2
|
Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC, Viatte S, Takahashi M, Ohmura K, Murasawa A, Hashimoto M, Ito H, Hammoudeh M, Emadi SA, Masri BK, Halabi H, Badsha H, Uthman IW, Wu X, Lin L, Li T, Plant D, Barton A, Orozco G, Verstappen SMM, Bowes J, MacGregor AJ, Honda S, Koido M, Tomizuka K, Kamatani Y, Tanaka H, Tanaka E, Suzuki A, Maeda Y, Yamamoto K, Miyawaki S, Xie G, Zhang J, Amos CI, Keystone E, Wolbink G, van der Horst-Bruinsma I, Cui J, Liao KP, Carroll RJ, Lee HS, Bang SY, Siminovitch KA, de Vries N, Alfredsson L, Rantapää-Dahlqvist S, Karlson EW, Bae SC, Kimberly RP, Edberg JC, Mariette X, Huizinga T, Dieudé P, Schneider M, Kerick M, Denny JC, Matsuda K, Matsuo K, Mimori T, Matsuda F, Fujio K, Tanaka Y, Kumanogoh A, Traylor M, Lewis CM, Eyre S, Xu H, Saxena R, Arayssi T, Kochi Y, Ikari K, Harigai M, Gregersen PK, Yamamoto K, Louis Bridges S, Padyukov L, Martin J, Klareskog L, Okada Y, Raychaudhuri S. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nat Genet 2022; 54:1640-1651. [PMID: 36333501 PMCID: PMC10165422 DOI: 10.1038/s41588-022-01213-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 12/01/2021] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-ancestry genetic research of RA promises to improve power to detect genetic signals, fine-mapping resolution and performances of polygenic risk scores (PRS). Here, we present a large-scale genome-wide association study (GWAS) of RA, which includes 276,020 samples from five ancestral groups. We conducted a multi-ancestry meta-analysis and identified 124 loci (P < 5 × 10-8), of which 34 are novel. Candidate genes at the novel loci suggest essential roles of the immune system (for example, TNIP2 and TNFRSF11A) and joint tissues (for example, WISP1) in RA etiology. Multi-ancestry fine-mapping identified putatively causal variants with biological insights (for example, LEF1). Moreover, PRS based on multi-ancestry GWAS outperformed PRS based on single-ancestry GWAS and had comparable performance between populations of European and East Asian ancestries. Our study provides several insights into the etiology of RA and improves the genetic predictability of RA.
Collapse
Affiliation(s)
- Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Kensuke Yamaguchi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tiffany Amariuta
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chun Lai Too
- Immunogenetics Unit, Allergy and Immunology Research Center, Institute for Medical Research, National Institutes of Health Complex, Ministry of Health, Kuala Lumpur, Malaysia
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Vincent A Laufer
- Department of Clinical Immunology and Rheumatology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Ian C Scott
- Haywood Academic Rheumatology Centre, Haywood Hospital, Midlands Partnership NHS Foundation Trust, Burslem, UK
- Primary Care Centre Versus Arthritis, School of Medicine, Keele University, Keele, UK
| | - Sebastien Viatte
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Meiko Takahashi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Murasawa
- Department of Rheumatology, Niigata Rheumatic Center, Niigata, Japan
| | - Motomu Hashimoto
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Immunology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Hiromu Ito
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Orthopaedic Surgery, Kurashiki Central Hospital, Kurashiki, Japan
| | - Mohammed Hammoudeh
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Samar Al Emadi
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Basel K Masri
- Department of Internal Medicine, Jordan Hospital, Amman, Jordan
| | - Hussein Halabi
- Section of Rheumatology, Department of Internal Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Humeira Badsha
- Dr. Humeira Badsha Medical Center, Emirates Hospital, Dubai, United Arab Emirates
| | - Imad W Uthman
- Department of Rheumatology, American University of Beirut, Beirut, Lebanon
| | - Xin Wu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Li Lin
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Darren Plant
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Suzanne M M Verstappen
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
- Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | | | - Suguru Honda
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Eiichi Tanaka
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Satoru Miyawaki
- Department of Neurosurgery, Faculty of Medicine, the University of Tokyo, Tokyo, Japan
| | - Gang Xie
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Jinyi Zhang
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Gertjan Wolbink
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center (ARC), Reade, Amsterdam, the Netherlands
| | - Irene van der Horst-Bruinsma
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location Vrije Universiteit, Amsterdam, the Netherlands
| | - Jing Cui
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Katherine P Liao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Katherine A Siminovitch
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Niek de Vries
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location AMC/University of Amsterdam, Amsterdam, the Netherlands
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Robert P Kimberly
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey C Edberg
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xavier Mariette
- Department of Rheumatology, Université Paris-Saclay, Assistance Pubique - Hôpitaux de Paris, Hôpital Bicêtre, INSERM UMR1184, Le Kremlin Bicêtre, France
| | - Tom Huizinga
- Leiden University Medical Center, Leiden, the Netherlands
| | - Philippe Dieudé
- University of Paris Cité, Inserm, PHERE, F-75018, Paris, France
- Department of Rheumatology, Hôpital Bichat, APHP, Paris, France
| | - Matthias Schneider
- Department of Rheumatology & Hiller Research Unit Rheumatology, UKD, Heinrich-Heine University, Düsseldorf, Germany
| | - Martin Kerick
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
- All of Us Research Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Department of Preventive Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Matthew Traylor
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Cathryn M Lewis
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
- School of Clinical Medicine Tsinghua University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Thurayya Arayssi
- Department of Internal Medicine, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Orthopedic Surgery, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
- Division of Multidisciplinary Management of Rheumatic Diseases, Tokyo Women's Medical University, Tokyo, Japan
| | - Masayoshi Harigai
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Division of Rheumatology, Department of Internal Medicine, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - S Louis Bridges
- Department of Medicine, Hospital for Special Surgery, New York, NY, USA
- Division of Rheumatology, Weill Cornell Medicine, New York, NY, USA
| | - Leonid Padyukov
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Javier Martin
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Lars Klareskog
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, 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.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
| |
Collapse
|