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Kottyan LC, Zoller EE, Bene J, Lu X, Kelly JA, Rupert AM, Lessard CJ, Vaughn SE, Marion M, Weirauch MT, Namjou B, Adler A, Rasmussen A, Glenn S, Montgomery CG, Hirschfield GM, Xie G, Coltescu C, Amos C, Li H, Ice JA, Nath SK, Mariette X, Bowman S, Rischmueller M, Lester S, Brun JG, Gøransson LG, Harboe E, Omdal R, Cunninghame-Graham DS, Vyse T, Miceli-Richard C, Brennan MT, Lessard JA, Wahren-Herlenius M, Kvarnström M, Illei GG, Witte T, Jonsson R, Eriksson P, Nordmark G, Ng WF, Anaya JM, Rhodus NL, Segal BM, Merrill JT, James JA, Guthridge JM, Scofield RH, Alarcon-Riquelme M, Bae SC, Boackle SA, Criswell LA, Gilkeson G, Kamen DL, Jacob CO, Kimberly R, Brown E, Edberg J, Alarcón GS, Reveille JD, Vilá LM, Petri M, Ramsey-Goldman R, Freedman BI, Niewold T, Stevens AM, Tsao BP, Ying J, Mayes MD, Gorlova OY, Wakeland W, Radstake T, Martin E, Martin J, Siminovitch K, Moser Sivils KL, Gaffney PM, Langefeld CD, Harley JB, Kaufman KM. The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. Hum Mol Genet 2014; 24:582-96. [PMID: 25205108 DOI: 10.1093/hmg/ddu455] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Exploiting genotyping, DNA sequencing, imputation and trans-ancestral mapping, we used Bayesian and frequentist approaches to model the IRF5-TNPO3 locus association, now implicated in two immunotherapies and seven autoimmune diseases. Specifically, in systemic lupus erythematosus (SLE), we resolved separate associations in the IRF5 promoter (all ancestries) and with an extended European haplotype. We captured 3230 IRF5-TNPO3 high-quality, common variants across 5 ethnicities in 8395 SLE cases and 7367 controls. The genetic effect from the IRF5 promoter can be explained by any one of four variants in 5.7 kb (P-valuemeta = 6 × 10(-49); OR = 1.38-1.97). The second genetic effect spanned an 85.5-kb, 24-variant haplotype that included the genes IRF5 and TNPO3 (P-valuesEU = 10(-27)-10(-32), OR = 1.7-1.81). Many variants at the IRF5 locus with previously assigned biological function are not members of either final credible set of potential causal variants identified herein. In addition to the known biologically functional variants, we demonstrated that the risk allele of rs4728142, a variant in the promoter among the lowest frequentist probability and highest Bayesian posterior probability, was correlated with IRF5 expression and differentially binds the transcription factor ZBTB3. Our analytical strategy provides a novel framework for future studies aimed at dissecting etiological genetic effects. Finally, both SLE elements of the statistical model appear to operate in Sjögren's syndrome and systemic sclerosis whereas only the IRF5-TNPO3 gene-spanning haplotype is associated with primary biliary cirrhosis, demonstrating the nuance of similarity and difference in autoimmune disease risk mechanisms at IRF5-TNPO3.
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Affiliation(s)
- Leah C Kottyan
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology and US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Erin E Zoller
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology and
| | - Jessica Bene
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology and
| | - Xiaoming Lu
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology and
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Andrew M Rupert
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Christopher J Lessard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA Department of Pathology and
| | - Samuel E Vaughn
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology and
| | - Miranda Marion
- Department of Biostatistical Sciences and Center for Public Health Genomics and
| | - Matthew T Weirauch
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology and US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bahram Namjou
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology and
| | - Adam Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Astrid Rasmussen
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Stuart Glenn
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Courtney G Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | - Gang Xie
- Mount Sinai Hospital Samuel Lunenfeld Research Institute, Toronto, ON, Canada
| | | | - Chris Amos
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - He Li
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA Department of Pathology and
| | - John A Ice
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Xavier Mariette
- Department of Rheumatology, Hôpitaux Universitaires Paris-Sud, INSERM U1012, Le Kremlin Bicêtre, France
| | - Simon Bowman
- Rheumatology Department, University Hospital Birmingham, Birmingham, UK
| | | | | | - Sue Lester
- The Queen Elizabeth Hospital, Adelaide, Australia The University of Adelaide, Adelaide, Australia
| | - Johan G Brun
- Institute of Internal Medicine, University of Bergen, Bergen, Norway Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Lasse G Gøransson
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Erna Harboe
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Roald Omdal
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | | | - Tim Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Corinne Miceli-Richard
- Department of Rheumatology, Hôpitaux Universitaires Paris-Sud, INSERM U1012, Le Kremlin Bicêtre, France
| | - Michael T Brennan
- Department of Oral Medicine, Carolinas Medical Center, Charlotte, NC, USA
| | | | | | | | - Gabor G Illei
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | | | - Roland Jonsson
- Department of Rheumatology, Haukeland University Hospital, Bergen, Norway Broegelmann Research Laboratory, The Gade Institute, University of Bergen, Bergen, Norway
| | - Per Eriksson
- Department of Rheumatology, Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | - Gunnel Nordmark
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Wan-Fai Ng
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia
| | - Nelson L Rhodus
- Department of Oral Surgery, University of Minnesota School of Dentistry, Minneapolis, MN, USA
| | - Barbara M Segal
- Division of Rheumatology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Joan T Merrill
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Judith A James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA Division of Veterans Affairs Medical Center, Oklahoma City, OK, USA Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Marta Alarcon-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucia, Granada, Spain
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Lindsey A Criswell
- Division of Rheumatology, Rosalind Russell Medical Research Center for Arthritis, University of California San Francisco, San Francisco, CA, USA
| | - Gary Gilkeson
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Diane L Kamen
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Chaim O Jacob
- Divison of Gastrointestinal and Liver Diseases, Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Robert Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Elizabeth Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Graciela S Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John D Reveille
- Division of Rheumatology and Clinical Immunogenetics, The Univeristy of Texas Health Science Center at Houston, Houston, TX, USA
| | - Luis M Vilá
- University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, USA
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins, Baltimore, MD, USA
| | | | | | - Timothy Niewold
- Division of Rheumatology and Immunology, Mayo Clinic, Rochester, MN, USA
| | - Anne M Stevens
- University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Betty P Tsao
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Jun Ying
- MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Maureen D Mayes
- MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Olga Y Gorlova
- MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Ward Wakeland
- University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Timothy Radstake
- Department of Rheumatology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Ezequiel Martin
- Instituto de Parasitología y Biomedicina López Neyra Avda, Granada, Spain and
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López Neyra Avda, Granada, Spain and
| | - Katherine Siminovitch
- Mount Sinai Hospital Samuel Lunenfeld Research Institute, Toronto, ON, Canada Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Kathy L Moser Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences and Center for Public Health Genomics and
| | - John B Harley
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology and US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Kenneth M Kaufman
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology and US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
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