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Ramos PS, Criswell LA, Moser KL, Comeau ME, Williams AH, Pajewski NM, Chung SA, Graham RR, Zidovetzki R, Kelly JA, Kaufman KM, Jacob CO, Vyse TJ, Tsao BP, Kimberly RP, Gaffney PM, Alarcón-Riquelme ME, Harley JB, Langefeld CD. A comprehensive analysis of shared loci between systemic lupus erythematosus (SLE) and sixteen autoimmune diseases reveals limited genetic overlap. PLoS Genet 2011; 7:e1002406. [PMID: 22174698 PMCID: PMC3234215 DOI: 10.1371/journal.pgen.1002406] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 10/18/2011] [Indexed: 12/18/2022] Open
Abstract
In spite of the well-known clustering of multiple autoimmune disorders in families, analyses of specific shared genes and polymorphisms between systemic lupus erythematosus (SLE) and other autoimmune diseases (ADs) have been limited. Therefore, we comprehensively tested autoimmune variants for association with SLE, aiming to identify pleiotropic genetic associations between these diseases. We compiled a list of 446 non–Major Histocompatibility Complex (MHC) variants identified in genome-wide association studies (GWAS) of populations of European ancestry across 17 ADs. We then tested these variants in our combined Caucasian SLE cohorts of 1,500 cases and 5,706 controls. We tested a subset of these polymorphisms in an independent Caucasian replication cohort of 2,085 SLE cases and 2,854 controls, allowing the computation of a meta-analysis between all cohorts. We have uncovered novel shared SLE loci that passed multiple comparisons adjustment, including the VTCN1 (rs12046117, P = 2.02×10−06) region. We observed that the loci shared among the most ADs include IL23R, OLIG3/TNFAIP3, and IL2RA. Given the lack of a universal autoimmune risk locus outside of the MHC and variable specificities for different diseases, our data suggests partial pleiotropy among ADs. Hierarchical clustering of ADs suggested that the most genetically related ADs appear to be type 1 diabetes with rheumatoid arthritis and Crohn's disease with ulcerative colitis. These findings support a relatively distinct genetic susceptibility for SLE. For many of the shared GWAS autoimmune loci, we found no evidence for association with SLE, including IL23R. Also, several established SLE loci are apparently not associated with other ADs, including the ITGAM-ITGAX and TNFSF4 regions. This study represents the most comprehensive evaluation of shared autoimmune loci to date, supports a relatively distinct non–MHC genetic susceptibility for SLE, provides further evidence for previously and newly identified shared genes in SLE, and highlights the value of studies of potentially pleiotropic genes in autoimmune diseases. It is well known that multiple autoimmune disorders cluster in families. However, all of the genetic variants that explain this clustering have not been discovered, and the specific genetic variants shared between systemic lupus erythematosus (SLE) and other autoimmune diseases (ADs) are not known. In order to better understand the genetic factors that explain this predisposition to autoimmunity, we performed a comprehensive evaluation of shared autoimmune genetic variants. First we considered results from 17 ADs and compiled a list with 446 significant genetic variants from these studies. We identified some genetic variants extensively shared between ADs, as well as the ADs that share the most variants. The genetic overlap between SLE and other ADs was modest. Next we tested how important all the 446 genetic variants were in our collection with a minimum of 1,500 SLE patients. Among the most significant variants in SLE, the majority had already been identified in previous studies, but we also discovered variants in two important immune genes. In summary, our data identified diseases with common genetic risk factors and novel SLE effects, and this supports a relatively distinct genetic susceptibility for SLE. This study helps delineate the genetic architecture of ADs.
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Affiliation(s)
- Paula S Ramos
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America.
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Tan W, Sunahori K, Zhao J, Deng Y, Kaufman KM, Kelly JA, Langefeld CD, Williams AH, Comeau ME, Ziegler JT, Marion MC, Bae SC, Lee JH, Lee JS, Chang DM, Song YW, Yu CY, Kimberly RP, Edberg JC, Brown EE, Petri MA, Ramsey-Goldman R, Vilá LM, Reveille JD, Alarcón-Riquelme ME, Harley JB, Boackle SA, Stevens AM, Scofield RH, Merrill JT, Freedman BI, Anaya JM, Criswell LA, Jacob CO, Vyse TJ, Niewold TB, Gaffney PM, Moser KL, Gilkeson GS, Kamen DL, James JA, Grossman JM, Hahn BH, Tsokos GC, Tsao BP, Alarcón GS. Association of PPP2CA polymorphisms with systemic lupus erythematosus susceptibility in multiple ethnic groups. ACTA ACUST UNITED AC 2011; 63:2755-63. [PMID: 21590681 DOI: 10.1002/art.30452] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE T cells from patients with systemic lupus erythematosus (SLE) express increased amounts of PP2Ac, which contributes to decreased production of interleukin-2 (IL-2). Because IL-2 is important in the regulation of several aspects of the immune response, it has been proposed that PP2Ac contributes to the expression of SLE. This study was designed to determine whether genetic variants of PPP2AC are linked to the expression of SLE and specific clinical manifestations and account for the increased expression of PP2Ac. METHODS We conducted a trans-ethnic study of 8,695 SLE cases and 7,308 controls of 4 different ancestries. Eighteen single-nucleotide polymorphisms (SNPs) across PPP2CA were genotyped using an Illumina custom array. PPP2CA expression in SLE and control T cells was analyzed by real-time polymerase chain reaction. RESULTS A 32-kb haplotype comprising multiple SNPs of PPP2CA showed significant association with SLE in Hispanic Americans, European Americans, and Asians, but not in African Americans. Conditional analyses revealed that SNP rs7704116 in intron 1 showed consistently strong association with SLE across Asian, European American, and Hispanic American populations (odds ratio 1.3 [95% confidence interval 1.14-1.31], meta-analysis P=3.8×10(-7)). In European Americans, the largest ethnic data set studied, the risk A allele of rs7704116 was associated with the presence of renal disease, anti-double-stranded DNA, and anti-RNP antibodies. PPP2CA expression was ∼2-fold higher in SLE patients carrying the rs7704116 AG genotype than those carrying the GG genotype (P=0.007). CONCLUSION Our data provide the first evidence of an association between PPP2CA polymorphisms and elevated PP2Ac transcript levels in T cells, which implicates a new molecular pathway for SLE susceptibility in European Americans, Hispanic Americans, and Asians.
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Affiliation(s)
- Wenfeng Tan
- David Geffen School of Medicine, Department of Medicine, University of California, Los Angeles, CA 90095-1670, USA
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55
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Zhao J, Wu H, Khosravi M, Cui H, Qian X, Kelly JA, Kaufman KM, Langefeld CD, Williams AH, Comeau ME, Ziegler JT, Marion MC, Adler A, Glenn SB, Alarcón-Riquelme ME, Pons-Estel BA, Harley JB, Bae SC, Bang SY, Cho SK, Jacob CO, Vyse TJ, Niewold TB, Gaffney PM, Moser KL, Kimberly RP, Edberg JC, Brown EE, Alarcon GS, Petri MA, Ramsey-Goldman R, Vilá LM, Reveille JD, James JA, Gilkeson GS, Kamen DL, Freedman BI, Anaya JM, Merrill JT, Criswell LA, Scofield RH, Stevens AM, Guthridge JM, Chang DM, Song YW, Park JA, Lee EY, Boackle SA, Grossman JM, Hahn BH, Goodship THJ, Cantor RM, Yu CY, Shen N, Tsao BP. Association of genetic variants in complement factor H and factor H-related genes with systemic lupus erythematosus susceptibility. PLoS Genet 2011; 7:e1002079. [PMID: 21637784 PMCID: PMC3102741 DOI: 10.1371/journal.pgen.1002079] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 03/28/2011] [Indexed: 01/24/2023] Open
Abstract
Systemic lupus erythematosus (SLE), a complex polygenic autoimmune disease, is associated with increased complement activation. Variants of genes encoding complement regulator factor H (CFH) and five CFH-related proteins (CFHR1-CFHR5) within the chromosome 1q32 locus linked to SLE, have been associated with multiple human diseases and may contribute to dysregulated complement activation predisposing to SLE. We assessed 60 SNPs covering the CFH-CFHRs region for association with SLE in 15,864 case-control subjects derived from four ethnic groups. Significant allelic associations with SLE were detected in European Americans (EA) and African Americans (AA), which could be attributed to an intronic CFH SNP (rs6677604, in intron 11, Pmeta = 6.6×10−8, OR = 1.18) and an intergenic SNP between CFHR1 and CFHR4 (rs16840639, Pmeta = 2.9×10−7, OR = 1.17) rather than to previously identified disease-associated CFH exonic SNPs, including I62V, Y402H, A474A, and D936E. In addition, allelic association of rs6677604 with SLE was subsequently confirmed in Asians (AS). Haplotype analysis revealed that the underlying causal variant, tagged by rs6677604 and rs16840639, was localized to a ∼146 kb block extending from intron 9 of CFH to downstream of CFHR1. Within this block, the deletion of CFHR3 and CFHR1 (CFHR3-1Δ), a likely causal variant measured using multiplex ligation-dependent probe amplification, was tagged by rs6677604 in EA and AS and rs16840639 in AA, respectively. Deduced from genotypic associations of tag SNPs in EA, AA, and AS, homozygous deletion of CFHR3-1Δ (Pmeta = 3.2×10−7, OR = 1.47) conferred a higher risk of SLE than heterozygous deletion (Pmeta = 3.5×10−4, OR = 1.14). These results suggested that the CFHR3-1Δ deletion within the SLE-associated block, but not the previously described exonic SNPs of CFH, might contribute to the development of SLE in EA, AA, and AS, providing new insights into the role of complement regulators in the pathogenesis of SLE. Systemic lupus erythematosus (SLE) is a complex autoimmune disease, associated with increased complement activation. Previous studies have provided evidence for the presence of SLE susceptibility gene(s) in the chromosome 1q31-32 locus. Within 1q32, genes encoding complement regulator factor H (CFH) and five CFH-related proteins (CFHR1-CFHR5) may contribute to the development of SLE, because genetic variants of these genes impair complement regulation and predispose to various human diseases. In this study, we tested association of genetic variants in the region containing CFH and CFHRs with SLE. We identified genetic variants predisposing to SLE in European American, African American, and Asian populations, which might be attributed to the deletion of CFHR3 and CFHR1 genes but not previously identified disease-associated exonic variants of CFH. This study provides the first evidence for consistent association between CFH/CFHRs and SLE across multi-ancestral SLE datasets, providing new insights into the role of complement regulators in the pathogenesis of SLE.
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Affiliation(s)
- Jian Zhao
- Division of Rheumatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Hui Wu
- Division of Rheumatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Melanie Khosravi
- Division of Rheumatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Huijuan Cui
- Joint Molecular Rheumatology Laboratory of Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institutes for Biological Sciences, and Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxia Qian
- Joint Molecular Rheumatology Laboratory of Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institutes for Biological Sciences, and Chinese Academy of Sciences, Shanghai, China
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Kenneth M. Kaufman
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- United States Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, United States of America
| | - Carl D. Langefeld
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Wake Forest, North Carolina, United States of America
| | - Adrienne H. Williams
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Wake Forest, North Carolina, United States of America
| | - Mary E. Comeau
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Wake Forest, North Carolina, United States of America
| | - Julie T. Ziegler
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Wake Forest, North Carolina, United States of America
| | - Miranda C. Marion
- Department of Biostatistical Sciences, Wake Forest University Health Sciences, Wake Forest, North Carolina, United States of America
| | - Adam Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Stuart B. Glenn
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Marta E. Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Center for Genomics and Oncological Research, Pfizer-University of Granada-Junta de Andalucia, Granada, Spain
| | | | | | | | - John B. Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- United States Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Soo-Kyung Cho
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Chaim O. Jacob
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Timothy J. Vyse
- Divisions of Genetics and Molecular Medicine and Immunology, King's College London, London, United Kingdom
| | - Timothy B. Niewold
- Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, United States of America
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Kathy L. Moser
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Robert P. Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jeffrey C. Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Elizabeth E. Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Graciela S. Alarcon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michelle A. Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Luis M. Vilá
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - John D. Reveille
- Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Judith A. James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Gary S. Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Diane L. Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Barry I. Freedman
- Department of Internal Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Juan-Manuel Anaya
- Center for Autoimmune Disease Research, Universidad del Rosario, Bogota, Colombia
| | - Joan T. Merrill
- Clinical Pharmacology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Lindsey A. Criswell
- Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - R. Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- United States Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, United States of America
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Anne M. Stevens
- Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Joel M. Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | | | - Yeong Wook Song
- Division of Rheumatology, Seoul National University, Seoul, Korea
| | - Ji Ah Park
- Division of Rheumatology, Seoul National University, Seoul, Korea
| | - Eun Young Lee
- Division of Rheumatology, Seoul National University, Seoul, Korea
| | - Susan A. Boackle
- Division of Rheumatology, School of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Jennifer M. Grossman
- Division of Rheumatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Bevra H. Hahn
- Division of Rheumatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | | | - Rita M. Cantor
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Chack-Yung Yu
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Nan Shen
- Joint Molecular Rheumatology Laboratory of Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institutes for Biological Sciences, and Chinese Academy of Sciences, Shanghai, China
| | - Betty P. Tsao
- Division of Rheumatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Thompson SD, Sudman M, Ramos PS, Marion MC, Ryan M, Tsoras M, Weiler T, Wagner M, Keddache M, Haas JP, Mueller C, Prahalad S, Bohnsack J, Wise CA, Punaro M, Zhang D, Rosé CD, Comeau ME, Divers J, Glass DN, Langefeld CD. The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1. ACTA ACUST UNITED AC 2010; 62:3265-76. [PMID: 20722033 DOI: 10.1002/art.27688] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To test for associations between non-major histocompatibility complex susceptibility loci previously reported in autoimmune diseases and juvenile idiopathic arthritis (JIA). METHODS Published autoimmune disease genome-wide association studies were reviewed, and 519 single-nucleotide polymorphisms (SNPs) were selected for association testing. The initial cohort included 809 JIA cases and 3,535 controls of non-Hispanic, European ancestry. Of the SNPs, 257 were successfully genotyped, while 168 were imputed with quality. Based on findings in the initial cohort, replication was sought for 21 SNPs in a second cohort of 1,015 JIA cases and 1,569 controls collected in the US and Germany. For the initial cohort, tests for association were adjusted for potential confounding effects of population structure by including principal components derived from a genome-wide association study as covariates in logistic regression models. Odds ratios (ORs) and 95% confidence intervals were calculated. RESULTS Testing for association of previously reported autoimmune disease genetic associations in the initial cohort suggested associations with JIA in 13 distinct loci. Of these, 7 were validated in the replication cohort. Meta-analysis results for the replicating loci included PTPN22 (rs6679677 [OR 1.58, P = 1.98 × 10(-12) ], rs2476601 [OR 1.64, P = 1.90 × 10(-13) ], and rs2488457 [OR 1.32, P = 6.74 × 10(-8) ]), PTPN2 (rs1893217 [OR = 1.33, P = 1.60 × 10(-9) ] and rs7234029 [OR 1.35, P = 1.86 × 10(-10) ]), ADAD1-IL2-IL21 (rs17388568 [OR 1.24, P = 1.13 × 10(-6) ] and rs13143866 [OR 0.83, P = 1.95 × 10(-4) ]), STAT4 (rs3821236 [OR = 1.27, P = 2.36 × 10(-6) ] and rs7574865 [OR = 1.31, P = 2.21 × 10(-6) ]), C12orf30 (rs17696736 [OR = 1.19, P = 2.59 × 10(-5) ]), COG6 (rs7993214 [OR = 0.76, P = 1.10 × 10(-5) ]), and ANGPT1 (rs1010824 [OR = 0.79, P = 2.91 × 10(-4) ]). These polymorphisms have been reported in diseases such as rheumatoid arthritis, type 1 diabetes mellitus, Crohn's disease, and multiple sclerosis. CONCLUSION General susceptibility loci for autoimmunity are shared across diseases, including JIA, suggesting the potential for common therapeutic targets and mechanisms.
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Affiliation(s)
- Susan D Thompson
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.
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