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1. Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis

Author

Simon P. Hart, Vilmundur Gudnason, Yingze Zhang, Hiroto Hatabu, Rebecca Braybrooke, R. Gisli Jenkins, Shwu-Fan Ma, Michael Ng, Carlos Flores, George T. O'Connor, Ma'en Obeidat, Nik Hirani, Brian D. Hobbs, Megan L. Paynton, Amy Dressen, Ayodeji Adegunsoye, Helen Booth, Dominic Furniss, Philippe Joubert, Eunice Oballa, Ian Sayers, Martin D. Tobin, Krina T. Zondervan, Richard Hubbard, Xuan Li, Yohan Bossé, John D. Newell, Beatriz Guillen-Guio, Ann B. Millar, Wim Timens, Mary E. Strek, Gunnar Gudmundsson, Philip L. Molyneaux, Gary M. Hunninghake, Ani Manichaikul, Tasha E. Fingerlin, Rachel K. Putman, Richard J. Allen, Vidyia Navaratnam, Maria Molina-Molina, Don D. Sin, Helen Parfrey, Luke M. Kraven, Moira K. B. Whyte, Xuting R. Sheng, Phuwanat Sakornsakolpat, David J. Lederer, David C. Nickle, Ian P. Hall, Brian L. Yaspan, Louise V. Wain, Toby M. Maher, Gauri Saini, Ke Hao, Michael Hill, Naftali Kaminski, Andrew P. Morris, Hanfei Xu, Justin M. Oldham, David A. Schwartz, Robin J. McAnulty, Michael H. Cho, Victor E. Ortega, Margaret Neighbors, Imre Noth, William A. Fahy, Action for Pulmonary Fibrosis, National Institute for Health Research, British Lung Foundation, Groningen Research Institute for Asthma and COPD (GRIAC), Guided Treatment in Optimal Selected Cancer Patients (GUTS), Læknadeild (HÍ), Faculty of Medicine (UI), Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Háskóli Íslands, and University of Iceland

Subjects
Male, Pathology, Epidemiology, Respiratory System, Kinesins, Gene Expression, Genome-wide association study, Cell Cycle Proteins, TOR Serine-Threonine Kinases/metabolism, VARIANTS, Critical Care and Intensive Care Medicine, Idiopathic pulmonary fibrosis, 0302 clinical medicine, KIF15, TELOMERES, genetics, 030212 general & internal medicine, Respiratory system, 11 Medical and Health Sciences, RISK, TOR Serine-Threonine Kinases, Intracellular Signaling Peptides and Proteins, respiratory system, Middle Aged, MAD1L1, 3. Good health, medicine.anatomical_structure, SURVIVAL, epidemiology, Female, Life Sciences & Biomedicine, Kinesin/genetics, Signal Transduction, Pulmonary and Respiratory Medicine, medicine.medical_specialty, Spindle Apparatus, DIAGNOSIS, Risk Assessment, REGION, 03 medical and health sciences, Critical Care Medicine, General & Internal Medicine, medicine, Genetics, Erfðafræði, Humans, Genetic Predisposition to Disease, Aged, Cell Cycle Proteins/genetics, Lungnasjúkdómar, Lung, Science & Technology, DEPTOR, business.industry, MUTATIONS, Case-control study, Editorials, RTEL1, medicine.disease, Epithelium, Idiopathic Pulmonary Fibrosis, respiratory tract diseases, Genarannsóknir, 030228 respiratory system, EVENT, Case-Control Studies, GAIN, business, Intracellular Signaling Peptides and Proteins/genetics, Idiopathic Pulmonary Fibrosis/genetics, Genome-Wide Association Study
Abstract

Publisher's version (útgefin grein), Rationale: Idiopathic pulmonary fibrosis (IPF) is a complex lung disease characterized by scarring of the lung that is believed to result from an atypical response to injury of the epithelium. Genome-wide association studies have reported signals of association implicating multiple pathways including host defense, telomere maintenance, signaling, and cell-cell adhesion. Objectives: To improve our understanding of factors that increase IPF susceptibility by identifying previously unreported genetic associations. Methods: We conducted genome-wide analyses across three independent studies and meta-analyzed these results to generate the largest genome-wide association study of IPF to date (2,668 IPF cases and 8,591 controls). We performed replication in two independent studies (1,456 IPF cases and 11,874 controls) and functional analyses (including statistical fine-mapping, investigations into gene expression, and testing for enrichment of IPF susceptibility signals in regulatory regions) to determine putatively causal genes. Polygenic risk scores were used to assess the collective effect of variants not reported as associated with IPF. Measurements and Main Results: We identified and replicated threenewgenome-wide significant (P, R.J.A. is an Action for Pulmonary Fibrosis Research Fellow. L.V.W. holds a GSK/British Lung Foundation Chair in Respiratory Research. R.G.J. is supported by a National Institute for Health Research (NIHR) Research Professorship (NIHR reference RP-2017-08-ST2-014). I.N. is supported by the NHLBI (R01HL130796). B.G.-G. is funded by Agencia Canaria de Investigación, Innovación y Sociedad de la Información (TESIS2015010057) cofunded by European Social Fund. J.M.O. is supported by the NHLBI (K23HL138190). C.F. is supported by the Spanish Ministry of Science, Innovation and Universities (grant RTC-2017-6471-1; Ministerio de Ciencia e Innovacion/Agencia Estatal de Investigación/Fondo Europeo de Desarrollo Regional, Unión Europea) cofinanced by the European Regional Development Funds “A way of making Europe” from the European Union and by agreement OA17/008 with Instituto Tecnológico y de Energías Renovables to strengthen scientific and technological education, training, research, development and innovation in Genomics, Personalized Medicine and Biotechnology. The Spain Biobank array genotyping service was performed at CEGEN-PRB3-ISCIII, which is supported by PT17/0019, of the PE I+D+i 2013–2016, funded by Instituto de Salud Carlos III, and cofinanced by the European Regional Development Funds. P.L.M. is an Action for Pulmonary Fibrosis Research Fellow. M.O. is a fellow of the Parker B. Francis Foundation and a Scholar of the Michael Smith Foundation for Health Research. B.D.H. is supported by NIH K08 HL136928, Parker B. Francis Research Opportunity Award. M.H.C. and G.M.H. are supported by NHLBI grants R01HL113264 (M.H.C.), R01HL137927 (M.H.C.), R01HL135142 (M.H.C. and G.M.H.), R01111024 (G.M.H.), and R01130974 (G.M.H.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. The funding body has no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. T.M.M. is supported by an NIHR Clinician Scientist Fellowship (NIHR Ref: CS-2013-13-017) and a British Lung Foundation Chair in Respiratory Research (C17-3). M.D.T. is supported by a Wellcome Trust Investigator Award (WT202849/Z/16/Z). The research was partially supported by the NIHR Leicester Biomedical Research Centre; the views expressed are those of the author(s) and not necessarily those of the National Health Service (NHS), the NIHR, or the Department of Health. I.P.H. was partially supported by the NIHR Nottingham Biomedical Research Centre; the views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health. I.S. is supported by Medical Research Council (G1000861) and Asthma UK (AUK-PG-2013-188). D.F. was supported by an Intermediate Fellowship from the Wellcome Trust (097152/Z/11/Z). This work was partially supported by the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre. V.N. is funded by an NIHR Clinical Lectureship. G.G. is supported by project grant 141513-051 from the Icelandic Research Fund and Landspitali Scientific Fund A-2016-023, A-2017-029, and A-2018-025. D.J.L. and A.M. are supported by Multi-Ethnic Study of Atherosclerosis (MESA) and the MESA SNP Health Association Resource (SHARe) project are conducted and supported by the NHLBI in collaboration with MESA investigators. Support for MESA is provided by contracts HHSN268201500003I, N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162, N01-HC-95163, N01-HC-95164, N01-HC-95165, N01-HC-95166, N01-HC-95167, N01-HC-95168, N01-HC-95169, UL1-TR-000040, UL1-TR-001079, UL1-TR-001420, UL1-TR-001881, and DK063491. Funding for SHARe genotyping was provided by NHLBI Contract N02-HL-64278. Genotyping was performed at Affymetrix (Santa Clara, California) and the Broad Institute of Harvard and Massachusetts Institute of Technology (Boston, Massachusetts) using the Affymetrix Genome-Wide Human SNP Array 6.0. This work was supported by NIH grants R01 HL131565 (A.M.), R01 HL103676 (D.J.L.), and R01 HL137234 (D.J.L.).

Published
2020
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2. MUC5B Promoter Variant and Rheumatoid Arthritis with Interstitial Lung Disease

Author

Yaping Wang, Annick Clement, Nadia Nathan, Joanne J. van der Vis, Huguette Lioté, Aryeh Fischer, Dominique Valeyre, David A. Schwartz, Jan C. Grutters, Timothy B Niewold, Michael A. Nalls, Ivette Buendía-Roldán, Dimitrios Boumpas, Vincent Cottin, Marie-Christophe Boissier, Theofanis Karageorgas, Mayra Mejía, Yaël A de Man, Kevin D. Deane, Effrosyni D. Manali, Katarina M. Antoniou, Joshua J. Solomon, Jay H. Ryu, Pierre-Antoine Juge, Martin Soubrier, Jean Sibilia, Hilario Nunes, Marie-Pierre Debray, Christophe Richez, Spyros Papiris, Steven Gazal, Catherine Boileau, Deborah Assayag, Nathalie Saidenberg-Kermanac’h, Tasha E. Fingerlin, Claire Dromer, Marvin I. Schwarz, Esther Ebstein, Michael Holers, Tracy J. Doyle, Ivan O. Rosas, Bruno Crestani, Hiroshi Furukawa, Evgenia Dobrinskikh, Cornelis Blauwendraat, Paul J. Wolters, Naoyuki Tsuchiya, Thierry Schaeverbeke, Ramcés Falfán-Valencia, Lidwine Wemeau-Stervinou, Gabriel Thabut, Shigeto Tohma, Coline H.M. van Moorsel, Montserrat I González-Pérez, Andrew J. Gross, Benoit Wallaert, Shomi Oka, Caroline Kannengiesser, Joyce S. Lee, Enrique Ambrocio-Ortiz, Aline Frazier, Sylvain Marchand-Adam, René-Marc Flipo, Eric L. Matteson, Pascal Richette, S. Amselem, Raphael Borie, Jorge Rojas-Serrano, Yannick Allanore, Sébastien Ottaviani, Philippe Dieudé, Avram D Walts, AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Physiopathologie et Epidémiologie des Maladies Respiratoires (PHERE (UMR_S_1152 / U1152)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Colorado School of Medicine, Université de Tsukuba = University of Tsukuba, Sagamihara National Hospital [Kanagawa, Japan], Harvard T.H. Chan School of Public Health, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], University of Athens, 'Attikon' Hospital, National and Kapodistrian University of Athens (NKUA), University of Crete [Heraklion] (UOC), St. Antonius Hospital [Nieuwegein], Nanjing Medical University, Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Hôpital Avicenne [AP-HP], Physiopathologie, Cibles et Thérapies de la Polyarthrite Rhumatoïde, Université Paris 13 (UP13)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Hôpital Lariboisière-Fernand-Widal [APHP], Biologie de l'Os et du Cartilage : Régulations et Ciblages Thérapeutiques (BIOSCAR (UMR_S_1132 / U1132)), AP-HP - Hôpital Cochin Broca Hôtel Dieu [Paris], Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital de Hautepierre [Strasbourg], Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg (UNISTRA), CHU Bordeaux [Bordeaux], Immunology from Concept and Experiments to Translation (ImmunoConcept), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), CHU Tenon [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Maladies génétiques d'expression pédiatrique (U933), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Trousseau [APHP], CHU Clermont-Ferrand, Unité de Nutrition Humaine (UNH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Infections Virales et Pathologie Comparée - UMR 754 (IVPC), Institut National de la Recherche Agronomique (INRA)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Hôpital Louis Pradel [CHU - HCL], Hospices Civils de Lyon (HCL), National Jewish Health (NJH), Mayo Clinic and Mayo College of Medicine, Rochester, New York University School of Medicine, NYU System (NYU), McGill University = Université McGill [Montréal, Canada], University of California [San Francisco] (UC San Francisco), University of California (UC), Brigham & Women’s Hospital [Boston] (BWH), Harvard Medical School [Boston] (HMS), National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Societe Francaise de Rhumatologie, Club Rhumatismes Inflammation, la Chancellerie des Universites de Paris (legs Poix), Sorbonne Paris Cite (FPI-SPC Program), Agence Nationale de la Recherche ANR-10-LABX-46 ANR-10-EQPX-07-01 ANR-14-CE10-0006 ANR-10-INBS-09, France Genomique National Infrastructure, Pfizer, Chugai, Centre de Resources Biologiques Hopital Bichat Paris FranceFondation Arthritis, Département Hospitalo-Universitaire Fibrose Inflammation Remodelage, National Heart, Lung, and Blood Institute (UH2/3-HL123442, R01-HL097163, R21/R33-HL120770, P01-HL092870, and K23-HL138131), National Institute of Arthritis and Musculoskeletal and Skin Diseases (K23-AR051461), National Institute of Allergy and Infectious Diseases (U01-AI101981), U.S. Department of Defense (W81XWH-17-1-0597), National Center for Advancing Translational Science (UCSF-CTI KL2TR000143), the Nina Ireland Program for Lung Health, the Intramural Research Program of the National Institute of Aging, part of the National Institutes of Health, Department of Health and Human Services (Z01-AG000949–02), and the Japanese Society for the Promotion of Science., Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE)-Université Claude Bernard Lyon 1 (UCBL), Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE), and Societe Francaise de Rhumatologie, Club Rhumatismes Inflammation, la Chancellerie des Universites de Paris (legs Poix), Sorbonne Paris Cite (FPI-SPC Program), Agence Nationale de la Recherche ANR-10-LABX-46 ANR-10-EQPX-07-01 ANR-14-CE10-0006 ANR-10-INBS-09, France Genomique National Infrastructure, Pfizer, Chugai, Centre de Resources Biologiques Hopital Bichat Paris France

Subjects
Male, Lung Diseases, medicine.medical_specialty, Genotype, [SDV]Life Sciences [q-bio], Population, Arthritis, behavioral disciplines and activities, Gastroenterology, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Promoter Regions, 03 medical and health sciences, Idiopathic pulmonary fibrosis, 0302 clinical medicine, Genetic, Internal medicine, Gain of Function Mutation, Odds Ratio, Medicine, Humans, Genetic Predisposition to Disease, Rheumatoid/complications/*genetics, Risk factor, education, Aged, 030203 arthritis & rheumatology, Lung/chemistry/pathology, education.field_of_study, business.industry, Interstitial lung disease, General Medicine, Odds ratio, respiratory system, Middle Aged, medicine.disease, respiratory tract diseases, 3. Good health, body regions, Minor allele frequency, 030228 respiratory system, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Rheumatoid arthritis, Female, Interstitial/complications/*genetics, Mucin-5B/analysis/*genetics, business, Idiopathic Pulmonary Fibrosis/genetics
Abstract

International audience; BACKGROUND: Given the phenotypic similarities between rheumatoid arthritis (RA)-associated interstitial lung disease (ILD) (hereafter, RA-ILD) and idiopathic pulmonary fibrosis, we hypothesized that the strongest risk factor for the development of idiopathic pulmonary fibrosis, the gain-of-function MUC5B promoter variant rs35705950, would also contribute to the risk of ILD among patients with RA. METHODS: Using a discovery population and multiple validation populations, we tested the association of the MUC5B promoter variant rs35705950 in 620 patients with RA-ILD, 614 patients with RA without ILD, and 5448 unaffected controls. RESULTS: Analysis of the discovery population revealed an association of the minor allele of the MUC5B promoter variant with RA-ILD when patients with RA-ILD were compared with unaffected controls (adjusted odds ratio, 3.8; 95% confidence interval [CI], 2.8 to 5.2; P=9.7x10(-17)). The MUC5B promoter variant was also significantly overrepresented among patients with RA-ILD, as compared with unaffected controls, in an analysis of the multiethnic case series (adjusted odds ratio, 5.5; 95% CI, 4.2 to 7.3; P=4.7x10(-35)) and in a combined analysis of the discovery population and the multiethnic case series (adjusted odds ratio, 4.7; 95% CI, 3.9 to 5.8; P=1.3x10(-49)). In addition, the MUC5B promoter variant was associated with an increased risk of ILD among patients with RA (adjusted odds ratio in combined analysis, 3.1; 95% CI, 1.8 to 5.4; P=7.4x10(-5)), particularly among those with evidence of usual interstitial pneumonia on high-resolution computed tomography (adjusted odds ratio in combined analysis, 6.1; 95% CI, 2.9 to 13.1; P=2.5x10(-6)). However, no significant association with the MUC5B promoter variant was observed for the diagnosis of RA alone. CONCLUSIONS: We found that the MUC5B promoter variant was associated with RA-ILD and more specifically associated with evidence of usual interstitial pneumonia on imaging. (Funded by Societe Francaise de Rhumatologie and others.).

Published
2018
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