Tyk2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits
Copyright: © 2015 Diogo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Despite the success of genome-wid...
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| Published in: | PloS one Vol. 10; no. 4; p. e0122271 |
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| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
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07-04-2015
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| Abstract | Copyright: © 2015 Diogo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3 x 10(-21)), A928V (rs35018800, OR = 0.53, P = 1.2 x 10(-9)), and I684S (rs12720356, OR = 0.86, P = 4.6 x 10(-7)). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6 x 10(-18)), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P(omnibus) = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases. |
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| AbstractList | Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3x10-21), A928V (rs35018800, OR = 0.53, P = 1.2x10-9), and I684S (rs12720356, OR = 0.86, P = 4.6x10-7). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6x10-18), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; Pomnibus = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases. Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3x10.sup.-21 ), A928V (rs35018800, OR = 0.53, P = 1.2x10.sup.-9 ), and I684S (rs12720356, OR = 0.86, P = 4.6x10.sup.-7). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, P.sub.omnibus = 6x10.sup.-18 ), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P.sub.omnibus = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases. Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3x10 -21 ), A928V (rs35018800, OR = 0.53, P = 1.2x10 -9 ), and I684S (rs12720356, OR = 0.86, P = 4.6x10 -7 ). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, P omnibus = 6x10 -18 ), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P omnibus = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases. Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3 x 10(-21)), A928V (rs35018800, OR = 0.53, P = 1.2 x 10(-9)), and I684S (rs12720356, OR = 0.86, P = 4.6 x 10(-7)). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6 x 10(-18)), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P(omnibus) = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases. Copyright: © 2015 Diogo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3 x 10(-21)), A928V (rs35018800, OR = 0.53, P = 1.2 x 10(-9)), and I684S (rs12720356, OR = 0.86, P = 4.6 x 10(-7)). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6 x 10(-18)), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P(omnibus) = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases. |
| Audience | Academic |
| Author | Lee, Annette Klareskog, Lars Mardis, Elaine R. Kosoy, Roman Deluca, Tracie L. Gainer, Vivian Worthington, Jane Coenen, Marieke J. H. Mikuls, Ted R. O'Laughlin, Michelle Barton, Anne Pappas, Dimitrios A. Greenberg, Jeffrey D. Graham, Robert R. Bastarache, Lisa Raychaudhuri, Soumya Larson, David E. Fulton, Lucinda L. Seldin, Michael F. Kohane, Isaac Cui, Jing Nurmohamed, Michael T. Diogo, Dorothée Gregersen, Peter K. Bowes, John de Vries, Niek Okada, Yukinori Murphy, Shawn N. Fulton, Robert S. Zhernakova, Alexandra Fronick, Catrina C. Tak, Paul P. Liao, Katherine P. Kiemeney, Lambertus A. Plenge, Robert M. Eyre, Steve Padyukov, Leonid Crusius, J. Bart A. Kurreeman, Fina Stahl, Eli A. Franke, Barbara Karlson, Elizabeth W. Mariette, Xavier Richard-Miceli, Corrine Martin, Javier Cagan, Andrew Canhao, Helena Bhangale, Tushar R. Denny, Joshua C. Behrens, Timothy Ransom, Michael Fonseca, João Kremer, Joel M. Ortmann, Ward |
| AuthorAffiliation | 4 Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America 7 The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America 16 Université Paris-Sud, Orsay, France 25 Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America 9 Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom 17 APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France 15 Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands 3 Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America 1 Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America 20 Amsterdam Rheumatology and I |
| AuthorAffiliation_xml | – name: 29 Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden – name: 16 Université Paris-Sud, Orsay, France – name: 25 Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America – name: 6 ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America – name: 12 The Albany Medical College and The Center for Rheumatology, Albany, New York, United States of America – name: 30 Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America – name: 1 Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America – name: 7 The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America – name: 17 APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France – name: 18 Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal – name: 11 Columbia University, College of Physicians and Surgeons, New York, New York, United States of America – name: 4 Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America – name: 8 New York University Hospital for Joint Diseases, New York, New York, United States of America – name: 5 Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America – name: 20 Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology & Rheumatology, Academic Medical Center /University of Amsterdam, Amsterdam, The Netherlands – name: 3 Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America – name: 9 Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom – name: 22 Amsterdam Rheumatology and Immunology Center, Department of Rheumatology, Reade, Amsterdam, The Netherlands – name: 24 Division of Rheumatology and Immunology, Omaha VA and University of Nebraska Medical Center, Omaha, Nebraska, United States of America – name: 28 Genetics Department, University Medical Center and Groningen University, Groningen, The Netherlands – name: 2 Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America – name: 10 The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America – name: 23 Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands – name: 21 Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands – name: 27 Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Granada, 18100, Spain – name: 15 Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands – name: 19 Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal – name: 26 Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America – name: National Institute of Dental and Craniofacial Research, UNITED STATES – name: 14 Radboud University Medical Center, Donders Centre for Neurosciences, Department of Psychiatry and Human Genetics, Nijmegen, The Netherlands – name: 13 Radboud university medical center, Radboud Institute for Health Sciences, Department of Human Genetics, Nijmegen, The Netherlands |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25849893$$D View this record in MEDLINE/PubMed http://kipublications.ki.se/Default.aspx?queryparsed=id:131098005$$DView record from Swedish Publication Index |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Competing Interests: The authors would like to emphasize that Drs T. Behrens, R.R. Graham, T.R. Bhangale and W. Ortmann are employed by Genentech Inc. Dr. J.D. Greenberg is an employee and shareholder in Corrona and has received consulting fees from AstraZeneca, Celgene, Novartis and Pfizer. Dr D.A. Pappas is an employee of Corrona, LLC, and Novartis instructor. J.M. Kremer is a shareholder in Corrona and receives employment compensation. However, this does not alter the authors' adherence to PLOS ONE policies on sharing data and materials. Current address: Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan Current address: Division of Psychiatric Genomics, Mt. Sinai School of Medicine, New York, New York, United States of America Current address: Merck Research Laboratories, Boston, Massachusetts, United States of America Conceived and designed the experiments: DD RMP. Performed the experiments: DD RMP JCD KPL SR. Analyzed the data: DD LB. Contributed reagents/materials/analysis tools: RPG RSF JDG SE JB JC AL DAP JMK AB MJHC BF LAK XM CRM HC JEF NdV PPT JBAC MTN FK TRM YO EAS DEL TLD MO CCF LLF RK MR TRB WO AC VG EWK IK SNM JM AZ LK LP JW ERM MFS PKG TB. Wrote the paper: DD RPM. Current address: University of Cambridge, Cambridge, United Kingdom, and GlaxoSmithkline, Stevenage, United Kingdom |
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| Snippet | Copyright: © 2015 Diogo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits... Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA)... |
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| SubjectTerms | Analysis Arthritis Arthritis, Rheumatoid - enzymology Arthritis, Rheumatoid - genetics Autoimmune diseases Autoimmunity Autoimmunity - genetics Biological effects Cell Adhesion Molecules - genetics Chromosome 19 Chronic conditions Electronic Health Records Electronic medical records Exons - genetics Gastrointestinal diseases Genetic Loci - genetics Genetic Pleiotropy Genetic Predisposition to Disease - genetics Genome-wide association studies Genomes Genomics Genotyping Humans Inflammatory bowel diseases Intestine Loci Medical treatment Medicin och hälsovetenskap Pathogenesis Polymorphism, Single Nucleotide Protein-tyrosine kinase Rheumatoid arthritis Rheumatoid factor Systemic lupus erythematosus TYK2 Kinase - genetics Tyk2 protein Tyrosine |
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| Title | Tyk2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits |
| URI | http://hdl.handle.net/10451/53176 https://www.ncbi.nlm.nih.gov/pubmed/25849893 https://www.proquest.com/docview/1671014222 https://search.proquest.com/docview/1672090375 https://pubmed.ncbi.nlm.nih.gov/PMC4388675 http://kipublications.ki.se/Default.aspx?queryparsed=id:131098005 https://doaj.org/article/beb6d79c3e184701a89299ca92e0df4f http://dx.doi.org/10.1371/journal.pone.0122271 |
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