HLA-DRB1*1101, Regulatory Variants of the MHC, and a Regulatory Region Near an Intergenic Long Noncoding RNA on Chromosome 1 Are Risk Factors for Systemic Juvenile Idiopathic Arthritis

Michael J. Ombrello¹, Elaine F. Remmers², Ioanna Tachmazidou³, Alexei Grom⁴, Dirk Föll⁵, Alberto Martini⁶, Marco Gattorno⁷, Seza Ozen⁸, Sampath Prahalad^9,10, Andrew S. Zeft¹¹, John F. Bohnsack¹², Norman T. Ilowite¹³, Jane L. Park¹⁴, Elizabeth D. Mellins¹⁵, Ricardo A. G. Russo¹⁶, Claudio A. Len¹⁷, Sheila K. Feitosa de Oliveira¹⁸, Rae SM Yeung¹⁹, Lucy R. Wedderburn^20,21, Jordi Anton²², Tobias Schwarz²³, Buhm Han²⁴, Richard H. Duerr²⁵, Jean-Paul Achkar²⁶, M. Ilyas Kamboh²⁷, Kenneth M. Kaufman²⁸, Leah C. Kottyan²⁸, Dalila Pinto²⁹, Stephen Scherer³⁰, Marta E. Alarcón-Riquelme³¹, Elisa Docampo Martinez³², Xavier Estivill³³, Ahmet Gul³⁴, Colleen Satorius³⁵, Paul I.W. de Bakker^36,37,38, Soumya Raychaudhuri^37,39,40, Carl D. Langefeld⁴¹, Susan D. Thompson⁴², Eleftheria Zeggini³, Wendy Thomson⁴³, Daniel L. Kastner⁴⁴, Patricia Woo⁴⁵ and International Childhood Arthritis Genetics (INCHARGE) Consortium, ¹Translational Genetics and Genomics Unit, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, ²Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, ³The Wellcome Trust Sanger Institute, Cambridge, United Kingdom, ⁴Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, ⁵Pediatric Rheumatology and Immunology, University Children's Hospital Muenster, Muenster, Germany, ⁶University of Genova, Genova, Italy, ⁷Pediatric Rheumatology, Instituto Giannina Gaslini, Genoa, Italy, ⁸Deptartment. of Pediatric Rheumatology, Hacettepe University, Ankara, Turkey, ⁹Emory University School of Medicine, Atlanta, GA, ¹⁰Children's Healthcare of Atlanta, Atlanta, GA, ¹¹Pediatrics Rheumatology, Cleveland Clinic, Cleveland, OH, ¹²Pediatriacs, University of Utah, Salt Lake City, UT, ¹³Pediatrics, Albert Einstein College of Medicine, Bronx, NY, ¹⁴Pediatric Rheumatology, Stanford University Medical Center, Stanford, CA, ¹⁵Dept of Pediatrics CCSR, Stanford University Medical Center, Stanford, CA, ¹⁶Immunology & Rheumatology, Hospital de Pediatria Garrahan, Buenos Aires, Argentina, ¹⁷Universidade Federal de São Paulo/Escola Paulista de Medicina, São Paulo, Brazil, ¹⁸Pediatric Rheumatology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil, ¹⁹Rheumatology, The Hospital for Sick Children, Toronto, ON, Canada, ²⁰University College London (UCL) Institute of Child Health, London, United Kingdom, ²¹Great Ormond Street Hospital, London, United Kingdom, ²²Pediatric Rheumatology Unit. Hospital Sant Joan de Déu. Universitat de Barcelona, Barcelona, Spain, ²³Pediatric rheumathology and osteology, University of Wuerzburg, Wuerzburg, Germany, ²⁴Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, ²⁵Department of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, ²⁶Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH, ²⁷Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, ²⁸Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, ²⁹Genetics and Genomi Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, ³⁰The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada, ³¹Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, ³²Unit of Animal Genomics, GIGA-Université de Liège, LIege, Belgium, ³³Genetic Causes of Disease Laboratory, Center for Genomic Regulation, Barcelona, Spain, ³⁴Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey, ³⁵National Human Genome Research Institute, Bethesda, MD, ³⁶Brighan and Women's Hospital, Harvard Medical School, Boston, MA, ³⁷Broad Institute of MIT and Harvard, Cambridge, MA, ³⁸University Medical Center Utrecht, Utrecht, Netherlands, ³⁹Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, ⁴⁰Manchester Academic Health Sciences Centre, Manchester, United Kingdom, ⁴¹Center for Public Health Genomics and Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, ⁴²Division and Center for Autoimmune Disease Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, ⁴³Institute of Inflammation and Repair, The University of Manchester, Manchester, United Kingdom, ⁴⁴Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD, ⁴⁵Paediatric Rheumatology Unit, University College London, London, United Kingdom

Meeting: 2014 ACR/ARHP Annual Meeting

Keywords: Autoinflammation, genomics and major histocompatibility complex (MHC), Systemic JIA

Session Information

Title: Pediatric Rheumatology - Pathogenesis and Genetics

Session Type: Abstract Submissions (ACR)

Background/Purpose: Systemic juvenile idiopathic arthritis (sJIA) is a severe inflammatory disease of unknown etiology. We utilized a genomic approach to interrogate the molecular pathogenesis of this disorder.

Methods: Single nucleotide polymorphism (SNP) genotypes from Illumina arrays were obtained in 988 children with sJIA and 431 healthy subjects and combined with in silico SNP data from 7579 healthy subjects. The collection was divided into 9 strata by country of origin, and after stringent quality control, we performed genome-wide SNP imputation and association testing in each stratum, followed by meta-analysis. A second round of imputation using a more densely genotyped reference panel was performed in regions with p< 1E-7. To investigate the role of specific major histocompatibility complex (MHC) proteins, we imputed classical HLA alleles and their subordinate amino acid positions. To assess whether sJIA-associated noncoding MHC variation conferred risk through regulatory mechanisms, we used RegulomeDB to analyze MHC SNPs with p < 1E-5. RegulomeDB integrates and queries regulatory information from over 100 tissues and cell lines, including DNAse hypersensitivity, transcription factor (TF) ChIP-seq and histone ChIP-seq data from ENCODE, plus expression quantitative trait loci (eQTL) data.

Results: Meta-analyses of >1.3M SNPs identified significant associations (p < 1.5E-8) between sJIA and 6 SNPs between BTNL2 and HLA-DQA1, as well as a susceptibility locus in a noncoding region of chromosome 1 nearest to the long intergenic noncoding RNA, LOC284661. Conditional analysis of the phase 2 imputation data identified HLA-DRB1 (p_peak = 1.6E-10)and HLA-DQA2 (p_regression = 4.6E-7) as independent susceptibility loci. It also revealed a 10kb sJIA-associated region on chromosome 1 that contained 8 sJIA-associated SNPs (p < 1.5E-8). Conditional analyses of imputed HLA alleles identified HLA-DRB1*1101 (p_peak = 3.1E-9) and HLA-DPB1*03 (p_regression = 3.2E-4) as independent risk factors, while position 58 of HLA-DRB1, which defines the -DRB1*11 alleles, was also significantly associated with sJIA (p = 1.4E-7). Using RegulomeDB to examine 886 MHC SNPs with p < 1E-5, we found 13 sJIA-associated SNPs with strong evidence that they influenced transcription factor binding and were also linked to expression of a gene target (RegulomeDB scores 1a - 1f). These SNPs were located nearest to HLA-DQA1, HLA-DRB1, HLA-DRA, TNXB, NOTCH4 and C2. 12 of 13 SNPs were cis eQTLs for 1 or more MHC class II (MHCII) genes in lymphoblastoid cell lines (LCLs) and/or monocytes, 8 of which were eQTLs for HLA-DRB5. 3 of 13 SNPs resided within TF ChIP-seq peaks in GM12878 LCLs. 7 of 13 SNPs resided in H3K27ac ChIP-seq peaks (marks of active enhancers) in GM12878 LCLs and/or monocytes, 6 of which were cell-type specific. In all, 9 of 13 SNPs were located within histone modification signatures that were specific to GM12878 LCLs.

Conclusion: This study implicates the MHCII locus and a region of chromosome 1 upstream of LOC284661 in sJIA susceptibility. The data suggest that the MHCII locus influences sJIA susceptibility through both protein coding variation and noncoding variation that alters gene expression.

Disclosure:

M. J. Ombrello,
None;

E. F. Remmers,
None;

I. Tachmazidou,
None;

A. Grom,