitamin D: the importance of model assumptions. Lancet Diabetes Endocrinol 2023; 11:14-15. [PMID: 36528344 DOI: 10.1016/s2213-8587(22)00342-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3T 1E2, Canada; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC H3T 1E2, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3T 1E2, Canada; Department of Human Genetics, McGill University, Montréal, QC H3T 1E2, Canada; Department of Twin Research, King's College London, London, UK; 5 Prime Sciences, Montreal, QC, Canada.
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22
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Chen Y, Lu T, Pettersson-Kymmer U, Stewart ID, Butler-Laporte G, Nakanishi T, Cerani A, Liang KYH, Yoshiji S, Willett JDS, Su CY, Raina P, Greenwood CMT, Farjoun Y, Forgetta V, Langenberg C, Zhou S, Ohlsson C, Richards JB. Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases. Nat Genet 2023; 55:44-53. [PMID: 36635386 PMCID: PMC7614162 DOI: 10.1038/s41588-022-01270-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 11/18/2022] [Indexed: 01/14/2023]
Abstract
Metabolic processes can influence disease risk and provide therapeutic targets. By conducting genome-wide association studies of 1,091 blood metabolites and 309 metabolite ratios, we identified associations with 690 metabolites at 248 loci and associations with 143 metabolite ratios at 69 loci. Integrating metabolite-gene and gene expression information identified 94 effector genes for 109 metabolites and 48 metabolite ratios. Using Mendelian randomization (MR), we identified 22 metabolites and 20 metabolite ratios having estimated causal effect on 12 traits and diseases, including orotate for estimated bone mineral density, α-hydroxyisovalerate for body mass index and ergothioneine for inflammatory bowel disease and asthma. We further measured the orotate level in a separate cohort and demonstrated that, consistent with MR, orotate levels were positively associated with incident hip fractures. This study provides a valuable resource describing the genetic architecture of metabolites and delivers insights into their roles in common diseases, thereby offering opportunities for therapeutic targets.
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Affiliation(s)
- Yiheng Chen
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | | | - Isobel D Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Agustin Cerani
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Kevin Y H Liang
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
| | - Satoshi Yoshiji
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Julian Daniel Sunday Willett
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
- McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Chen-Yang Su
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Computer Science, McGill University, Montreal, Quebec, Canada
| | - Parminder Raina
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
- McMaster Institute for Research on Aging, McMaster University, Hamilton, Ontario, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Quantitative Life Sciences Program, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Yossi Farjoun
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Fulcrum Genomics, Boulder, CO, USA
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
- Computational Medicine, Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Claes Ohlsson
- Sahlgrenska Osteoporosis Centre, Centre of Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
- 5 Prime Sciences Inc, Montreal, Quebec, Canada.
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada.
- Department of Medicine, McGill University, Montreal, Quebec, Canada.
- Department of Twin Research, King's College London, London, UK.
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23
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Gómez-Carballa A, Pardo-Seco J, Pischedda S, Rivero-Calle I, Butler-Laporte G, Richards JB, Viz-Lasheras S, Martinón-Torres F, Salas A. Sex-biased expression of the TLR7 gene in severe COVID-19 patients: Insights from transcriptomics and epigenomics. Environ Res 2022; 215:114288. [PMID: 36152884 PMCID: PMC9508271 DOI: 10.1016/j.envres.2022.114288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 06/16/2023]
Abstract
There is abundant epidemiological data indicating that the incidence of severe cases of coronavirus disease (COVID-19) is significantly higher in males than females worldwide. Moreover, genetic variation at the X-chromosome linked TLR7 gene has been associated with COVID-19 severity. It has been suggested that the sex-biased incidence of COVID-19 might be related to the fact that TLR7 escapes X-chromosome inactivation during early embryogenesis in females, thus encoding a doble dose of its gene product compared to males. We analyzed TLR7 expression in two acute phase cohorts of COVID-19 patients that used two different technological platforms, one of them in a multi-tissue context including saliva, nasal, and blood samples, and a third cohort that included different post-infection timepoints of long-COVID-19 patients. We additionally explored methylation patterns of TLR7 using epigenomic data from an independent cohort of COVID-19 patients stratified by severity and sex. In line with genome-wide association studies, we provide supportive evidence indicating that TLR7 has altered CpG methylation patterns and it is consistently downregulated in males compared to females in the most severe cases of COVID-19.
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Affiliation(s)
- A Gómez-Carballa
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - J Pardo-Seco
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - S Pischedda
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - I Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - G Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada; Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - J B Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada; Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - S Viz-Lasheras
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - F Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - A Salas
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain; Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain.
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24
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Borie R, Cardwell J, Konigsberg IR, Moore CM, Zhang W, Sasse SK, Gally F, Dobrinskikh E, Walts A, Powers J, Brancato J, Rojas M, Wolters PJ, Brown KK, Blackwell TS, Nakanishi T, Richards JB, Gerber AN, Fingerlin TE, Sachs N, Pulit SL, Zappala Z, Schwartz DA, Yang IV. Colocalization of Gene Expression and DNA Methylation with Genetic Risk Variants Supports Functional Roles of MUC5B and DSP in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2022; 206:1259-1270. [PMID: 35816432 PMCID: PMC9746850 DOI: 10.1164/rccm.202110-2308oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: Common genetic variants have been associated with idiopathic pulmonary fibrosis (IPF). Objectives: To determine functional relevance of the 10 IPF-associated common genetic variants we previously identified. Methods: We performed expression quantitative trait loci (eQTL) and methylation quantitative trait loci (mQTL) mapping, followed by co-localization of eQTL and mQTL with genetic association signals and functional validation by luciferase reporter assays. Illumina multi-ethnic genotyping arrays, mRNA sequencing, and Illumina 850k methylation arrays were performed on lung tissue of participants with IPF (234 RNA and 345 DNA samples) and non-diseased controls (188 RNA and 202 DNA samples). Measurements and Main Results: Focusing on genetic variants within 10 IPF-associated genetic loci, we identified 27 eQTLs in controls and 24 eQTLs in cases (false-discovery-rate-adjusted P < 0.05). Among these signals, we identified associations of lead variants rs35705950 with expression of MUC5B and rs2076295 with expression of DSP in both cases and controls. mQTL analysis identified CpGs in gene bodies of MUC5B (cg17589883) and DSP (cg08964675) associated with the lead variants in these two loci. We also demonstrated strong co-localization of eQTL/mQTL and genetic signal in MUC5B (rs35705950) and DSP (rs2076295). Functional validation of the mQTL in MUC5B using luciferase reporter assays demonstrates that the CpG resides within a putative internal repressor element. Conclusions: We have established a relationship of the common IPF genetic risk variants rs35705950 and rs2076295 with respective changes in MUC5B and DSP expression and methylation. These results provide additional evidence that both MUC5B and DSP are involved in the etiology of IPF.
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Affiliation(s)
| | | | | | - Camille M. Moore
- Department of Biostatistics and Bioinformatics and
- Center for Genes, Environment, and Health
| | | | | | - Fabienne Gally
- Department of Medicine
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | | | | | | | | | - Mauricio Rojas
- Department of Internal Medicine, Ohio State College of Medicine, The Ohio State University, Columbus, Ohio
| | - Paul J. Wolters
- Department of Medicine, University of California, San Francisco, California
| | | | - Timothy S. Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tomoko Nakanishi
- Department of Human Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Canada
| | - J. Brent Richards
- Department of Human Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Canada
| | - Anthony N. Gerber
- Department of Medicine
- Department of Medicine, and
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | - Tasha E. Fingerlin
- Department of Biostatistics and Bioinformatics and
- Center for Genes, Environment, and Health
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | - Norman Sachs
- Cell Biology, Vertex Pharmaceuticals, San Diego, California; and
| | - Sara L. Pulit
- Computational Genomics, Vertex Pharmaceuticals, Boston, Massachusetts
| | - Zachary Zappala
- Computational Genomics, Vertex Pharmaceuticals, Boston, Massachusetts
| | - David A. Schwartz
- Department of Medicine
- Department of Microbiology and Immunology, University of Colorado Anschutz Medical Campus; Aurora, Colorado
| | - Ivana V. Yang
- Department of Medicine
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado
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25
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Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJM, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A, Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet 2022; 18:e1010367. [PMID: 36327219 PMCID: PMC9632827 DOI: 10.1371/journal.pgen.1010367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/29/2022] [Indexed: 11/05/2022] Open
Abstract
Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.
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Grants
- 409511 CIHR
- RG/13/13/30194 British Heart Foundation
- C18281/A29019 Cancer Research UK
- 100558 CIHR
- MC_PC_20004 Medical Research Council
- 365825 CIHR
- UL1 TR001873 NCATS NIH HHS
- RG/18/13/33946 British Heart Foundation
- CH/12/2/29428 British Heart Foundation
- CanCOGeN HostSeq
- Fonds de Recherche Québec Santé (FRQS)
- Génome Québec
- Public Health Agency of Canada
- Canadian Institutes of Health Research (CIHR)
- Lady Davis Institute of the Jewish General Hospital
- Canadian Foundation for Innovation
- NIH Foundation
- McGill Interdisciplinary Initiative in Infection and Immunity (MI4)
- Jewish General Hospital Foundation
- McGill University
- Calcul Québec and Compute Canada
- Compute Canada
- Vagelos College of Physicians & Surgeons Office for Research
- Biomedical Informatics Resource of the Columbia University Irving Institute for Clinical and Translational Research (CTSA)
- National Center for Advancing Translational Sciences, National Institutes of Health
- German Research Foundation
- NGS Competence Center Tübingen
- West German Genome Center
- Stiftung Universitätsmedizin Essen
- Technical University of Munich
- BONFOR program of the Medical Faculty, University of Bonn
- Emmy-Noether programm of the German Research Foundation
- State of Saarland
- Dr. Rolf M. Schwiete Foundation
- Munich Clinician Scientist Programm
- Netzwerk-Universitaetsmedizin-COVIM
- Federal Ministry of Education and Research
- Swiss National Science Foundation
- Leenaards Foundation
- Santos-Suarez Foundation
- Carigest
- MIUR project “Dipartimenti di Eccellenza 2018-2020”
- Bando Ricerca COVID-19 Toscana
- charity fund 2020 from Intesa San Paolo
- Italian Ministry of University and Research
- Istituto Buddista Italiano Soka Gakkai
- Instituto de Salud Carlos III
- GePEM
- DIAVIR
- Resvi-Omics
- ReSVinext
- Enterogen
- Agencia Gallega para la Gestión del Conocimiento en Salud
- BI-BACVIR
- CovidPhy
- Agencia Gallega de Innovación (GAIN):
- GEN-COVID
- Framework Partnership Agreement between the Consellería de Sanidad de la XUNTA de Galicia
- GENVIP-IDIS
- consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias
- F. Hoffmann-La Roche Ltd
- U.S. Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, and Biomedical Advanced Research and Development Authority
- Nevada Governor's Office of Economic Development
- Renown Health and the Renown Health Foundation
- Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research)
- Grant for Development of New Faculty Staff, Ratchadaphiseksomphot Endowment Fund
- e-ASIA Joint Research Program (National Science and Technology Development Agency)
- Health Systems Research Institute, TSRI Fund
- Thailand Research Fund
- Ratchadapiseksompotch Fund
- Ratchadapiseksompotch Fund, Faculty of Medicine,Chulalongkorn University, Bangkok, Thailand
- Health Systems Research Institute
- Ratchadapisek Sompoch Endowment Fund, Chulalongkorn University
- NHS Blood and Transplant
- National Institute for Health Research
- UK Medical Research Council
- Japan Agency for Medical Research and Development
- Japan Science and Technology Agency
- National Center for Global Health and Medicine
- Agency for Medical Research and Development
- Polish National Science Centre
- Medical Research Agency
- Perelman School of Medicine at University of Pennsylvania
- Smilow family
- National Center for Advancing Translational Sciences of the National Institutes of Health
- Polish Medical Research Agency
- Qatar Foundation for Education, Science and Community Development
- Saudi Ministry of Health
- King Abdulaziz City for Science and Technology
- European Union’s Horizon 2020 research and innovation program
- Science for Life Laboratory
- Swedish Research Council
- Knut and Alice Wallenberg Foundation
- OCRC
- Microsoft COVID Compute Funding
- Illumina
- UCLA David Geffen School of Medicine - Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Award Program
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Affiliation(s)
- Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Jack A. Kosmicki
- Regeneron Genetics Center, Tarrytown, New York, United States of America
| | | | - Theodore Drivas
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Simone Furini
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Axel Schmidt
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | - Urszula Korotko
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Elifnaz Çelik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Kousik Kundu
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Junghyun Jung
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amy D. Stockwell
- Genentech Inc, South San Francisco, California, United States of America
| | - Laura G. Sloofman
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Daniel M. Jordan
- Mount Sinai Clnical Intelligence Center, Charles Bronfman Institute for Personalized Medicine, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Ryan C. Thompson
- Icahn Institute of Data Science and Genomics Technology, New York city, New York, United States of America
| | - Diane Del Valle
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Nicole Simons
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Seunghee Kim-Schulze
- Department of Oncological Science, Human Immune Monitoring Center, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Miriam Merad
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Noam D. Beckmann
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Alexander W. Charney
- Mount Sinai Clinical Intelligence Center; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | | | - Timothy Chang
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Tess D. Pottinger
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Fabian Brand
- Institute of Genomic Statistics and Bioinformatics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Francesca Fava
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Karolina Chwialkowska
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Niemira
- Centre for Clinical Research, Medical University of Bialystok, Bialystok, Poland
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | | | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachussets, United States of America
| | - Konrad J. Karczewski
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kumar Veerapen
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Robert JM Eveleigh
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Langlais
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Mark Lathrop
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Robert Frithiof
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Hultström
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Miklos Lipcsey
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Hedenstierna Laboratory, CIRRUS, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - William Lee
- Helix, San Mateo, California, United States of America
| | | | - Simon White
- Helix, San Mateo, California, United States of America
| | | | | | | | - Iva Neveux
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | - Shaun Dabe
- Renown Health, Reno, Nevada, United States of America
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susanne Motameny
- West German Genome Center, site Cologne, University of Cologne, Cologne, Germany
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nora Aljawini
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mansour S. Almutairi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Yaseen M. Arabi
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Saleh A. Alqahtani
- Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fawz S. Al Harthi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Amal Almutairi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fatima Alqubaishi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sarah Alotaibi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Albandari Binowayn
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ebtehal A. Alsolm
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hadeel El Bardisy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohammad Fawzy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fang Cai
- Genentech Inc, South San Francisco, California, United States of America
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adam Butterworth
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | | | | | | | | | | | - Daniel H. Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stephanie Arteaga
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alexis Stephens
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Manish J. Butte
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul C. Boutros
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Takafumi N. Yamaguchi
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Shu Tao
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stefan Eng
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Timothy Sanders
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul J. Tung
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Michael E. Broudy
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Yu Pan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alfredo Gonzalez
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Nikhil Chavan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Ruth Johnson
- Department of Computer Science, McGill University, Montréal, Québec, Canada
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Computational Medicine, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Pathology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Brian Yaspan
- Genentech Inc, South San Francisco, California, United States of America
| | - Sandra Smieszek
- Vanda Pharmaceuticals, Washington, District of Columbia, United States of America
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Stephanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Maciej Dabrowski
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
| | - Pawel Zawadzki
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | | | - Elżbieta Kaja
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Department of Medical Chemistry and Laboratory Medicine, Poznań University of Medical Sciences, Poznań, Poland
| | - Pajaree Chariyavilaskul
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voraphoj Nilaratanakul
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research) and Division of Infectious Diseases, Department of Medicine,Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, and Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chureerat Phokaew
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masaya Sugiyama
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Takanori Hasegawa
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Joseph J. Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | | | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
- West German Genome Center, site Bonn, University of Bonn, Bonn, Germany
| | - Eva C. Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Miroslaw Kwasniewski
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Anurag Verma
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Department of Genetics & Development, Columbia University, New York city, New York, United States of America
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Alessandra Renieri
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | | | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- * E-mail:
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26
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Hultström M, Lipcsey M, Morrison DR, Nakanishi T, Butler-Laporte G, Chen Y, Yoshiji S, Forgetta V, Farjoun Y, Wallin E, Larsson IM, Larsson A, Marton A, Titze JM, Nihlén S, Richards JB, Frithiof R. Dehydration is associated with production of organic osmolytes and predicts physical long-term symptoms after COVID-19: a multicenter cohort study. Crit Care 2022; 26:322. [PMID: 36271419 PMCID: PMC9585783 DOI: 10.1186/s13054-022-04203-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Background We have previously shown that iatrogenic dehydration is associated with a shift to organic osmolyte production in the general ICU population. The aim of the present investigation was to determine the validity of the physiological response to dehydration known as aestivation and its relevance for long-term disease outcome in COVID-19. Methods The study includes 374 COVID-19 patients from the Pronmed cohort admitted to the ICU at Uppsala University Hospital. Dehydration data was available for 165 of these patients and used for the primary analysis. Validation was performed in Biobanque Québécoise de la COVID-19 (BQC19) using 1052 patients with dehydration data. Dehydration was assessed through estimated osmolality (eOSM = 2Na + 2 K + glucose + urea), and correlated to important endpoints including death, invasive mechanical ventilation, acute kidney injury, and long COVID-19 symptom score grouped by physical or mental. Results Increasing eOSM was correlated with increasing role of organic osmolytes for eOSM, while the proportion of sodium and potassium of eOSM were inversely correlated to eOSM. Acute outcomes were associated with pronounced dehydration, and physical long-COVID was more strongly associated with dehydration than mental long-COVID after adjustment for age, sex, and disease severity. Metabolomic analysis showed enrichment of amino acids among metabolites that showed an aestivating pattern. Conclusions Dehydration during acute COVID-19 infection causes an aestivation response that is associated with protein degradation and physical long-COVID. Trial registration: The study was registered à priori (clinicaltrials.gov: NCT04316884 registered on 2020-03-13 and NCT04474249 registered on 2020-06-29). Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13054-022-04203-w.
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Affiliation(s)
- Michael Hultström
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, ANOPIVA, Ing70, 2Tr, 75185 Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Lady Davis Institute of Medical Research, Jewish General Hospital, McGill University, Montreal, QC Canada
| | - Miklos Lipcsey
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, ANOPIVA, Ing70, 2Tr, 75185 Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Hedenstierna Laboratory, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Dave R. Morrison
- grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Lady Davis Institute of Medical Research, Jewish General Hospital, McGill University, Montreal, QC Canada
| | - Tomoko Nakanishi
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute of Medical Research, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC Canada ,grid.258799.80000 0004 0372 2033Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan ,grid.54432.340000 0001 0860 6072Japan Society for the Promotion of Science, Tokyo, Japan
| | - Guillaume Butler-Laporte
- grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Lady Davis Institute of Medical Research, Jewish General Hospital, McGill University, Montreal, QC Canada
| | - Yiheng Chen
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute of Medical Research, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC Canada
| | - Satoshi Yoshiji
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute of Medical Research, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC Canada ,grid.258799.80000 0004 0372 2033Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan ,grid.54432.340000 0001 0860 6072Japan Society for the Promotion of Science, Tokyo, Japan
| | - Vincenzo Forgetta
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute of Medical Research, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC Canada ,5 Prime Sciences, Montreal, QC Canada
| | - Yossi Farjoun
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute of Medical Research, Jewish General Hospital, McGill University, Montreal, QC Canada ,5 Prime Sciences, Montreal, QC Canada ,grid.66859.340000 0004 0546 1623The Broad Institute of Harvard and MIT, Cambridge, MA USA ,Fulcrum Genomics, Bolder, CO USA
| | - Ewa Wallin
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, ANOPIVA, Ing70, 2Tr, 75185 Uppsala, Sweden
| | - Ing-Marie Larsson
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, ANOPIVA, Ing70, 2Tr, 75185 Uppsala, Sweden
| | - Anders Larsson
- grid.8993.b0000 0004 1936 9457Clinical Chemistry, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Adriana Marton
- grid.428397.30000 0004 0385 0924Program in Cardiovascular and Metabolic Disorders, Duke- NUS Medical School, Singapore, Singapore
| | - Jens Marc Titze
- grid.428397.30000 0004 0385 0924Program in Cardiovascular and Metabolic Disorders, Duke- NUS Medical School, Singapore, Singapore ,grid.189509.c0000000100241216Division of Nephrology, Duke University Medical Center, Durham, NC USA
| | - Sandra Nihlén
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, ANOPIVA, Ing70, 2Tr, 75185 Uppsala, Sweden
| | - J. Brent Richards
- grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Lady Davis Institute of Medical Research, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC Canada ,grid.13097.3c0000 0001 2322 6764Department of Twin Research, King’s College London, London, UK ,5 Prime Sciences, Montreal, QC Canada
| | - Robert Frithiof
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, ANOPIVA, Ing70, 2Tr, 75185 Uppsala, Sweden
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27
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Smith-Byrne K, Cerani A, Guida F, Zhou S, Agudo A, Aleksandrova K, Barricarte A, Barranco MR, Bochers CH, Gram IT, Han J, Amos CI, Hung RJ, Grankvist K, Nøst TH, Imaz L, Chirlaque-López MD, Johansson M, Kaaks R, Kühn T, Martin RM, McKay JD, Pala V, Robbins HA, Sandanger TM, Schibli D, Schulze MB, Travis RC, Vineis P, Weiderpass E, Brennan P, Johansson M, Richards JB. Circulating Isovalerylcarnitine and Lung Cancer Risk: Evidence from Mendelian Randomization and Prediagnostic Blood Measurements. Cancer Epidemiol Biomarkers Prev 2022; 31:1966-1974. [PMID: 35839461 PMCID: PMC9530646 DOI: 10.1158/1055-9965.epi-21-1033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/09/2021] [Accepted: 07/13/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Tobacco exposure causes 8 of 10 lung cancers, and identifying additional risk factors is challenging due to confounding introduced by smoking in traditional observational studies. MATERIALS AND METHODS We used Mendelian randomization (MR) to screen 207 metabolites for their role in lung cancer predisposition using independent genome-wide association studies (GWAS) of blood metabolite levels (n = 7,824) and lung cancer risk (n = 29,266 cases/56,450 controls). A nested case-control study (656 cases and 1,296 matched controls) was subsequently performed using prediagnostic blood samples to validate MR association with lung cancer incidence data from population-based cohorts (EPIC and NSHDS). RESULTS An MR-based scan of 207 circulating metabolites for lung cancer risk identified that blood isovalerylcarnitine (IVC) was associated with a decreased odds of lung cancer after accounting for multiple testing (log10-OR = 0.43; 95% CI, 0.29-0.63). Molar measurement of IVC in prediagnostic blood found similar results (log10-OR = 0.39; 95% CI, 0.21-0.72). Results were consistent across lung cancer subtypes. CONCLUSIONS Independent lines of evidence support an inverse association of elevated circulating IVC with lung cancer risk through a novel methodologic approach that integrates genetic and traditional epidemiology to efficiently identify novel cancer biomarkers. IMPACT Our results find compelling evidence in favor of a protective role for a circulating metabolite, IVC, in lung cancer etiology. From the treatment of a Mendelian disease, isovaleric acidemia, we know that circulating IVC is modifiable through a restricted protein diet or glycine and L-carnatine supplementation. IVC may represent a modifiable and inversely associated biomarker for lung cancer.
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Affiliation(s)
- Karl Smith-Byrne
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Agustin Cerani
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada/Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Florence Guida
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Sirui Zhou
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada/Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Antonio Agudo
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Institut Català d'Oncologia, Spain
| | - Krasimira Aleksandrova
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
- University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Aurelio Barricarte
- Navarra Institute for Health Research (IdiSNA) Pamplona, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Miguel Rodríguez Barranco
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Escuela Andaluza de Salud Pública (EASP), Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Christoph H. Bochers
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada/Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- University of Victoria–Genome British Columbia Proteomics Centre, Victoria, BC, Canada/Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Inger Torhild Gram
- Faculty of Health Sciences, Department of Community Medicine, University of Tromsø, The Arctic University of Norway, Norway
| | - Jun Han
- University of Victoria–Genome British Columbia Proteomics Centre, Victoria, BC, Canada/Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Christopher I. Amos
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Rayjean J. Hung
- Prosserman Centre for Health Research, Mount Sinai Hospital, Toronto, Canada
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Therese Haugdhal Nøst
- Faculty of Health Sciences, Department of Community Medicine, University of Tromsø, The Arctic University of Norway, Norway
| | - Liher Imaz
- Ministry of Health of the Basque Government, Public Health Division of Gipuzkoa, Donostia-San Sebastian, Spain
- Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
| | - María Dolores Chirlaque-López
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia University, Murcia, Spain
| | | | - Rudolf Kaaks
- German Cancer Research Center (DKFZ), Heidelberg, Department of Cancer Epidemiology
- Translational Lung Research Center (TLRC) Heidelberg, Member of the German Center for Lung Research (DZL), Germany
| | - Tilman Kühn
- German Cancer Research Center (DKFZ), Heidelberg, Department of Cancer Epidemiology
| | - Richard M. Martin
- Clinical Epidemiology & Public Health, University of Bristol, Bristol, United Kingdom
| | - James D. McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Valeria Pala
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano
| | - Hilary A. Robbins
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Torkjel M. Sandanger
- Faculty of Health Sciences, Department of Community Medicine, University of Tromsø, The Arctic University of Norway, Norway
| | - David Schibli
- University of Victoria–Genome British Columbia Proteomics Centre, Victoria, BC, Canada/Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Matthias B. Schulze
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
- University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Ruth C. Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Elisabete Weiderpass
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - J. Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada/Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Division of Endocrinology, Department of Medicine & Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, Strand, London, United Kingdom
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28
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Butler-Laporte G, Gonzalez-Kozlova E, Su CY, Zhou S, Nakanishi T, Brunet-Ratnasingham E, Morrison D, Laurent L, Afilalo J, Afilalo M, Henry D, Chen Y, Carrasco-Zanini J, Farjoun Y, Pietzner M, Kimchi N, Afrasiabi Z, Rezk N, Bouab M, Petitjean L, Guzman C, Xue X, Tselios C, Vulesevic B, Adeleye O, Abdullah T, Almamlouk N, Moussa Y, DeLuca C, Duggan N, Schurr E, Brassard N, Durand M, Del Valle DM, Thompson R, Cedillo MA, Schadt E, Nie K, Simons NW, Mouskas K, Zaki N, Patel M, Xie H, Harris J, Marvin R, Cheng E, Tuballes K, Argueta K, Scott I, Greenwood CMT, Paterson C, Hinterberg M, Langenberg C, Forgetta V, Mooser V, Marron T, Beckmann N, Kenigsberg E, Charney AW, Kim-schulze S, Merad M, Kaufmann DE, Gnjatic S, Richards JB. The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals. Clin Proteomics 2022; 19:34. [PMID: 36171541 PMCID: PMC9516500 DOI: 10.1186/s12014-022-09371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/15/2021] [Accepted: 08/21/2022] [Indexed: 02/02/2023] Open
Abstract
INTRODUCTION Severe COVID-19 leads to important changes in circulating immune-related proteins. To date it has been difficult to understand their temporal relationship and identify cytokines that are drivers of severe COVID-19 outcomes and underlie differences in outcomes between sexes. Here, we measured 147 immune-related proteins during acute COVID-19 to investigate these questions. METHODS We measured circulating protein abundances using the SOMAscan nucleic acid aptamer panel in two large independent hospital-based COVID-19 cohorts in Canada and the United States. We fit generalized additive models with cubic splines from the start of symptom onset to identify protein levels over the first 14 days of infection which were different between severe cases and controls, adjusting for age and sex. Severe cases were defined as individuals with COVID-19 requiring invasive or non-invasive mechanical respiratory support. RESULTS 580 individuals were included in the analysis. Mean subject age was 64.3 (sd 18.1), and 47% were male. Of the 147 proteins, 69 showed a significant difference between cases and controls (p < 3.4 × 10-4). Three clusters were formed by 108 highly correlated proteins that replicated in both cohorts, making it difficult to determine which proteins have a true causal effect on severe COVID-19. Six proteins showed sex differences in levels over time, of which 3 were also associated with severe COVID-19: CCL26, IL1RL2, and IL3RA, providing insights to better understand the marked differences in outcomes by sex. CONCLUSIONS Severe COVID-19 is associated with large changes in 69 immune-related proteins. Further, five proteins were associated with sex differences in outcomes. These results provide direct insights into immune-related proteins that are strongly influenced by severe COVID-19 infection.
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Affiliation(s)
- Guillaume Butler-Laporte
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada
| | - Edgar Gonzalez-Kozlova
- grid.59734.3c0000 0001 0670 2351Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Chen-Yang Su
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Computer Science, McGill University, Montréal, Québec Canada
| | - Sirui Zhou
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada
| | - Tomoko Nakanishi
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montréal, Québec Canada ,grid.258799.80000 0004 0372 2033Graduate School of Medicine, McGill International Collaborative School in Genomic Medicine, Kyoto University, KyotoKyoto, Japan ,grid.54432.340000 0001 0860 6072Japan Society for the Promotion of Science, Tokyo, Japan
| | - Elsa Brunet-Ratnasingham
- grid.410559.c0000 0001 0743 2111Research Centre of the Centre Hospitalier de L’Université de Montréal, Montréal, Québec Canada
| | - David Morrison
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Laetitia Laurent
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Jonathan Afilalo
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada
| | - Marc Afilalo
- grid.414980.00000 0000 9401 2774Department of Emergency Medicine, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Danielle Henry
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Yiheng Chen
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montréal, Québec Canada
| | - Julia Carrasco-Zanini
- grid.5335.00000000121885934MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Yossi Farjoun
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Maik Pietzner
- grid.5335.00000000121885934MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK ,grid.484013.a0000 0004 6879 971XComputational Medicine, Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Nofar Kimchi
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Zaman Afrasiabi
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Nardin Rezk
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Meriem Bouab
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Louis Petitjean
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Charlotte Guzman
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Xiaoqing Xue
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Chris Tselios
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Branka Vulesevic
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Olumide Adeleye
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Tala Abdullah
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Noor Almamlouk
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Yara Moussa
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Chantal DeLuca
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Naomi Duggan
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Erwin Schurr
- grid.63984.300000 0000 9064 4811Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec Canada
| | - Nathalie Brassard
- grid.410559.c0000 0001 0743 2111Research Centre of the Centre Hospitalier de L’Université de Montréal, Montréal, Québec Canada
| | - Madeleine Durand
- grid.410559.c0000 0001 0743 2111Research Centre of the Centre Hospitalier de L’Université de Montréal, Montréal, Québec Canada
| | - Diane Marie Del Valle
- grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ryan Thompson
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Mario A. Cedillo
- grid.59734.3c0000 0001 0670 2351Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Eric Schadt
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Kai Nie
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nicole W. Simons
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Konstantinos Mouskas
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nicolas Zaki
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Manishkumar Patel
- grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Hui Xie
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Jocelyn Harris
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Robert Marvin
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Esther Cheng
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Kevin Tuballes
- grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Kimberly Argueta
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ieisha Scott
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | | | - Celia M. T. Greenwood
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada
| | - Clare Paterson
- grid.437866.80000 0004 0625 700XSomaLogic Inc, Boulder, CO USA
| | | | - Claudia Langenberg
- grid.5335.00000000121885934MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK ,grid.437866.80000 0004 0625 700XSomaLogic Inc, Boulder, CO USA
| | - Vincenzo Forgetta
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Vincent Mooser
- grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montréal, Québec Canada
| | - Thomas Marron
- grid.59734.3c0000 0001 0670 2351Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.416167.30000 0004 0442 1996Early Phase Trials Unit, Mount Sinai Hospital, New York, NY USA
| | - Noam Beckmann
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ephraim Kenigsberg
- grid.59734.3c0000 0001 0670 2351Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Alexander W. Charney
- grid.59734.3c0000 0001 0670 2351Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Seunghee Kim-schulze
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Miriam Merad
- grid.59734.3c0000 0001 0670 2351Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Daniel E. Kaufmann
- grid.410559.c0000 0001 0743 2111Research Centre of the Centre Hospitalier de L’Université de Montréal, Montréal, Québec Canada ,grid.14848.310000 0001 2292 3357Department of Medicine, Université de Montréal, Montréal, Québec Canada
| | - Sacha Gnjatic
- grid.59734.3c0000 0001 0670 2351Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - J Brent Richards
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montréal, Québec Canada ,grid.13097.3c0000 0001 2322 6764Department of Twin Research, King’s College London, London, UK ,5 Prime Sciences, Montreal, Québec Canada ,grid.14709.3b0000 0004 1936 8649McGill University, King’s College London (Honorary), Jewish General Hospital, Pavilion H-4133755 Côte-Ste-Catherine, Montréal, Québec H3T 1E2 Canada
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Lu T, Forgetta V, Greenwood CMT, Richards JB. Identifying Causes of Fracture Beyond Bone Mineral Density: Evidence From Human Genetics. J Bone Miner Res 2022; 37:1592-1602. [PMID: 35689460 DOI: 10.1002/jbmr.4632] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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] [Received: 09/07/2021] [Revised: 05/28/2022] [Accepted: 06/04/2022] [Indexed: 11/10/2022]
Abstract
New therapies may help to prevent osteoporotic fractures other than through increasing bone mineral density (BMD). Because fracture risk has an important genetic component, we aim to identify loci increasing fracture risk that do not decrease BMD, using a recently-proposed structural equation model adapted to remove genetic influences of BMD on fracture risk. We used summary statistics of the largest genome-wide association studies (GWASs) for BMD and for fracture in these analyses. We next estimated the genetic correlation between the non-BMD or BMD-related genetic effects and other clinical risk factors for fracture. Last, based on white British participants in the UK Biobank, we conducted genetic risk score analyses to assess whether the aggregated genetic effects conferred increased major osteoporotic fracture risk. We found that only three loci affecting fracture risk exhibited genetic effects not mediated by BMD: SOST, CPED1-WNT16, and RSPO3, while these three loci simultaneously conferred BMD-related effects. No strong genetic associations between non-BMD or BMD-related effects and 16 clinical risk factors were observed. However, non-BMD effects might be genetic correlated with hip bone size. In the UK Biobank, a 1 standard deviation (1-SD) increase in the non-BMD genetic risk score conferred an odds ratio of 1.17 for incident major osteoporotic fracture, compared to 1.29 by a BMD-related genetic risk score. Our study suggests that the majority of common genetic predisposition toward fracture risk acts upon BMD. Although non-BMD genetic effects may exist, they are not strongly correlated with most traditional clinical risk factors. Risk loci harboring non-BMD genetic effects may influence other perspectives of bone quality, or confer effects that existing GWASs fail to capture, but they demonstrate weaker impact on fracture risk than BMD-related genetic effects. These findings suggest that most successful drug development programs for osteoporosis should focus on pathways identified through BMD-associated loci. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada.,Quantitative Life Sciences Program, McGill University, Montreal, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada.,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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Lu T, Forgetta V, Richards JB, Greenwood CMT. Capturing additional genetic risk from family history for improved polygenic risk prediction. Commun Biol 2022; 5:595. [PMID: 35710731 PMCID: PMC9203758 DOI: 10.1038/s42003-022-03532-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/17/2022] [Accepted: 05/24/2022] [Indexed: 12/01/2022] Open
Abstract
Family history of complex traits may reflect transmitted rare pathogenic variants, intra-familial shared exposures to environmental and lifestyle factors, as well as a common genetic predisposition. We developed a latent factor model to quantify trait heritability in excess of that captured by a common variant-based polygenic risk score, but inferable from family history. For 941 children in the Avon Longitudinal Study of Parents and Children cohort, a joint predictor combining a polygenic risk score for height and mid-parental height was able to explain ~55% of the total variance in sex-adjusted adult height z-scores, close to the estimated heritability. Marginal yet consistent risk prediction improvements were also achieved among ~400,000 European ancestry participants for 11 complex diseases in the UK Biobank. Our work showcases a paradigm for risk calculation, and supports incorporation of family history into polygenic risk score-based genetic risk prediction models.
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada. .,Quantitative Life Sciences Program, McGill University, Montreal, QC, Canada.
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada.,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada. .,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada. .,Department of Human Genetics, McGill University, Montreal, QC, Canada. .,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.
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Ghanbari F, Yazdanpanah N, Yazdanpanah M, Richards JB, Manousaki D. Connecting Genomics and Proteomics to Identify Protein Biomarkers for Adult and Youth-Onset Type 2 Diabetes: A Two-Sample Mendelian Randomization Study. Diabetes 2022; 71:1324-1337. [PMID: 35234851 DOI: 10.2337/db21-1046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022]
Abstract
Type 2 diabetes shows an increasing prevalence in both adults and children. Identification of biomarkers for both youth and adult-onset type 2 diabetes is crucial for development of screening tools or drug targets. In this study, using two-sample Mendelian randomization (MR), we identified 22 circulating proteins causally linked to adult type 2 diabetes and 11 proteins with suggestive evidence for association with youth-onset type 2 diabetes. Among these, colocalization analysis further supported a role in type 2 diabetes for C-type mannose receptor 2 (MR odds ratio [OR] 0.85 [95% CI 0.79-0.92] per genetically predicted SD increase in protein level), MANS domain containing 4 (MR OR 0.90 [95% CI 0.88-0.92]), sodium/potassium-transporting ATPase subunit β2 (MR OR 1.10 [95% CI 1.06-1.15]), endoplasmic reticulum oxidoreductase 1β (MR OR 1.09 [95% CI 1.05-1.14]), spermatogenesis-associated protein 20 (MR OR 1.12 [95% CI 1.06-1.18]), haptoglobin (MR OR 0.96 [95% CI 0.94-0.98]), and α1-3-N-acetylgalactosaminyltransferase and α1-3-galactosyltransferase (MR OR 1.04 [95% CI 1.03-1.05]). Our findings support a causal role in type 2 diabetes for a set of circulating proteins, which represent promising type 2 diabetes drug targets.
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Affiliation(s)
- Faegheh Ghanbari
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Nahid Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Mojgan Yazdanpanah
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology and Biostatistics, McGill University, Montreal, Quebec, Canada
- Department of Twin Research, King's College London, London, U.K
| | - Despoina Manousaki
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
- Departments of Pediatrics, Biochemistry and Molecular Medicine, University of Montreal, Montreal, Canada
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Bouillon R, Manousaki D, Rosen C, Trajanoska K, Rivadeneira F, Richards JB. Reply to 'The emerging evidence for non-skeletal health benefits of vitamin D supplementation in adults'. Nat Rev Endocrinol 2022; 18:324. [PMID: 35194177 DOI: 10.1038/s41574-022-00647-w] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Roger Bouillon
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KULeuven, Leuven, Belgium.
| | - Despoina Manousaki
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Cliff Rosen
- Maine Medical Center Research Institute, Scarborough, ME, USA
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Fernando Rivadeneira
- Translational Skeletal Genomics, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - J Brent Richards
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montreal, Quebec, Canada
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Forgetta V, Li R, Darmond-Zwaig C, Belisle A, Balion C, Roshandel D, Wolfson C, Lettre G, Pare G, Paterson AD, Griffith LE, Verschoor C, Lathrop M, Kirkland S, Raina P, Richards JB, Ragoussis J. Cohort profile: genomic data for 26 622 individuals from the Canadian Longitudinal Study on Aging (CLSA). BMJ Open 2022; 12:e059021. [PMID: 35273064 PMCID: PMC8915305 DOI: 10.1136/bmjopen-2021-059021] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
PURPOSE The Canadian Longitudinal Study on Aging (CLSA) Comprehensive cohort was established to provide unique opportunities to study the genetic and environmental contributions to human disease as well as ageing process. The aim of this report was to describe the genomic data included in CLSA. PARTICIPANTS A total of 26 622 individuals from the CLSA Comprehensive cohort of men and women aged 45-85 recruited between 2010 and 2015 underwent genome-wide genotyping of DNA samples collected from blood. Comprehensive quality control metrics were measured for genetic markers and samples, respectively. The genotypes were imputed to the TOPMed reference panel. Sex chromosome abnormalities were identified by copy number profiling. Classical human leukocyte antigen gene haplotypes were imputed at two-field (four-digit). FINDINGS TO DATE Of the 26 622 genotyped participants, 24 655 (92.6%) were identified as having European ancestry. These genomic data were linked to physical, lifestyle, medical, economic, environmental and psychosocial factors collected longitudinally in CLSA. The combined analysis, including CLSA genomic data, uncovered over 100 novel loci associated with key parameters to define glaucoma. The CLSA genomic dataset validated the contribution of a polygenic risk score to screen individuals with high fracture risk. It is also a valuable resource to directly identify common genetic variations associated with conditions related to complex traits. Taking advantage of the comprehensive interview and physical information collected in CLSA, this genomic dataset has been linked to psychosocial factors to investigate both the independent and interactive effects on cardiovascular disease. FUTURE PLANS The CLSA overall is ongoing. Follow-up data will continue to be collected from participants in the current genomic subcohort, including the DNA methylation and metabolomic data. Ongoing studies focus on elucidating the role of genetic factors in cognitive decline and cardiovascular diseases. This genomic data resource is available on request through the CLSA data access application process.
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Affiliation(s)
- Vincenzo Forgetta
- Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada
| | - Rui Li
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Corinne Darmond-Zwaig
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Alexandre Belisle
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Cynthia Balion
- Hamilton Regional Laboratory Medicine Program, McMaster University, St. Joseph's Hospital St. Luke's Wing, Hamilton, ON, Canada
| | - Delnaz Roshandel
- Genetics & Genomic Biology, The Hospital for Sick Children Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christina Wolfson
- Department of Medicine & of Epidemiology and Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
| | - Guillaume Lettre
- Montréal Heart Institute and Université de Montréal, Montréal, QC, Canada
| | - Guillaume Pare
- Hamilton Regional Laboratory Medicine Program, McMaster University, St. Joseph's Hospital St. Luke's Wing, Hamilton, ON, Canada
| | - Andrew D Paterson
- Genetics & Genomic Biology, The Hospital for Sick Children Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Lauren E Griffith
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Chris Verschoor
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Mark Lathrop
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Susan Kirkland
- Department of Community Health and Epidemiology, Division of Geriatric Medicine, Dalhousie University, Halifax, NS, Canada
| | - Parminder Raina
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - J Brent Richards
- Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada
- Department of Medicine & of Epidemiology and Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jiannis Ragoussis
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Bioengineering, McGill University, Montréal, QC, Canada
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Abstract
Vitamin D supplementation can prevent and cure nutritional rickets in infants and children. Preclinical and observational data suggest that the vitamin D endocrine system has a wide spectrum of skeletal and extra-skeletal activities. There is consensus that severe vitamin D deficiency (serum 25-hydroxyvitamin D (25OHD) concentration <30 nmol/l) should be corrected, whereas most guidelines recommend serum 25OHD concentrations of >50 nmol/l for optimal bone health in older adults. However, the causal link between vitamin D and many extra-skeletal outcomes remains unclear. The VITAL, ViDA and D2d randomized clinical trials (combined number of participants >30,000) indicated that vitamin D supplementation of vitamin D-replete adults (baseline serum 25OHD >50 nmol/l) does not prevent cancer, cardiovascular events, falls or progression to type 2 diabetes mellitus. Post hoc analysis has suggested some extra-skeletal benefits for individuals with vitamin D deficiency. Over 60 Mendelian randomization studies, designed to minimize bias from confounding, have evaluated the consequences of lifelong genetically lowered serum 25OHD concentrations on various outcomes and most studies have found null effects. Four Mendelian randomization studies found an increased risk of multiple sclerosis in individuals with genetically lowered serum 25OHD concentrations. In conclusion, supplementation of vitamin D-replete individuals does not provide demonstrable health benefits. This conclusion does not contradict older guidelines that severe vitamin D deficiency should be prevented or corrected.
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Affiliation(s)
- Roger Bouillon
- Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium.
| | - Despoina Manousaki
- Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Cliff Rosen
- Maine Medical Center Research Institute, Scarborough, ME, USA
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Fernando Rivadeneira
- Translational Skeletal Genomics, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - J Brent Richards
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montreal, Quebec, Canada
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Huffman JE, Butler-Laporte G, Khan A, Pairo-Castineira E, Drivas TG, Peloso GM, Nakanishi T, Ganna A, Verma A, Baillie JK, Kiryluk K, Richards JB, Zeberg H. Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19. Nat Genet 2022; 54:125-127. [PMID: 35027740 PMCID: PMC8837537 DOI: 10.1038/s41588-021-00996-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [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: 03/14/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023]
Abstract
The OAS1/2/3 cluster has been identified as a risk locus for severe COVID-19 among individuals of European ancestry, with a protective haplotype of approximately 75 kilobases (kb) derived from Neanderthals in the chromosomal region 12q24.13. This haplotype contains a splice variant of OAS1, which occurs in people of African ancestry independently of gene flow from Neanderthals. Using trans-ancestry fine-mapping approaches in 20,779 hospitalized cases, we demonstrate that this splice variant is likely to be the SNP responsible for the association at this locus, thus strongly implicating OAS1 as an effector gene influencing COVID-19 severity.
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Affiliation(s)
- Jennifer E Huffman
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Guillaume Butler-Laporte
- Departments of Medicine, Human Genetics, Epidemiology, Biostatistics and Occupational Health, McGill University, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Theodore G Drivas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania,, Philadelphia, PA, USA
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gina M Peloso
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Tomoko Nakanishi
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania,, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - J Brent Richards
- Departments of Medicine, Human Genetics, Epidemiology, Biostatistics and Occupational Health, McGill University, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Department of Twin Research, King's College London, London, UK
| | - Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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Yazdanpanah N, Yazdanpanah M, Wang Y, Forgetta V, Pollak M, Polychronakos C, Richards JB, Manousaki D. Clinically Relevant Circulating Protein Biomarkers for Type 1 Diabetes: Evidence From a Two-Sample Mendelian Randomization Study. Diabetes Care 2022; 45:169-177. [PMID: 34758976 DOI: 10.2337/dc21-1049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/18/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To identify circulating proteins influencing type 1 diabetes susceptibility using Mendelian randomization (MR). RESEARCH DESIGN AND METHODS We used a large-scale two-sample MR study, using cis genetic determinants (protein quantitative trait loci [pQTL]) of up to 1,611 circulating proteins from five large genome-wide association studies, to screen for causal associations of these proteins with type 1 diabetes risk in 9,684 case subjects with type 1 diabetes and 15,743 control subjects. Further, pleiotropy-robust MR methods were used in sensitivity analyses using both cis and trans-pQTL. RESULTS We found that a genetically predicted SD increase in signal regulatory protein gamma (SIRPG) level was associated with increased risk of type 1 diabetes risk (MR odds ratio [OR] 1.66 [95% 1.36-2.03]; P = 7.1 × 10-7). The risk of type 1 diabetes increased almost twofold per genetically predicted standard deviation (SD) increase in interleukin-27 Epstein-Barr virus-induced 3 (IL27-EBI3) protein levels (MR OR 1.97 [95% CI 1.48-2.62]; P = 3.7 × 10-6). However, an SD increase in chymotrypsinogen B1 (CTRB1) was associated with decreased risk of type 1 diabetes (MR OR 0.84 [95% CI 0.77-0.90]; P = 6.1 × 10-6). Sensitivity analyses using MR methods testing for pleiotropy while including trans-pQTL showed similar results. While the MR-Egger suggested no pleotropic effect (P value MR-Egger intercept = 0.31), there was evidence of pleiotropy in MR-PRESSO (P value global test = 0.006). CONCLUSIONS We identified three novel circulating protein biomarkers associated with type 1 diabetes risk using an MR approach. These biomarkers are promising targets for development of drugs and/or of screening tools for early prediction of type 1 diabetes.
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Affiliation(s)
- Nahid Yazdanpanah
- 1Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Mojgan Yazdanpanah
- 1Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Ye Wang
- 2Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Vincenzo Forgetta
- 2Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Michael Pollak
- 2Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,3Department of Medicine, McGill University, Montreal, Quebec, Canada.,4Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Constantin Polychronakos
- 5Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,6Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,7Centre of Excellence in Translational Immunology, Montreal, Quebec, Canada
| | - J Brent Richards
- 2Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,3Department of Medicine, McGill University, Montreal, Quebec, Canada.,6Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,8Department of Epidemiology and Biostatistics, McGill University, Montreal, Quebec, Canada.,9Department of Twin Research, King's College London, London, U.K
| | - Despoina Manousaki
- 1Research Center of the Sainte-Justine University Hospital, University of Montreal, Montreal, Quebec, Canada.,10Departments of Pediatrics, Biochemistry and Molecular Medicine, University of Montreal, Montreal, Quebec, Canada
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Yoshiji S, Tanaka D, Minamino H, Lu T, Butler-Laporte G, Murakami T, Fujita Y, Richards JB, Inagaki N. Causal associations between body fat accumulation and COVID-19 severity: A Mendelian randomization study. Front Endocrinol (Lausanne) 2022; 13:899625. [PMID: 35992131 PMCID: PMC9381824 DOI: 10.3389/fendo.2022.899625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/29/2022] [Indexed: 12/05/2022] Open
Abstract
Previous studies reported associations between obesity measured by body mass index (BMI) and coronavirus disease 2019 (COVID-19). However, BMI is calculated only with height and weight and cannot distinguish between body fat mass and fat-free mass. Thus, it is not clear if one or both of these measures are mediating the relationship between obesity and COVID-19. Here, we used Mendelian randomization (MR) to compare the independent causal relationships of body fat mass and fat-free mass with COVID-19 severity. We identified single nucleotide polymorphisms associated with body fat mass and fat-free mass in 454,137 and 454,850 individuals of European ancestry from the UK Biobank, respectively. We then performed two-sample MR to ascertain their effects on severe COVID-19 (cases: 4,792; controls: 1,054,664) from the COVID-19 Host Genetics Initiative. We found that an increase in body fat mass by one standard deviation was associated with severe COVID-19 (odds ratio (OR)body fat mass = 1.61, 95% confidence interval [CI]: 1.28-2.04, P = 5.51 × 10-5; ORbody fat-free mass = 1.31, 95% CI: 0.99-1.74, P = 5.77 × 10-2). Considering that body fat mass and fat-free mass were genetically correlated with each other (r = 0.64), we further evaluated independent causal effects of body fat mass and fat-free mass using multivariable MR and revealed that only body fat mass was independently associated with severe COVID-19 (ORbody fat mass = 2.91, 95% CI: 1.71-4.96, P = 8.85 × 10-5 and ORbody fat-free mass = 1.02, 95%CI: 0.61-1.67, P = 0.945). In summary, this study demonstrates the causal effects of body fat accumulation on COVID-19 severity and indicates that the biological pathways influencing the relationship between COVID-19 and obesity are likely mediated through body fat mass.
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Affiliation(s)
- Satoshi Yoshiji
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Kyoto-McGill International Collaborative Program in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Daisuke Tanaka
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroto Minamino
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Tianyuan Lu
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Quantitative Life Sciences Program, McGill University, Montréal, QC, Canada
| | - Guillaume Butler-Laporte
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
| | - Takaaki Murakami
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihito Fujita
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - J. Brent Richards
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Centre for Clinical Epidemiology, Department of Medicine, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
- 5 Prime Sciences, Montréal, QC, Canada
- *Correspondence: J. Brent Richards, ; Nobuya Inagaki,
| | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- *Correspondence: J. Brent Richards, ; Nobuya Inagaki,
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Kim PG, Niroula A, Shkolnik V, McConkey M, Lin AE, Słabicki M, Kemp JP, Bick A, Gibson CJ, Griffin G, Sekar A, Brooks DJ, Wong WJ, Cohen DN, Uddin MM, Shin WJ, Pirruccello J, Tsai JM, Agrawal M, Kiel DP, Bouxsein ML, Richards JB, Evans DM, Wein MN, Charles JF, Jaiswal S, Natarajan P, Ebert BL. Dnmt3a-mutated clonal hematopoiesis promotes osteoporosis. J Exp Med 2021; 218:e20211872. [PMID: 34698806 PMCID: PMC8552148 DOI: 10.1084/jem.20211872] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/18/2022] Open
Abstract
Osteoporosis is caused by an imbalance of osteoclasts and osteoblasts, occurring in close proximity to hematopoietic cells in the bone marrow. Recurrent somatic mutations that lead to an expanded population of mutant blood cells is termed clonal hematopoiesis of indeterminate potential (CHIP). Analyzing exome sequencing data from the UK Biobank, we found CHIP to be associated with increased incident osteoporosis diagnoses and decreased bone mineral density. In murine models, hematopoietic-specific mutations in Dnmt3a, the most commonly mutated gene in CHIP, decreased bone mass via increased osteoclastogenesis. Dnmt3a-/- demethylation opened chromatin and altered activity of inflammatory transcription factors. Bone loss was driven by proinflammatory cytokines, including Irf3-NF-κB-mediated IL-20 expression from Dnmt3a mutant macrophages. Increased osteoclastogenesis due to the Dnmt3a mutations was ameliorated by alendronate or IL-20 neutralization. These results demonstrate a novel source of osteoporosis-inducing inflammation.
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Affiliation(s)
- Peter Geon Kim
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Abhishek Niroula
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Veronica Shkolnik
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Marie McConkey
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Amy E. Lin
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - John P. Kemp
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Alexander Bick
- Division of Genetic Medicine, Vanderbilt University, Nashville, TN
| | | | - Gabriel Griffin
- Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Aswin Sekar
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Daniel J. Brooks
- Center for Advanced Orthopedic Studies, Beth Israel Deaconess Medical Center, Boston, MA
| | - Waihay J. Wong
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Drew N. Cohen
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Md Mesbah Uddin
- Broad Institute of Harvard and MIT, Cambridge, MA
- Center for Genomic Medicine, Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Wesley J. Shin
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - James Pirruccello
- Center for Genomic Medicine, Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jonathan M. Tsai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Mridul Agrawal
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | - Douglas P. Kiel
- Broad Institute of Harvard and MIT, Cambridge, MA
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA
| | - Mary L. Bouxsein
- Center for Advanced Orthopedic Studies, Beth Israel Deaconess Medical Center, Boston, MA
| | - J. Brent Richards
- Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital, and Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - David M. Evans
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Marc N. Wein
- Broad Institute of Harvard and MIT, Cambridge, MA
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Julia F. Charles
- Department of Orthopaedic Surgery, Brigham and Women’s Hospital, Boston, MA
| | - Siddhartha Jaiswal
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA
| | - Pradeep Natarajan
- Broad Institute of Harvard and MIT, Cambridge, MA
- Center for Genomic Medicine, Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
- Howard Hughes Medical Institute, Boston, MA
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40
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Butler-Laporte G, Richards JB. WITHDRAWN: Targeting of vitamin D supplementation to individuals with deficiency. Lancet Diabetes Endocrinol 2021; 9:803-804. [PMID: 34717823 DOI: 10.1016/s2213-8587(21)00282-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/21/2022]
Affiliation(s)
- Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2; Department of Epidemiology, Biostatistics and Occupational Health, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2; Department of Epidemiology, Biostatistics and Occupational Health, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Department of Twin Research, King's College London, London, UK.
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Brunet-Ratnasingham E, Anand SP, Gantner P, Dyachenko A, Moquin-Beaudry G, Brassard N, Beaudoin-Bussières G, Pagliuzza A, Gasser R, Benlarbi M, Point F, Prévost J, Laumaea A, Niessl J, Nayrac M, Sannier G, Orban C, Messier-Peet M, Butler-Laporte G, Morrison DR, Zhou S, Nakanishi T, Boutin M, Descôteaux-Dinelle J, Gendron-Lepage G, Goyette G, Bourassa C, Medjahed H, Laurent L, Rébillard RM, Richard J, Dubé M, Fromentin R, Arbour N, Prat A, Larochelle C, Durand M, Richards JB, Chassé M, Tétreault M, Chomont N, Finzi A, Kaufmann DE. Integrated immunovirological profiling validates plasma SARS-CoV-2 RNA as an early predictor of COVID-19 mortality. Sci Adv 2021; 7:eabj5629. [PMID: 34826237 PMCID: PMC8626074 DOI: 10.1126/sciadv.abj5629] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Despite advances in COVID-19 management, identifying patients evolving toward death remains challenging. To identify early predictors of mortality within 60 days of symptom onset (DSO), we performed immunovirological assessments on plasma from 279 individuals. On samples collected at DSO11 in a discovery cohort, high severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA (vRNA), low receptor binding domain–specific immunoglobulin G and antibody-dependent cellular cytotoxicity, and elevated cytokines and tissue injury markers were strongly associated with mortality, including in patients on mechanical ventilation. A three-variable model of vRNA, with predefined adjustment by age and sex, robustly identified patients with fatal outcome (adjusted hazard ratio for log-transformed vRNA = 3.5). This model remained robust in independent validation and confirmation cohorts. Since plasma vRNA’s predictive accuracy was maintained at earlier time points, its quantitation can help us understand disease heterogeneity and identify patients who may benefit from new therapies.
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Affiliation(s)
- Elsa Brunet-Ratnasingham
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Sai Priya Anand
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Pierre Gantner
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Alina Dyachenko
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Gaël Moquin-Beaudry
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Department of Neuroscience, Université de Montréal, Montréal, QC, Canada
| | - Nathalie Brassard
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Guillaume Beaudoin-Bussières
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Amélie Pagliuzza
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Romain Gasser
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Mehdi Benlarbi
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Floriane Point
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Jérémie Prévost
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Annemarie Laumaea
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Julia Niessl
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Manon Nayrac
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Gérémy Sannier
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Catherine Orban
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- Centre hospitalier de l’Université de Montréal (CHUM), Montréal, QC, Canada
| | - Marc Messier-Peet
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Centre hospitalier de l’Université de Montréal (CHUM), Montréal, QC, Canada
| | - Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - David R. Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Sirui Zhou
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, 102-0083 Tokyo, Japan
| | - Marianne Boutin
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Jade Descôteaux-Dinelle
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Gabrielle Gendron-Lepage
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Guillaume Goyette
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Catherine Bourassa
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Halima Medjahed
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Laetitia Laurent
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Rose-Marie Rébillard
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Department of Neuroscience, Université de Montréal, Montréal, QC, Canada
| | - Jonathan Richard
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Rémi Fromentin
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Nathalie Arbour
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Department of Neuroscience, Université de Montréal, Montréal, QC, Canada
| | - Alexandre Prat
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Department of Neuroscience, Université de Montréal, Montréal, QC, Canada
| | - Catherine Larochelle
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Department of Neuroscience, Université de Montréal, Montréal, QC, Canada
| | - Madeleine Durand
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Centre hospitalier de l’Université de Montréal (CHUM), Montréal, QC, Canada
| | - J. Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Twin Research, King’s College London, London, UK
| | - Michaël Chassé
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Centre hospitalier de l’Université de Montréal (CHUM), Montréal, QC, Canada
| | - Martine Tétreault
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Department of Neuroscience, Université de Montréal, Montréal, QC, Canada
| | - Nicolas Chomont
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- Corresponding author. (N.C.); (A.F.); (D.E.K.)
| | - Andrés Finzi
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Corresponding author. (N.C.); (A.F.); (D.E.K.)
| | - Daniel E. Kaufmann
- Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- Centre hospitalier de l’Université de Montréal (CHUM), Montréal, QC, Canada
- Département de Médecine, Université de Montréal, Montréal, QC, Canada
- Corresponding author. (N.C.); (A.F.); (D.E.K.)
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Chen Y, Forgetta V, Richards JB, Zhou S. Health Effects of Calcium: Evidence From Mendelian Randomization Studies. JBMR Plus 2021; 5:e10542. [PMID: 34761146 PMCID: PMC8567492 DOI: 10.1002/jbm4.10542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/23/2021] [Accepted: 08/03/2021] [Indexed: 12/24/2022] Open
Abstract
Calcium is widely used in conjunction with vitamin D to prevent osteoporosis. The use of calcium supplementation is also promoted for its potential benefits in lowering the risk for metabolic syndromes and cancers. However, the causal link between calcium and various health outcomes remains unclear. This review focuses on the evidence from 24 Mendelian randomization (MR) studies that were designed to minimize bias from confounding and reverse causation. These MR studies evaluated the effect of lifelong genetically higher serum calcium levels on various health outcomes. Overall, available MR studies found no conclusive effects of serum calcium levels on bone mineral density and fracture, ischemic stroke and heart failure, cancers, type 2 diabetes, Parkinson disease, or offspring birth weight. However, a higher serum calcium concentration was reported to have estimated causal effects on increased risks for coronary artery disease (especially myocardial infarction), migraine, renal colic, allergy/adverse effect of penicillin, and reduced risks for osteoarthrosis and osteoarthritis. In conclusion, supplementation of calcium in individuals from the general population is not predicted to influence the risk of most investigated diseases to date. Moreover, long-term high serum calcium concentrations may result in adverse health outcomes. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Yiheng Chen
- Department of Human GeneticsMcGill UniversityMontréalQCCanada
- Lady Davis Institute, Jewish General HospitalMcGill UniversityMontréalQCCanada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General HospitalMcGill UniversityMontréalQCCanada
| | - J. Brent Richards
- Department of Human GeneticsMcGill UniversityMontréalQCCanada
- Lady Davis Institute, Jewish General HospitalMcGill UniversityMontréalQCCanada
- Department of Epidemiology, Biostatistics and Occupational HealthMcGill UniversityMontréalQCCanada
- Department of Twin ResearchKing's College LondonLondonUK
| | - Sirui Zhou
- Lady Davis Institute, Jewish General HospitalMcGill UniversityMontréalQCCanada
- Department of Epidemiology, Biostatistics and Occupational HealthMcGill UniversityMontréalQCCanada
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Skrivankova VW, Richmond RC, Woolf BAR, Davies NM, Swanson SA, VanderWeele TJ, Timpson NJ, Higgins JPT, Dimou N, Langenberg C, Loder EW, Golub RM, Egger M, Davey Smith G, Richards JB. Strengthening the reporting of observational studies in epidemiology using mendelian randomisation (STROBE-MR): explanation and elaboration. BMJ 2021; 375:n2233. [PMID: 34702754 PMCID: PMC8546498 DOI: 10.1136/bmj.n2233] [Citation(s) in RCA: 342] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/02/2021] [Indexed: 12/15/2022]
Affiliation(s)
| | - Rebecca C Richmond
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Benjamin A R Woolf
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Psychological Science, University of Bristol, Bristol, UK
| | - Neil M Davies
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- K G Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sonja A Swanson
- Department of Epidemiology, Erasmus MC, Rotterdam, Netherlands
| | - Tyler J VanderWeele
- Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Nicholas J Timpson
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Julian P T Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Niki Dimou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, Lyon, France
| | - Claudia Langenberg
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | | | - Robert M Golub
- JAMA, Chicago, IL, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - J Brent Richards
- Departments of Medicine, Human Genetics, Epidemiology & Biostatistics, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, University of London, London, UK
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Skrivankova VW, Richmond RC, Woolf BAR, Yarmolinsky J, Davies NM, Swanson SA, VanderWeele TJ, Higgins JPT, Timpson NJ, Dimou N, Langenberg C, Golub RM, Loder EW, Gallo V, Tybjaerg-Hansen A, Davey Smith G, Egger M, Richards JB. Strengthening the Reporting of Observational Studies in Epidemiology Using Mendelian Randomization: The STROBE-MR Statement. JAMA 2021; 326:1614-1621. [PMID: 34698778 DOI: 10.1001/jama.2021.18236] [Citation(s) in RCA: 710] [Impact Index Per Article: 236.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Importance Mendelian randomization (MR) studies use genetic variation associated with modifiable exposures to assess their possible causal relationship with outcomes and aim to reduce potential bias from confounding and reverse causation. Objective To develop the STROBE-MR Statement as a stand-alone extension to the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guideline for the reporting of MR studies. Design, Setting, and Participants The development of the STROBE-MR Statement followed the Enhancing the Quality and Transparency of Health Research (EQUATOR) framework guidance and used the STROBE Statement as a starting point to draft a checklist tailored to MR studies. The project was initiated in 2018 by reviewing the literature on the reporting of instrumental variable and MR studies. A group of 17 experts, including MR methodologists, MR study design users, developers of previous reporting guidelines, and journal editors, participated in a workshop in May 2019 to define the scope of the Statement and draft the checklist. The draft checklist was published as a preprint in July 2019 and discussed on the preprint platform, in social media, and at the 4th Mendelian Randomization Conference. The checklist was then revised based on comments, further refined through 2020, and finalized in July 2021. Findings The STROBE-MR checklist is organized into 6 sections (Title and Abstract, Introduction, Methods, Results, Discussion, and Other Information) and includes 20 main items and 30 subitems. It covers both 1-sample and 2-sample MR studies that assess 1 or multiple exposures and outcomes, and addresses MR studies that follow a genome-wide association study and are reported in the same article. The checklist asks authors to justify why MR is a helpful method to address the study question and state prespecified causal hypotheses. The measurement, quality, and selection of genetic variants must be described and attempts to assess validity of MR-specific assumptions should be well reported. An item on data sharing includes reporting when the data and statistical code required to replicate the analyses can be accessed. Conclusions and Relevance STROBE-MR provides guidelines for reporting MR studies. Improved reporting of these studies could facilitate their evaluation by editors, peer reviewers, researchers, clinicians, and other readers, and enhance the interpretation of their results.
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Affiliation(s)
| | - Rebecca C Richmond
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Benjamin A R Woolf
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Department of Psychological Science, University of Bristol, Bristol, United Kingdom
| | - James Yarmolinsky
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Neil M Davies
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Norway
| | - Sonja A Swanson
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Tyler J VanderWeele
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Julian P T Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- NIHR Bristol Biomedical Research Centre, Bristol, United Kingdom
| | - Nicholas J Timpson
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Niki Dimou
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Robert M Golub
- JAMA , Chicago, Illinois
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Elizabeth W Loder
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- BMJ , London, United Kingdom
| | - Valentina Gallo
- Campus Fryslân, University of Groningen, Leeuwarden, the Netherlands
- Institute of Population Health Sciences, Queen Mary, University of London, London, United Kingdom
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Anne Tybjaerg-Hansen
- Section for Molecular Genetics, Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- NIHR Bristol Biomedical Research Centre, Bristol, United Kingdom
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
| | - J Brent Richards
- Departments of Medicine, Human Genetics, Epidemiology, & Biostatistics, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Department of Twin Research and Genetic Epidemiology, King's College London, University of London, London, United Kingdom
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Nakanishi T, Pigazzini S, Degenhardt F, Cordioli M, Butler-Laporte G, Maya-Miles D, Bujanda L, Bouysran Y, Niemi ME, Palom A, Ellinghaus D, Khan A, Martínez-Bueno M, Rolker S, Amitrano S, Roade Tato L, Fava F, Spinner CD, Prati D, Bernardo D, Garcia F, Darcis G, Fernandez-Cadenas I, Holter JC, Banales JM, Frithiof R, Kiryluk K, Duga S, Asselta R, Pereira AC, Romero-Gómez M, Nafría-Jiménez B, Hov JR, Migeotte I, Renieri A, Planas AM, Ludwig KU, Buti M, Rahmouni S, Alarcón-Riquelme ME, Schulte EC, Franke A, Karlsen TH, Valenti L, Zeberg H, Richards JB, Ganna A. Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality. J Clin Invest 2021; 131:152386. [PMID: 34597274 DOI: 10.1172/jci152386] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND There is considerable variability in COVID-19 outcomes amongst younger adults-and some of this variation may be due to genetic predisposition. METHODS We combined individual level data from 13,888 COVID-19 patients (N=7,185 hospitalized) from 17 cohorts in nine countries to assess the association of the major common COVID-19 genetic risk factor (chromosome 3 locus tagged by rs10490770) with mortality, COVID-19-related complications and laboratory values. We next performed meta-analyses using FinnGen and the Columbia University COVID-19 Biobank. RESULTS We found that rs10490770 risk allele carriers experienced an increased risk of all-cause mortality (HR 1.4, 95%CI 1.2-1.7). Risk allele carriers had increased odds of several COVID-19 complications: severe respiratory failure (OR 2.1, 95%CI 1.6-2.6), venous thromboembolism (OR 1.7, 95%CI 1.2-2.4), and hepatic injury (OR 1.5, 95%CI 1.2-2.0). Risk allele carriers ≤60 years had higher odds of death or severe respiratory failure (OR 2.7, 95%CI 1.8-3.9) compared to those >60 years (OR 1.5, 95%CI 1.2-1.8, interaction-p=0.038). Amongst individuals ≤60 years who died or experienced severe respiratory failure, 32.3% were risk variant carriers, compared to 13.9% of those not experiencing these outcomes. The genetic risk improved the prediction of death or severe respiratory failure similarly to, or better than, most established clinical risk factors. CONCLUSIONS The major common COVID-19 genetic risk factor is associated with increased risks of morbidity and mortality, which are more pronounced amongst individuals ≤60 years. The effect was similar in magnitude and more common than most established clinical risk factors, suggesting potential implications for future clinical risk management.
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Affiliation(s)
- Tomoko Nakanishi
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Sara Pigazzini
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Mattia Cordioli
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
| | | | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Donostia University Hospital, University of Basque Country, San Sebastian, Spain
| | - Youssef Bouysran
- Centre de Génétique Humaine, Hôpital Erasme-Université Libre de Bruxelles, Brussels, Belgium
| | - Mari Ek Niemi
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Adriana Palom
- Department of Internal Medicine, Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - David Ellinghaus
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Atlas Khan
- Department of Medicine, Columbia University, New York, United States of America
| | | | - Selina Rolker
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Sara Amitrano
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Luisa Roade Tato
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digest, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Christoph D Spinner
- Department of Internal Medicine II, University Hospital rechts der Isar, Munich, Germany
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Università degli Studi di Milano, Milano, Italy
| | - David Bernardo
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digest, Instituto de Salud Carlos III, Madrid, Spain
| | - Federico Garcia
- Department of Pathology, Hospital Virgen del Camino, Pamplona, Spain
| | - Gilles Darcis
- Infectious Diseases Department, Liège University Hospital, Liège, Belgium
| | - Israel Fernandez-Cadenas
- Stroke Pharmacogenomics and Genetics Group, Biomedical Research Institute Sant Pau, Barcelona, Spain
| | - Jan Cato Holter
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jesus M Banales
- Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain
| | - Robert Frithiof
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University, New York, United States of America
| | - Stefano Duga
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Rosanna Asselta
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | | | | | - Johannes R Hov
- Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Isabelle Migeotte
- Centre de Génétique Humaine, Hôpital Erasme-Université Libre de Bruxelles, Brussels, Belgium
| | - Alessandra Renieri
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Anna M Planas
- Department of Brain Ischemia and Neurodegeneration, Institute for Biomedical Research of Barcelona, Barcelona, Spain
| | | | - Maria Buti
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digest, Instituto de Salud Carlos III, Madrid, Spain
| | - Souad Rahmouni
- GIGA-R, Laboratory of Immunology and Infectious Diseases, University of Liège, Liège, Belgium
| | | | - Eva C Schulte
- Institute of Virology, Technical University Munich/Helmholtz Zentrum, Munich, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Tom H Karlsen
- Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Solna, Sweden
| | | | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
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46
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Escribe C, Lu T, Keller-Baruch J, Forgetta V, Xiao B, Richards JB, Bhatnagar S, Oualkacha K, Greenwood CMT. Block coordinate descent algorithm improves variable selection and estimation in error-in-variables regression. Genet Epidemiol 2021; 45:874-890. [PMID: 34468045 PMCID: PMC9292988 DOI: 10.1002/gepi.22430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/22/2021] [Revised: 07/19/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022]
Abstract
Medical research increasingly includes high‐dimensional regression modeling with a need for error‐in‐variables methods. The Convex Conditioned Lasso (CoCoLasso) utilizes a reformulated Lasso objective function and an error‐corrected cross‐validation to enable error‐in‐variables regression, but requires heavy computations. Here, we develop a Block coordinate Descent Convex Conditioned Lasso (BDCoCoLasso) algorithm for modeling high‐dimensional data that are only partially corrupted by measurement error. This algorithm separately optimizes the estimation of the uncorrupted and corrupted features in an iterative manner to reduce computational cost, with a specially calibrated formulation of cross‐validation error. Through simulations, we show that the BDCoCoLasso algorithm successfully copes with much larger feature sets than CoCoLasso, and as expected, outperforms the naïve Lasso with enhanced estimation accuracy and consistency, as the intensity and complexity of measurement errors increase. Also, a new smoothly clipped absolute deviation penalization option is added that may be appropriate for some data sets. We apply the BDCoCoLasso algorithm to data selected from the UK Biobank. We develop and showcase the utility of covariate‐adjusted genetic risk scores for body mass index, bone mineral density, and lifespan. We demonstrate that by leveraging more information than the naïve Lasso in partially corrupted data, the BDCoCoLasso may achieve higher prediction accuracy. These innovations, together with an R package, BDCoCoLasso, make error‐in‐variables adjustments more accessible for high‐dimensional data sets. We posit the BDCoCoLasso algorithm has the potential to be widely applied in various fields, including genomics‐facilitated personalized medicine research.
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Affiliation(s)
- Célia Escribe
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Québec, Canada.,Operations Research Center, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Québec, Canada.,Quantitative Life Sciences Program, McGill University, Montreal, Québec, Canada
| | - Julyan Keller-Baruch
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Québec, Canada.,Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Québec, Canada
| | - Bowei Xiao
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Québec, Canada.,Quantitative Life Sciences Program, McGill University, Montreal, Québec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Québec, Canada.,Department of Human Genetics, McGill University, Montreal, Québec, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Québec, Canada.,Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Sahir Bhatnagar
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Québec, Canada.,Department of Diagnostic Radiology, McGill University, Montreal, Québec, Canada
| | - Karim Oualkacha
- Département de Mathématiques, Université du Québec à Montréal, Montreal, Québec, Canada
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Québec, Canada.,Department of Human Genetics, McGill University, Montreal, Québec, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Québec, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Québec, Canada
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47
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Wu H, Luan J, Forgetta V, Engert JC, Thanassoulis G, Mooser V, Wareham NJ, Langenberg C, Richards JB. Utility of Genetically Predicted Lp(a) (Lipoprotein [a]) and ApoB Levels for Cardiovascular Risk Assessment. Circ Genom Precis Med 2021; 14:e003312. [PMID: 34461734 DOI: 10.1161/circgen.121.003312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND Current lipid guidelines suggest measurement of Lp(a) (lipoprotein[a]) and ApoB (apolipoprotein B) for atherosclerotic cardiovascular disease risk assessment. Polygenic risk scores (PRSs) for Lp(a) and ApoB may identify individuals unlikely to have elevated Lp(a) or ApoB and thus reduce such suggested testing. METHODS PRSs were developed using least absolute shrinkage and selection operator regression among 273 222 and 356 958 UK Biobank participants of white British ancestry for Lp(a) and ApoB, respectively, and validated in separate sets of 60 771 UK Biobank and 15 050 European Prospective Investigation into Cancer and Nutrition-Norfolk participants. We then assessed the proportion of participants who, based on these PRSs, were unlikely to benefit from Lp(a) or ApoB measurements, according to current lipid guidelines. RESULTS In the UK Biobank and European Prospective Investigation into Cancer and Nutrition-Norfolk cohorts, the area under the receiver operating curve for the PRS-predicted Lp(a) and ApoB to identify individuals with elevated Lp(a) and ApoB was at least 0.91 (95% CI, 0.90-0.92) and 0.74 (95% CI, 0.73-0.75), respectively. The Lp(a) PRS and measured Lp(a) showed comparable association with atherosclerotic cardiovascular disease incidence, whereas the ApoB PRS was in general less predictive of atherosclerotic cardiovascular disease risk than measured ApoB. In the context of the European Society of Cardiology/European Atherosclerosis Society lipid guidelines, at a 95% sensitivity to identify individuals with elevated Lp(a) and ApoB levels, at least 54% of Lp(a) and 24% of ApoB testing could be reduced by prescreening with a PRS while maintaining a low false-negative rate. CONCLUSIONS A substantial proportion of suggested testing for elevated Lp(a) and a modest proportion of testing for elevated ApoB could potentially be reduced by prescreening individuals with PRSs.
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Affiliation(s)
- Haoyu Wu
- Department of Epidemiology, Biostatistics and Occupational Health (H.W., J.B.R.), McGill University, Montréal, Québec, Canada.,Center for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital (H.W., V.F., J.B.R.), McGill University, Montréal, Québec, Canada
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge, United Kingdom (J.L., N.J.W., C.L.)
| | - Vincenzo Forgetta
- Center for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital (H.W., V.F., J.B.R.), McGill University, Montréal, Québec, Canada
| | - James C Engert
- Department of Medicine (J.C.E., G.T.), McGill University, Montréal, Québec, Canada.,Department of Human Genetics (J.C.E., G.T., V.M., J.B.R.), McGill University, Montréal, Québec, Canada.,McGill University Health Centre Research Institute, Montreal, Québec, Canada (J.C.E., G.T.)
| | - George Thanassoulis
- Department of Medicine (J.C.E., G.T.), McGill University, Montréal, Québec, Canada.,Department of Human Genetics (J.C.E., G.T., V.M., J.B.R.), McGill University, Montréal, Québec, Canada.,McGill University Health Centre Research Institute, Montreal, Québec, Canada (J.C.E., G.T.)
| | - Vincent Mooser
- Department of Human Genetics (J.C.E., G.T., V.M., J.B.R.), McGill University, Montréal, Québec, Canada
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge, United Kingdom (J.L., N.J.W., C.L.)
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, United Kingdom (J.L., N.J.W., C.L.)
| | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health (H.W., J.B.R.), McGill University, Montréal, Québec, Canada.,Center for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital (H.W., V.F., J.B.R.), McGill University, Montréal, Québec, Canada.,Department of Human Genetics (J.C.E., G.T., V.M., J.B.R.), McGill University, Montréal, Québec, Canada.,Department of Twin Research, King's College London, United Kingdom (J.B.R.)
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48
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Nilsson KH, Henning P, El Shahawy M, Nethander M, Andersen TL, Ejersted C, Wu J, Gustafsson KL, Koskela A, Tuukkanen J, Souza PPC, Tuckermann J, Lorentzon M, Ruud LE, Lehtimäki T, Tobias JH, Zhou S, Lerner UH, Richards JB, Movérare-Skrtic S, Ohlsson C. RSPO3 is important for trabecular bone and fracture risk in mice and humans. Nat Commun 2021; 12:4923. [PMID: 34389713 PMCID: PMC8363747 DOI: 10.1038/s41467-021-25124-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 01/21/2021] [Accepted: 07/19/2021] [Indexed: 11/22/2022] Open
Abstract
With increasing age of the population, countries across the globe are facing a substantial increase in osteoporotic fractures. Genetic association signals for fractures have been reported at the RSPO3 locus, but the causal gene and the underlying mechanism are unknown. Here we show that the fracture reducing allele at the RSPO3 locus associate with increased RSPO3 expression both at the mRNA and protein levels, increased trabecular bone mineral density and reduced risk mainly of distal forearm fractures in humans. We also demonstrate that RSPO3 is expressed in osteoprogenitor cells and osteoblasts and that osteoblast-derived RSPO3 is the principal source of RSPO3 in bone and an important regulator of vertebral trabecular bone mass and bone strength in adult mice. Mechanistic studies revealed that RSPO3 in a cell-autonomous manner increases osteoblast proliferation and differentiation. In conclusion, RSPO3 regulates vertebral trabecular bone mass and bone strength in mice and fracture risk in humans.
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Affiliation(s)
- Karin H Nilsson
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Petra Henning
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Maha El Shahawy
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Faculty of Dentistry, Department of Oral Biology, Minia University, Minia, Egypt
| | - Maria Nethander
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Thomas Levin Andersen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Charlotte Ejersted
- Department of Endocrinology, Odense University Hospital, Odense, Denmark
| | - Jianyao Wu
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Karin L Gustafsson
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Antti Koskela
- Department of Anatomy and Cell Biology, Faculty of Medicine, Institute of Cancer Research and Translational Medicine, University of Oulu, Oulu, Finland
| | - Juha Tuukkanen
- Department of Anatomy and Cell Biology, Faculty of Medicine, Institute of Cancer Research and Translational Medicine, University of Oulu, Oulu, Finland
| | - Pedro P C Souza
- Innovation in Biomaterials Laboratory, Faculty of Dentistry, Federal University of Goiás, Goiâna, Brazil
| | - Jan Tuckermann
- Institute of Comparative Molecular Endocrinology (CME), University of Ulm, Ulm, Germany
| | - Mattias Lorentzon
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Department of Geriatric Medicine, Sahlgrenska University Hospital, Mölndal, Sweden
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | - Linda Engström Ruud
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jon H Tobias
- Musculoskeletal Research Unit, Translational Health Sciences, and Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sirui Zhou
- Department of Medicine, Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Ulf H Lerner
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - J Brent Richards
- Department of Medicine, Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Sofia Movérare-Skrtic
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
| | - Claes Ohlsson
- Sahlgrenska Osteoporosis Centre, Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Department of Drug Treatment, Sahlgrenska University Hospital, Gothenburg, Sweden.
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49
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Povysil G, Butler-Laporte G, Gharavi AG, Richards JB, Goldstein DB, Kiryluk K. Association of rare predicted loss-of-function variants of influenza-related type I IFN genes with critical COVID-19 pneumonia. Reply. J Clin Invest 2021; 131:e152475. [PMID: 34156980 DOI: 10.1172/jci152475] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
| | - Ali G Gharavi
- Department of Medicine and.,Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada.,Department of Twin Research, King's College London, London, United Kingdom
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, New York, USA.,Department of Genetics and Development, Columbia University, New York, New York, USA
| | - Krzysztof Kiryluk
- Department of Medicine and.,Institute for Genomic Medicine, Columbia University, New York, New York, USA
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50
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Povysil G, Butler-Laporte G, Shang N, Wang C, Khan A, Alaamery M, Nakanishi T, Zhou S, Forgetta V, Eveleigh RJ, Bourgey M, Aziz N, Jones SJ, Knoppers B, Scherer SW, Strug LJ, Lepage P, Ragoussis J, Bourque G, Alghamdi J, Aljawini N, Albes N, Al-Afghani HM, Alghamdi B, Almutairi MS, Mahmoud ES, Abu-Safieh L, El Bardisy H, Harthi FSA, Alshareef A, Suliman BA, Alqahtani SA, Almalik A, Alrashed MM, Massadeh S, Mooser V, Lathrop M, Fawzy M, Arabi YM, Mbarek H, Saad C, Al-Muftah W, Jung J, Mangul S, Badji R, Thani AA, Ismail SI, Gharavi AG, Abedalthagafi MS, Richards JB, Goldstein DB, Kiryluk K. Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19. J Clin Invest 2021; 131:147834. [PMID: 34043590 PMCID: PMC8279578 DOI: 10.1172/jci147834] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 01/19/2021] [Accepted: 05/25/2021] [Indexed: 12/25/2022] Open
Abstract
A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 with mild disease) and 15,033 ancestry-matched population controls across 4 independent COVID-19 biobanks. We tested whether rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only 1 rare pLOF mutation across these genes among 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We found no evidence of association of rare LOF variants in the 13 candidate genes with severe COVID-19 outcomes.
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Affiliation(s)
- Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Guillaume Butler-Laporte
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Chen Wang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Tomoko Nakanishi
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sirui Zhou
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
| | | | - Robert J.M. Eveleigh
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Naveed Aziz
- Canadian COVID Genomics Network, HostSeq Project, Canada
| | | | | | | | - Lisa J. Strug
- Canadian COVID Genomics Network, HostSeq Project, Canada
| | - Pierre Lepage
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | | | - Nora Aljawini
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nour Albes
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hani M. Al-Afghani
- Laboratory Department, Security Forces Hospital, General Directorate of Medical Services, Ministry of Interior, Makkah, Saudi Arabia
| | - Bader Alghamdi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mansour S. Almutairi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Ebrahim Sabri Mahmoud
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Leen Abu-Safieh
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hadeel El Bardisy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fawz S. Al Harthi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | | | - Bandar Ali Suliman
- College of Applied Medical Sciences, Taibah University, Madina, Saudi Arabia
| | - Saleh A. Alqahtani
- Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Abdulaziz Almalik
- Life Science and Environmental Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - May M. Alrashed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian COVID Genomics Network, HostSeq Project, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
| | - Mohamed Fawzy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Yaseen M. Arabi
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Wadha Al-Muftah
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Junghyun Jung
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Radja Badji
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Asma Al Thani
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Ali G. Gharavi
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
- Center for Precision Medicine and Genomics, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - J. Brent Richards
- Lady Davis Institute for Medical Research, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Twin Research, King’s College London, London, United Kingdom
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
- Department of Genetics & Development, Columbia University, New York, New York, USA
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
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