Evidence for PTPN22 R620W Polymorphism As the Sole Common Risk Variant for Rheumatoid Arthritis in the 1p13.2 Region JOSE-EZEQUIEL MARTÍN, BEHROOZ Z. ALIZADEH, MIGUEL A. GONZÁLEZ-GAY, ALEJANDRO BALSA, DORA PASCUAL-SALCEDO, MARÍA F. GONZÁLEZ-ESCRIBANO, LUIS RODRIGUEZ-RODRIGUEZ, BENJAMÍN FERNÁNDEZ-GUTIÉRREZ, ENRIQUE RAYA, MARIEKE J.H. COENEN, PIET van RIEL, TIMOTHY R.D.J. RADSTAKE, TORE K. KVIEN, MARTE K. VIKEN, BENEDICTE A. LIE, BOBBY P.C. KOELEMAN, and JAVIER MARTÍN ABSTRACT. Objective. The PTPN22 rs2476601 genetic variant has been associated with rheumatoid arthritis (RA) and other autoimmune diseases. Some reports suggest that this single-nucleotide polymorphism (SNP) may not be the only causal variant in the region of PTPN22. Our aim was to identify new independent RA-associated common gene variants in the PTPN22 region. Methods. We analyzed Wellcome Trust Case-Control Consortium genome-wide association study data for associations in the 397.2 kb PTPN22 region and selected 9 associated SNP (with p < 5 × 10–3) for replication and dependence analysis. The replication cohorts comprised 2857 patients with RA and 2994 controls from Spain, Netherlands, and Norway. Results. We found that 6 of the 9 selected SNP were associated in the Spanish cohort. Of these, 4 were also associated in the Dutch and Norwegian cohorts, and all 6 were associated with RA in the combined analysis. Conditional analyses showed that none of these associations was independent of rs2476601. Conclusion. The SNP rs2476601 located in the PTPN22 gene is the sole common genetic variant asso- ciated with RA in the 1p13.2 region, suggesting that neighbor genes of PTPN22 do not have a major influence in RA. (First Release Oct 1 2011; J Rheumatol 2011;38:2290–6; doi:10.3899/jrheum.110361) Key Indexing Terms: PTPN22 GENETIC SUSCEPTIBILITY RHEUMATOID ARTHRITIS LOGISTIC REGRESSION More than 100 genetic variants are now unambiguously asso- association of a genetic variation does not mean causal asso- ciated with complex human autoimmune diseases1. In recent ciation of the variant with the disease. The most common sce- years several genome-wide association studies (GWAS) have nario is that a single-nucleotide polymorphism (SNP) shows been carried out on rheumatoid arthritis (RA), giving rise to a association with the trait because it is in linkage disequilibri- number of new genetic associations2,3,4,5,6. Nevertheless, um with the causal variant. From the Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Medical Centre Groningen; M.A. González-Gay, MD, PhD, Department Granada, Spain; Department of Epidemiology, University Medical Centre of Rheumatology, Hospital Universitario Marqués de Valdecilla, IFIMAV; Groningen, Groningen, The Netherlands; Department of Rheumatology, A. Balsa, MD, PhD, Department of Rheumatology, Hospital La Paz; Hospital Universitario Marqués de Valdecilla, IFIMAV, Santander, Spain; D. Pascual-Salcedo, MD, PhD, Department of Immunology, Hospital La Department of Rheumatology and Department of Immunology, Hospital Paz; M.F. González-Escribano, MD, PhD, Department of Immunology, La Paz, Madrid, Spain; Department of Immunology, Hospital Virgen del Hospital Virgen del Rocio; L. Rodriguez-Rodriguez, MD, PhD; B. Rocio, Seville, Spain; Department of Rheumatology, Hospital Clinico San Fernández-Gutiérrez, MD, PhD, Department of Rheumatology, Hospital Carlos, Madrid, Spain; Department of Rheumatology, Hospital Clinico San Carlos; E. Raya, MD, PhD, Department of Rheumatology, Universitario Clinico San Cecilio, Granada, Spain; Department of Hospital Universitario Clinico San Cecilio; M.J.H. Coenen, PhD, Human Genetics and Department of Rheumatology, Radboud University, Department of Human Genetics, Radboud University; P. van Riel, MD, Nijmegen Medical Center, Nijmegen, The Netherlands; Department of PhD; T.R.D.J. Radstake, MD, PhD, Department of Rheumatology, Rheumatology, Diakonhjemmet Hospital, Oslo; Institute of Immunology, Radboud University, Nijmegen Medical Center; T.K. Kvien, MD, PhD, Oslo University Hospital Rikshospitalet, Oslo, Norway; and Department Department of Rheumatology, Diakonhjemmet Hospital; M.K. Viken, MD, of Medical Genetics, University Medical Centre Utrecht, Utrecht, The PhD; B.A. Lie, MD, PhD, Institute of Immunology, Oslo University Netherlands. Hospital Rikshospitalet; B.P.C. Koeleman, PhD, Department of Medical Supported by grant SAF2009-11110 and by Junta de Andalucía grant Genetics, University Medical Centre Utrecht; J. Martín, MD, PhD, CTS-4977; and by RETICS Program, RD08/0075 (RIER) from Instituto de Instituto de Parasitología y Biomedicina López-Neyra, CSIC. Salud Carlos III (ISCIII), within the VI PN de I+D+I 2008-2011 B.P.C. Koeleman and J. Martín contributed equally to this report. (FEDER). Dr. Koeleman is supported by the Dutch Diabetes Research Address correspondence to J-E. Martín, Instituto de Parasitologia y Foundation (grant 2008.40.001) and the Dutch Arthritis Foundation Biomedicina Lopez-Neyra, CSIC, Parque Tecnologico de Ciencias de la (Reumafonds, grant NR 09-1-408). Dr. Lie is supported by the Research Salud, Avenida del Conocimiento s/n 18100 Armilla, Granada, Spain. Council of Norway. E-mail: [email protected] J-E. Martín, BSc, Instituto de Parasitología y Biomedicina López-Neyra, Accepted for publication July 13, 2011. CSIC; B.Z. Alizadeh, PhD, Department of Epidemiology, University Personal non-commercial use only. The Journal of Rheumatology Copyright © 2011. All rights reserved. 2290 The Journal of Rheumatology 2011; 38:11; doi:10.3899/jrheum.110361 Downloaded on September 23, 2021 from www.jrheum.org Prior to the era of GWAS, SNP rs2476601 at PTPN22 was Populations. The WTCCC RA and control populations have been described2. found to be associated with autoimmune diseases such as The initial Spanish cohort comprised 941 patients with RA and 743 healthy RA7, systemic lupus erythematosus (SLE)8, type 1 diabetes9, controls. The Dutch replication cohort consisted of 962 patients with RA and 10,11 1130 healthy controls. The Norwegian replication cohort consisted of 953 and Graves’ disease . The risk allele encodes a nonsyn- patients with RA and 1121 healthy controls. All patients with RA met onymous gain-of-function variant of lymphoid tyrosine phos- American College of Rheumatology criteria21 and were recruited from phatase gene (Arg620), and functional studies have suggested Hospital Clínico San Carlos (Madrid, Spain), Hospital Xeral-Calde (Lugo, a role either in loss of tolerance to self or on regulatory T Spain), Hospital Universitario La Paz (Madrid, Spain), Hospital Clínico San cells9,12. Cecilio (Granada, Spain), Radboud University Nijmegen Medical Centre (Nijmegen, Netherlands), Diakonhjemmet Hospital (Oslo, Norway), and Nevertheless, it is suspected that other common variants blood banks from the corresponding regions and hospitals. All individuals may explain, at least in part, the association detected at the were white and all gave written informed consent for the study. This study PTPN22 locus. Studies have investigated additional causal was approved by the local ethics committees of the corresponding hospitals. variants in the PTPN22 region in RA13, type 1 diabetes14,15, Genotyping methods. All SNP were genotyped using TaqMan assays (Applied and Graves’ disease16, among others. Some studies suggest the Biosystems, Foster City, CA, USA) on an ABIprism 7900 HT real-time ther- presence of more than 1 variant associated with autoimmunity mocycler in the Spanish and Dutch cohorts. The Norwegian cohort was geno- in the 1p13.2 region where PTPN22 is located. No study to typed by MassARRAY technology (Sequenom, San Diego, CA, USA) of the Centre for Interactive Genetics, Norwegian University of Life Sciences date has been sufficiently large to fully dissect the complex (UMB), except for rs2476601, where genotypes were available from previous association of this region with RA. Conversely, a recent study publications22,23,24. 17 by Wan Taib, et al suggested that rs2476601 is the only inde- Data imputation. WTCCC data were imputed in order to increase the number pendent RA association in the 1p13.2 region. In addition to the of genotypes in the 1p13.2 region for the UK population. After performing widely demonstrated role of PTPN22 itself in autoimmune imputation tests in this region in the WTCCC cohort, removing genotyped processes, its genetic region is complex, with a relatively high SNP from the panel and comparing them to their imputed counterparts, we selected for optimal imputation using the Impute software as described25 tak- density of genes spanning roughly 0.4 Mb, including (from 5’ ing as reference panels the CEU and TSI (white) populations from the to 3’) MAGI3, PHTF1, RSBN1, PTPN22, BCL2L15, AP4B1, HapMap project26 (http://hapmap.ncbi.nlm.nih.gov/). After imputation, the DCLRE1B, HIPK1, and OLFML3. Not much is known about data were filtered as follows: all SNP with a call rate below 0.98, all SNP that the function of these genes, but 2 of them (BCL2L15 and deviated from Hardy-Weinberg equilibrium (p < 0.001), and all SNP with HIPK1) have roles in apoptotic processes, and thus could be minor allele frequency < 0.01 were excluded. involved in the pathogenesis of RA18,19,20. Data analysis. All data were filtered for quality using the following criteria: We aimed to identify new common genetic variants associ- Hardy-Weinberg equilibrium p value < 0.001 in controls, and success call rate per individual > 0.95 and per SNP > 0.95. Genotype and allele frequencies ated with RA in the