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Wang Y, Guga S, Wu K, Khaw Z, Tzoumkas K, Tombleson P, Comeau ME, Langefeld CD, Cunninghame Graham DS, Morris DL, Vyse TJ. COVID-19 and systemic lupus erythematosus genetics: A balance between autoimmune disease risk and protection against infection. PLoS Genet 2022; 18:e1010253. [PMID: 36327221 PMCID: PMC9632821 DOI: 10.1371/journal.pgen.1010253] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 05/16/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Genome wide association studies show there is a genetic component to severe COVID-19. We find evidence that the genome-wide genetic association signal with severe COVID-19 is correlated with that of systemic lupus erythematosus (SLE), having formally tested this using genetic correlation analysis by LD score regression. To identify the shared associated loci and gain insight into the shared genetic effects, using summary level data we performed meta-analyses, a local genetic correlation analysis and fine-mapping using stepwise regression and functional annotation. This identified multiple loci shared between the two traits, some of which exert opposing effects. The locus with most evidence of shared association is TYK2, a gene critical to the type I interferon pathway, where the local genetic correlation is negative. Another shared locus is CLEC1A, where the direction of effects is aligned, that encodes a lectin involved in cell signaling, and the anti-fungal immune response. Our analyses suggest that several loci with reciprocal effects between the two traits have a role in the defense response pathway, adding to the evidence that SLE risk alleles are protective against infection. We observed a correlation between the genetic associations with severe COVID-19 and those with systemic lupus erythematosus (SLE, Lupus), and aimed to discover which genetic loci were shared by these diseases and what biological processes were involved. This resulted in the discovery of several genetic loci, some of which had alleles that were risk for both diseases and some of which were risk for severe COVID-19 yet protective for SLE. The locus with most evidence of shared association (TYK2) is involved in interferon production, a process that is important in response to viral infection and known to be dysregulated in SLE patients. Other shared associated loci contained genes also involved in the defense response and the immune system signaling. These results add to the growing evidence that there are alleles in the human genome that provide protection against viral infection yet are risk for autoimmune disease.
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Affiliation(s)
- Yuxuan Wang
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
| | - Suri Guga
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
| | - Kejia Wu
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
| | - Zoe Khaw
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
| | - Konstantinos Tzoumkas
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
| | - Phil Tombleson
- NIHR GSTFT/KCL Biomedical Research Centre, London, United Kingdom
| | - Mary E. Comeau
- Department of Biostatistics and Data Science and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | | | - David L. Morris
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
- * E-mail:
| | - Timothy J. Vyse
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
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Chen L, Wang YF, Liu L, Bielowka A, Ahmed R, Zhang H, Tombleson P, Roberts AL, Odhams CA, Cunninghame Graham DS, Zhang X, Yang W, Vyse TJ, Morris DL. Genome-wide assessment of genetic risk for systemic lupus erythematosus and disease severity. Hum Mol Genet 2021; 29:1745-1756. [PMID: 32077931 PMCID: PMC7322569 DOI: 10.1093/hmg/ddaa030] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/30/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Using three European and two Chinese genome-wide association studies (GWAS), we investigated the performance of genetic risk scores (GRSs) for predicting the susceptibility and severity of systemic lupus erythematosus (SLE), using renal disease as a proxy for severity. We used four GWASs to test the performance of GRS both cross validating within the European population and between European and Chinese populations. The performance of GRS in SLE risk prediction was evaluated by receiver operating characteristic (ROC) curves. We then analyzed the polygenic nature of SLE statistically. We also partitioned patients according to their age-of-onset and evaluated the predictability of GRS in disease severity in each age group. We found consistently that the best GRS in the prediction of SLE used SNPs associated at the level of P < 1e−05 in all GWAS data sets and that SNPs with P-values above 0.2 were inflated for SLE true positive signals. The GRS results in an area under the ROC curve ranging between 0.64 and 0.72, within European and between the European and Chinese populations. We further showed a significant positive correlation between a GRS and renal disease in two independent European GWAS (Pcohort1 = 2.44e−08; Pcohort2 = 0.00205) and a significant negative correlation with age of SLE onset (Pcohort1 = 1.76e−12; Pcohort2 = 0.00384). We found that the GRS performed better in the prediction of renal disease in the ‘later onset’ compared with the ‘earlier onset’ group. The GRS predicts SLE in both European and Chinese populations and correlates with poorer prognostic factors: young age-of-onset and lupus nephritis.
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Affiliation(s)
- Lingyan Chen
- Department of Medical and Molecular Genetics, King's College London, London, UK.,MRC/BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Lu Liu
- Department of Dermatology, NO. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China.,Department of Dermatology, Huashan Hospital of Fudan University, Shanghai, China
| | - Adrianna Bielowka
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Rahell Ahmed
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Huoru Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Phil Tombleson
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Amy L Roberts
- Department of Medical and Molecular Genetics, King's College London, London, UK.,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | | | - Xuejun Zhang
- Department of Dermatology, NO. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China.,Department of Dermatology, Huashan Hospital of Fudan University, Shanghai, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - David L Morris
- Department of Medical and Molecular Genetics, King's College London, London, UK
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Vester SK, Beavil RL, Lynham S, Beavil AJ, Cunninghame Graham DS, McDonnell JM, Vyse TJ. Nucleolin acts as the receptor for C1QTNF4 and supports C1QTNF4-mediated innate immunity modulation. J Biol Chem 2021; 296:100513. [PMID: 33676896 PMCID: PMC8042453 DOI: 10.1016/j.jbc.2021.100513] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/16/2022] Open
Abstract
The C1q and TNF related 4 (C1QTNF4) protein is a structurally unique member of the C1QTNF family, a family of secreted proteins that have structural homology with both complement C1q and the tumor necrosis factor superfamily. C1QTNF4 has been linked to the autoimmune disease systemic lupus erythematosus through genetic studies; however, its role in immunity and inflammation remains poorly defined and a cell surface receptor of C1QTNF4 has yet to be identified. Here we report identification of nucleolin as a cell surface receptor of C1QTNF4 using mass spectrometric analysis. Additionally, we present evidence that the interaction between C1QTNF4 and nucleolin is mediated by the second C1q-like domain of C1QTNF4 and the C terminus of nucleolin. We show that monocytes and B cells are target cells of C1QTNF4 and observe extensive binding to dead cells. Imaging flow cytometry experiments in monocytes show that C1QTNF4 becomes actively internalized upon cell binding. Our results suggest that nucleolin may serve as a docking molecule for C1QTNF4 and act in a context-dependent manner through coreceptors. Taken together, these findings further our understanding of C1QTNF4's function in the healthy immune system and how dysfunction may contribute to the development of systemic lupus erythematosus.
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Affiliation(s)
- Susan K Vester
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Rebecca L Beavil
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, King's College London, London, UK
| | - Andrew J Beavil
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | | | - James M McDonnell
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, London, UK.
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Vyse TJ, Cunninghame Graham DS. Trans-Ancestral Fine-Mapping and Epigenetic Annotation as Tools to Delineate Functionally Relevant Risk Alleles at IKZF1 and IKZF3 in Systemic Lupus Erythematosus. Int J Mol Sci 2020; 21:ijms21218383. [PMID: 33182226 PMCID: PMC7664943 DOI: 10.3390/ijms21218383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Prioritizing tag-SNPs carried on extended risk haplotypes at susceptibility loci for common disease is a challenge. Methods: We utilized trans-ancestral exclusion mapping to reduce risk haplotypes at IKZF1 and IKZF3 identified in multiple ancestries from SLE GWAS and ImmunoChip datasets. We characterized functional annotation data across each risk haplotype from publicly available datasets including ENCODE, RoadMap Consortium, PC Hi-C data from 3D genome browser, NESDR NTR conditional eQTL database, GeneCards Genehancers and TF (transcription factor) binding sites from Haploregv4. Results: We refined the 60 kb associated haplotype upstream of IKZF1 to just 12 tag-SNPs tagging a 47.7 kb core risk haplotype. There was preferential enrichment of DNAse I hypersensitivity and H3K27ac modification across the 3′ end of the risk haplotype, with four tag-SNPs sharing allele-specific TF binding sites with promoter variants, which are eQTLs for IKZF1 in whole blood. At IKZF3, we refined a core risk haplotype of 101 kb (27 tag-SNPs) from an initial extended haplotype of 194 kb (282 tag-SNPs), which had widespread DNAse I hypersensitivity, H3K27ac modification and multiple allele-specific TF binding sites. Dimerization of Fox family TFs bound at the 3′ and promoter of IKZF3 may stabilize chromatin looping across the locus. Conclusions: We combined trans-ancestral exclusion mapping and epigenetic annotation to identify variants at both IKZF1 and IKZF3 with the highest likelihood of biological relevance. The approach will be of strong interest to other complex trait geneticists seeking to attribute biological relevance to risk alleles on extended risk haplotypes in their disease of interest.
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Odhams CA, Roberts AL, Vester SK, Duarte CST, Beales CT, Clarke AJ, Lindinger S, Daffern SJ, Zito A, Chen L, Jones LL, Boteva L, Morris DL, Small KS, Fernando MMA, Cunninghame Graham DS, Vyse TJ. Interferon inducible X-linked gene CXorf21 may contribute to sexual dimorphism in Systemic Lupus Erythematosus. Nat Commun 2019; 10:2164. [PMID: 31092820 PMCID: PMC6520347 DOI: 10.1038/s41467-019-10106-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease, characterised by increased expression of type I interferon (IFN)-regulated genes and a striking sex imbalance towards females. Through combined genetic, in silico, in vitro, and ex vivo approaches, we define CXorf21, a gene of hitherto unknown function, which escapes X-chromosome inactivation, as a candidate underlying the Xp21.2 SLE association. We demonstrate that CXorf21 is an IFN-response gene and that the sexual dimorphism in expression is magnified by immunological challenge. Fine-mapping reveals a single haplotype as a potential causal cis-eQTL for CXorf21. We propose that expression is amplified through modification of promoter and 3'-UTR chromatin interactions. Finally, we show that the CXORF21 protein colocalises with TLR7, a pathway implicated in SLE pathogenesis. Our study reveals modulation in gene expression affected by the combination of two hallmarks of SLE: CXorf21 expression increases in a both an IFN-inducible and sex-specific manner.
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Affiliation(s)
- Christopher A Odhams
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- Genomics England, Queen Mary University of London, Dawson Hall, London, EC1M 6BQ, UK
| | - Amy L Roberts
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Susan K Vester
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Carolina S T Duarte
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Charlie T Beales
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Alexander J Clarke
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Sonja Lindinger
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- University of Applied Sciences - FH Campus Wien, Favoritenstrasse 226, 1100, Wien, Austria
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria
| | - Samuel J Daffern
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Antonino Zito
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Lingyan Chen
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- MRC/BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Leonardo L Jones
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Lora Boteva
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
- MRC Human Genetics Unit MRC IGMM, University of Edinburgh Western General Hospital, Edinburgh, EH4 2XU, UK
| | - David L Morris
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Kerrin S Small
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Michelle M A Fernando
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | | | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK.
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Karrar S, Cunninghame Graham DS. Abnormal B Cell Development in Systemic Lupus Erythematosus: What the Genetics Tell Us. Arthritis Rheumatol 2018; 70:496-507. [PMID: 29207444 PMCID: PMC5900717 DOI: 10.1002/art.40396] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/29/2017] [Indexed: 12/15/2022]
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Odhams CA, Cunninghame Graham DS, Vyse TJ. Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease. PLoS Genet 2017; 13:e1007071. [PMID: 29059182 PMCID: PMC5695635 DOI: 10.1371/journal.pgen.1007071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 04/19/2017] [Revised: 11/02/2017] [Accepted: 10/11/2017] [Indexed: 01/12/2023] Open
Abstract
Genome-wide association studies have identified hundreds of risk loci for autoimmune disease, yet only a minority (~25%) share genetic effects with changes to gene expression (eQTLs) in immune cells. RNA-Seq based quantification at whole-gene resolution, where abundance is estimated by culminating expression of all transcripts or exons of the same gene, is likely to account for this observed lack of colocalisation as subtle isoform switches and expression variation in independent exons can be concealed. We performed integrative cis-eQTL analysis using association statistics from twenty autoimmune diseases (560 independent loci) and RNA-Seq data from 373 individuals of the Geuvadis cohort profiled at gene-, isoform-, exon-, junction-, and intron-level resolution in lymphoblastoid cell lines. After stringently testing for a shared causal variant using both the Joint Likelihood Mapping and Regulatory Trait Concordance frameworks, we found that gene-level quantification significantly underestimated the number of causal cis-eQTLs. Only 5.0-5.3% of loci were found to share a causal cis-eQTL at gene-level compared to 12.9-18.4% at exon-level and 9.6-10.5% at junction-level. More than a fifth of autoimmune loci shared an underlying causal variant in a single cell type by combining all five quantification types; a marked increase over current estimates of steady-state causal cis-eQTLs. Causal cis-eQTLs detected at different quantification types localised to discrete epigenetic annotations. We applied a linear mixed-effects model to distinguish cis-eQTLs modulating all expression elements of a gene from those where the signal is only evident in a subset of elements. Exon-level analysis detected disease-associated cis-eQTLs that subtly altered transcription globally across the target gene. We dissected in detail the genetic associations of systemic lupus erythematosus and functionally annotated the candidate genes. Many of the known and novel genes were concealed at gene-level (e.g. IKZF2, TYK2, LYST). Our findings are provided as a web resource.
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Affiliation(s)
- Christopher A. Odhams
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
| | - Deborah S. Cunninghame Graham
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
- Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, King’s College London, London, United Kingdom
| | - Timothy J. Vyse
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
- Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, King’s College London, London, United Kingdom
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Cortini A, Ellinghaus U, Malik TH, Cunninghame Graham DS, Botto M, Vyse TJ. B cell OX40L supports T follicular helper cell development and contributes to SLE pathogenesis. Ann Rheum Dis 2017; 76:2095-2103. [PMID: 28818832 PMCID: PMC5705841 DOI: 10.1136/annrheumdis-2017-211499] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/01/2017] [Indexed: 01/27/2023]
Abstract
Objectives TNFSF4 (encodes OX40L) is a susceptibility locus for systemic lupus erythematosus (SLE). Risk alleles increase TNFSF4 expression in cell lines, but the mechanism linking this effect to disease is unclear, and the OX40L-expressing cell types mediating the risk are not clearly established. Blockade of OX40L has been demonstrated to reduce disease severity in several models of autoimmunity, but not in SLE. We sought to investigate its potential therapeutic role in lupus. Methods We used a conditional knockout mouse system to investigate the function of OX40L on B and T lymphocytes in systemic autoimmunity. Results Physiologically, OX40L on both B and T cells contributed to the humoral immune response, but B cell OX40L supported the secondary humoral response and antibody affinity maturation. Our data also indicated that loss of B cell OX40L impeded the generation of splenic T follicular helper cells. We further show that in two models of SLE—a spontaneous congenic model and the H2-IAbm12 graft-versus-host-induced model—loss of B cell OX40L ameliorates the autoimmune phenotype. This improvement was, in each case, accompanied by a decline in T follicular helper cell numbers. Importantly, the germline knockout did not exhibit a markedly different phenotype from the B cell knockout in these models. Conclusions These findings contribute to a model in which genetically determined increased OX40L expression promotes human SLE by several mechanisms, contingent on its cellular expression. The improvement in pathology in two models of systemic autoimmunity indicates that OX40L is an excellent therapeutic target in SLE.
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Affiliation(s)
- Andrea Cortini
- Division of Medical and Molecular Genetics and Immunology, Infection and Inflammatory Disease, King's College London, London, UK
| | - Ursula Ellinghaus
- Division of Medical and Molecular Genetics and Immunology, Infection and Inflammatory Disease, King's College London, London, UK
| | - Talat H Malik
- Department of Medicine, Centre for Complement and Inflammation Research, Imperial College London, London, UK
| | - Deborah S Cunninghame Graham
- Division of Medical and Molecular Genetics and Immunology, Infection and Inflammatory Disease, King's College London, London, UK
| | - Marina Botto
- Department of Medicine, Centre for Complement and Inflammation Research, Imperial College London, London, UK
| | - Timothy James Vyse
- Division of Medical and Molecular Genetics and Immunology, Infection and Inflammatory Disease, King's College London, London, UK
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Li H, Reksten TR, Ice JA, Kelly JA, Adrianto I, Rasmussen A, Wang S, He B, Grundahl KM, Glenn SB, Miceli-Richard C, Bowman S, Lester S, Eriksson P, Eloranta ML, Brun JG, Gøransson LG, Harboe E, Guthridge JM, Kaufman KM, Kvarnström M, Cunninghame Graham DS, Patel K, Adler AJ, Farris AD, Brennan MT, Chodosh J, Gopalakrishnan R, Weisman MH, Venuturupalli S, Wallace DJ, Hefner KS, Houston GD, Huang AJW, Hughes PJ, Lewis DM, Radfar L, Vista ES, Edgar CE, Rohrer MD, Stone DU, Vyse TJ, Harley JB, Gaffney PM, James JA, Turner S, Alevizos I, Anaya JM, Rhodus NL, Segal BM, Montgomery CG, Scofield RH, Kovats S, Mariette X, Rönnblom L, Witte T, Rischmueller M, Wahren-Herlenius M, Omdal R, Jonsson R, Ng WF, Nordmark G, Lessard CJ, Sivils KL. Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons. PLoS Genet 2017. [PMID: 28640813 PMCID: PMC5501660 DOI: 10.1371/journal.pgen.1006820] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [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] [Indexed: 01/09/2023] Open
Abstract
Sjögren's syndrome (SS) is a common, autoimmune exocrinopathy distinguished by keratoconjunctivitis sicca and xerostomia. Patients frequently develop serious complications including lymphoma, pulmonary dysfunction, neuropathy, vasculitis, and debilitating fatigue. Dysregulation of type I interferon (IFN) pathway is a prominent feature of SS and is correlated with increased autoantibody titers and disease severity. To identify genetic determinants of IFN pathway dysregulation in SS, we performed cis-expression quantitative trait locus (eQTL) analyses focusing on differentially expressed type I IFN-inducible transcripts identified through a transcriptome profiling study. Multiple cis-eQTLs were associated with transcript levels of 2'-5'-oligoadenylate synthetase 1 (OAS1) peaking at rs10774671 (PeQTL = 6.05 × 10-14). Association of rs10774671 with SS susceptibility was identified and confirmed through meta-analysis of two independent cohorts (Pmeta = 2.59 × 10-9; odds ratio = 0.75; 95% confidence interval = 0.66-0.86). The risk allele of rs10774671 shifts splicing of OAS1 from production of the p46 isoform to multiple alternative transcripts, including p42, p48, and p44. We found that the isoforms were differentially expressed within each genotype in controls and patients with and without autoantibodies. Furthermore, our results showed that the three alternatively spliced isoforms lacked translational response to type I IFN stimulation. The p48 and p44 isoforms also had impaired protein expression governed by the 3' end of the transcripts. The SS risk allele of rs10774671 has been shown by others to be associated with reduced OAS1 enzymatic activity and ability to clear viral infections, as well as reduced responsiveness to IFN treatment. Our results establish OAS1 as a risk locus for SS and support a potential role for defective viral clearance due to altered IFN response as a genetic pathophysiological basis of this complex autoimmune disease.
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Affiliation(s)
- He Li
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Tove Ragna Reksten
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - John A. Ice
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Indra Adrianto
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Astrid Rasmussen
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Shaofeng Wang
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Bo He
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Kiely M. Grundahl
- 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
| | - Corinne Miceli-Richard
- Université Paris-Sud, AP-HP, Hôpitaux Universitaires Paris-Sud, INSERM U1012, Le Kremlin Bicêtre, France
| | - Simon Bowman
- Rheumatology Department, University Hospital Birmingham, Birmingham, United Kingdom
| | - Sue Lester
- The Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | - Per Eriksson
- Department of Rheumatology, Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Maija-Leena Eloranta
- Department of Medical Sciences, Rheumatology, SciLIfeLab, Uppsala University, Uppsala, Sweden
| | - Johan G. Brun
- Department of Clinical Science, 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
| | - Joel M. Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Kenneth M. Kaufman
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | | | | | - Ketan Patel
- Division of Oral and Maxillofacial Surgery, Department of Developmental and Surgical Science, University of Minnesota School of Dentistry, Minneapolis, Minnesota, United States of America
- Department of Oral and Maxillofacial Surgery, North Memorial Medical Center, Robbinsdale, Minnesota, United States of America
| | - Adam J. Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - A. Darise Farris
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Michael T. Brennan
- Department of Oral Medicine, Carolinas Medical Center, Charlotte, North Carolina, United States of America
| | - James Chodosh
- Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rajaram Gopalakrishnan
- Division of Oral Pathology, Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, Minnesota, United States of America
| | - Michael H. Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Swamy Venuturupalli
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Daniel J. Wallace
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Kimberly S. Hefner
- Hefner Eye Care and Optical Center, Oklahoma City, Oklahoma, United States of America
| | - Glen D. Houston
- Department of Oral and Maxillofacial Pathology, University of Oklahoma College of Dentistry, Oklahoma City, Oklahoma, United States of America
- Heartland Pathology Consultants, Edmond, Oklahoma, United States of America
| | - Andrew J. W. Huang
- Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, Missouri, United States of America
| | - Pamela J. Hughes
- Division of Oral and Maxillofacial Surgery, Department of Developmental and Surgical Science, University of Minnesota School of Dentistry, Minneapolis, Minnesota, United States of America
| | - David M. Lewis
- Department of Oral and Maxillofacial Pathology, University of Oklahoma College of Dentistry, Oklahoma City, Oklahoma, United States of America
| | - Lida Radfar
- Oral Diagnosis and Radiology Department, University of Oklahoma College of Dentistry, Oklahoma City, Oklahoma, United States of America
| | - Evan S. Vista
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- University of Santo Tomas Hospital, Manila, The Philippines
| | - Contessa E. Edgar
- The Biology Department, Oklahoma Baptist University, Oklahoma City, Oklahoma, United States of America
| | - Michael D. Rohrer
- Hard Tissue Research Laboratory, University of Minnesota School of Dentistry, Minneapolis, Minnesota, United States of America
| | - Donald U. Stone
- Department of Ophthalmology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Timothy J. Vyse
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - John B. Harley
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, 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 Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Sean Turner
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Ilias Alevizos
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, United States of America
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research, Universidad del Rosario, Bogotá, Colombia
| | - Nelson L. Rhodus
- Department of Oral Surgery, University of Minnesota School of Dentistry, Minneapolis, Minnesota, United States of America
| | - Barbara M. Segal
- Division of Rheumatology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Courtney G. Montgomery
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - R. Hal Scofield
- 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
- US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma, United States of America
| | - Susan Kovats
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Xavier Mariette
- Université Paris-Sud, AP-HP, Hôpitaux Universitaires Paris-Sud, INSERM U1012, Le Kremlin Bicêtre, France
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology, SciLIfeLab, Uppsala University, Uppsala, Sweden
| | - Torsten Witte
- Clinic for Immunology and Rheumatology, Hannover Medical School, Hannover, Germany
| | - Maureen Rischmueller
- The Queen Elizabeth Hospital, Adelaide, South Australia, Australia
- The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Roald Omdal
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Roland Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Wan-Fai Ng
- Institute of Cellular Medicine & NIHR Newcastle Biomedical Research Centre, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Gunnel Nordmark
- Department of Medical Sciences, Rheumatology, SciLIfeLab, Uppsala University, Uppsala, Sweden
| | - Christopher J. Lessard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Kathy L. Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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10
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Odhams CA, Cortini A, Chen L, Roberts AL, Viñuela A, Buil A, Small KS, Dermitzakis ET, Morris DL, Vyse TJ, Cunninghame Graham DS. Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus. Hum Mol Genet 2017; 26:1003-1017. [PMID: 28062664 PMCID: PMC5409091 DOI: 10.1093/hmg/ddw417] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022] Open
Abstract
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through the integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines. We use conditional analysis and a Bayesian colocalisation method to provide evidence of a shared causal-variant, then compare the ability of each quantification type to detect disease relevant eQTLs and eGenes. We discovered the greatest frequency of candidate-causal eQTLs using exon-level RNA-Seq, and identified novel SLE susceptibility genes (e.g. NADSYN1 and TCF7) that were concealed using microarrays, including four non-coding RNAs. Many of these eQTLs were found to influence the expression of several genes, supporting the notion that risk haplotypes may harbour multiple functional effects. Novel SLE associated splicing events were identified in the T-reg restricted transcription factor, IKZF2, and other candidate genes (e.g. WDFY4) through asQTL mapping using the Geuvadis cohort. We have significantly increased our understanding of the genetic control of gene-expression in SLE by maximising the leverage of RNA-Seq and performing integrative GWAS-eQTL analysis against gene, exon, and splice-junction quantifications. We conclude that to better understand the true functional consequence of regulatory variants, quantification by RNA-Seq should be performed at the exon-level as a minimum, and run in parallel with gene and splice-junction level quantification.
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Affiliation(s)
| | - Andrea Cortini
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Lingyan Chen
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Amy L Roberts
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Ana Viñuela
- Department of Twin Research, King's College London, London, UK
| | | | - Kerrin S Small
- Department of Twin Research, King's College London, London, UK
| | | | - David L Morris
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, London, UK.,Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK
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11
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Morris DL, Sheng Y, Zhang Y, Wang YF, Zhu Z, Tombleson P, Chen L, Cunninghame Graham DS, Bentham J, Roberts AL, Chen R, Zuo X, Wang T, Wen L, Yang C, Liu L, Yang L, Li F, Huang Y, Yin X, Yang S, Rönnblom L, Fürnrohr BG, Voll RE, Schett G, Costedoat-Chalumeau N, Gaffney PM, Lau YL, Zhang X, Yang W, Cui Y, Vyse TJ. Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus. Nat Genet 2016; 48:940-946. [PMID: 27399966 PMCID: PMC4966635 DOI: 10.1038/ng.3603] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/01/2016] [Indexed: 12/14/2022]
Abstract
Systemic lupus erythematosus (SLE; OMIM 152700) is a genetically complex autoimmune disease. Genome-wide association studies (GWASs) have identified more than 50 loci as robustly associated with the disease in single ancestries, but genome-wide transancestral studies have not been conducted. We combined three GWAS data sets from Chinese (1,659 cases and 3,398 controls) and European (4,036 cases and 6,959 controls) populations. A meta-analysis of these studies showed that over half of the published SLE genetic associations are present in both populations. A replication study in Chinese (3,043 cases and 5,074 controls) and European (2,643 cases and 9,032 controls) subjects found ten previously unreported SLE loci. Our study provides further evidence that the majority of genetic risk polymorphisms for SLE are contained within the same regions across both populations. Furthermore, a comparison of risk allele frequencies and genetic risk scores suggested that the increased prevalence of SLE in non-Europeans (including Asians) has a genetic basis.
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Affiliation(s)
- David L Morris
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Yujun Sheng
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China.,Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Yan Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Zhengwei Zhu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Philip Tombleson
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Lingyan Chen
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | | | - James Bentham
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Amy L Roberts
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Ruoyan Chen
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xianbo Zuo
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Tingyou Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Leilei Wen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Chao Yang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Lu Liu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Lulu Yang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Feng Li
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Yuanbo Huang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Xianyong Yin
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Sen Yang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Lars Rönnblom
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Barbara G Fürnrohr
- Department of Internal Medicine 3, University of Erlangen-Nuremberg, Erlangen, Germany.,Institute for Clinical Immunology, University of Erlangen-Nuremberg, Erlangen, Germany.,Division of Genetic Epidemiology, Medical University Innsbruck, Innsbruck, Austria.,Division of Biological Chemistry, Medical University Innsbruck, Innsbruck, Austria
| | - Reinhard E Voll
- Department of Internal Medicine 3, University of Erlangen-Nuremberg, Erlangen, Germany.,Institute for Clinical Immunology, University of Erlangen-Nuremberg, Erlangen, Germany.,Department of Rheumatology, University Hospital Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, University Hospital Freiburg, Freiburg, Germany.,Centre for Chronic Immunodeficiency, University Hospital Freiburg, Freiburg, Germany
| | - Georg Schett
- Department of Internal Medicine 3, University of Erlangen-Nuremberg, Erlangen, Germany.,Institute for Clinical Immunology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Nathalie Costedoat-Chalumeau
- AP-HP, Hôpital Cochin, Centre de référence maladies auto-immunes et systémiques rares, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.,The University of Hong Kong Shenzhen Hospital, Shenzhen, China
| | - Xuejun Zhang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China.,Department of Dermatology, Huashan Hospital of Fudan University, Shanghai, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yong Cui
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China.,Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine, King's College London, London, UK.,Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK
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12
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Günther C, Kind B, Reijns MAM, Berndt N, Martinez-Bueno M, Wolf C, Tüngler V, Chara O, Lee YA, Hübner N, Bicknell L, Blum S, Krug C, Schmidt F, Kretschmer S, Koss S, Astell KR, Ramantani G, Bauerfeind A, Morris DL, Cunninghame Graham DS, Bubeck D, Leitch A, Ralston SH, Blackburn EA, Gahr M, Witte T, Vyse TJ, Melchers I, Mangold E, Nöthen MM, Aringer M, Kuhn A, Lüthke K, Unger L, Bley A, Lorenzi A, Isaacs JD, Alexopoulou D, Conrad K, Dahl A, Roers A, Alarcon-Riquelme ME, Jackson AP, Lee-Kirsch MA. Defective removal of ribonucleotides from DNA promotes systemic autoimmunity. J Clin Invest 2014; 125:413-24. [PMID: 25500883 DOI: 10.1172/jci78001] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/09/2014] [Indexed: 01/22/2023] Open
Abstract
Genome integrity is continuously challenged by the DNA damage that arises during normal cell metabolism. Biallelic mutations in the genes encoding the genome surveillance enzyme ribonuclease H2 (RNase H2) cause Aicardi-Goutières syndrome (AGS), a pediatric disorder that shares features with the autoimmune disease systemic lupus erythematosus (SLE). Here we determined that heterozygous parents of AGS patients exhibit an intermediate autoimmune phenotype and demonstrated a genetic association between rare RNASEH2 sequence variants and SLE. Evaluation of patient cells revealed that SLE- and AGS-associated mutations impair RNase H2 function and result in accumulation of ribonucleotides in genomic DNA. The ensuing chronic low level of DNA damage triggered a DNA damage response characterized by constitutive p53 phosphorylation and senescence. Patient fibroblasts exhibited constitutive upregulation of IFN-stimulated genes and an enhanced type I IFN response to the immunostimulatory nucleic acid polyinosinic:polycytidylic acid and UV light irradiation, linking RNase H2 deficiency to potentiation of innate immune signaling. Moreover, UV-induced cyclobutane pyrimidine dimer formation was markedly enhanced in ribonucleotide-containing DNA, providing a mechanism for photosensitivity in RNase H2-associated SLE. Collectively, our findings implicate RNase H2 in the pathogenesis of SLE and suggest a role of DNA damage-associated pathways in the initiation of autoimmunity.
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13
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Lessard CJ, Li H, Adrianto I, Ice JA, Rasmussen A, Grundahl KM, Kelly JA, Dozmorov MG, Miceli-Richard C, Bowman S, Lester S, Eriksson P, Eloranta ML, Brun JG, Gøransson LG, Harboe E, Guthridge JM, Kaufman KM, Kvarnström M, Jazebi H, Cunninghame Graham DS, Grandits ME, Nazmul-Hossain ANM, Patel K, Adler AJ, Maier-Moore JS, Farris AD, Brennan MT, Lessard JA, Chodosh J, Gopalakrishnan R, Hefner KS, Houston GD, Huang AJW, Hughes PJ, Lewis DM, Radfar L, Rohrer MD, Stone DU, Wren JD, Vyse TJ, Gaffney PM, James JA, Omdal R, Wahren-Herlenius M, Illei GG, Witte T, Jonsson R, Rischmueller M, Rönnblom L, Nordmark G, Ng WF, Mariette X, Anaya JM, Rhodus NL, Segal BM, Scofield RH, Montgomery CG, Harley JB, Sivils KL. Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome. Nat Genet 2013; 45:1284-92. [PMID: 24097067 PMCID: PMC3867192 DOI: 10.1038/ng.2792] [Citation(s) in RCA: 349] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 09/11/2013] [Indexed: 12/11/2022]
Abstract
Sjögren’s syndrome is a common autoimmune disease (~0.7% of European Americans) typically presenting as keratoconjunctivitis sicca and xerostomia. In addition to strong association within the HLA region at 6p21 (Pmeta=7.65×10−114), we establish associations with IRF5-TNPO3 (Pmeta=2.73×10−19), STAT4 (Pmeta=6.80×10−15), IL12A (Pmeta =1.17×10−10), FAM167A-BLK (Pmeta=4.97×10−10), DDX6-CXCR5 (Pmeta=1.10×10−8), and TNIP1 (Pmeta=3.30×10−8). Suggestive associations with Pmeta<5×10−5 were observed with 29 regions including TNFAIP3, PTTG1, PRDM1, DGKQ, FCGR2A, IRAK1BP1, ITSN2, and PHIP amongst others. These results highlight the importance of genes involved in both innate and adaptive immunity in Sjögren’s syndrome.
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Affiliation(s)
- Christopher J Lessard
- 1] Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA. [2] Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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14
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Manjarrez-Orduño N, Marasco E, Chung SA, Katz MS, Kiridly JF, Simpfendorfer KR, Freudenberg J, Ballard DH, Nashi E, Hopkins TJ, Cunninghame Graham DS, Lee AT, Coenen MJH, Franke B, Swinkels DW, Graham RR, Kimberly RP, Gaffney PM, Vyse TJ, Behrens TW, Criswell LA, Diamond B, Gregersen PK. CSK regulatory polymorphism is associated with systemic lupus erythematosus and influences B-cell signaling and activation. Nat Genet 2012; 44:1227-30. [PMID: 23042117 PMCID: PMC3715052 DOI: 10.1038/ng.2439] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 09/11/2012] [Indexed: 12/11/2022]
Abstract
C-src tyrosine kinase, Csk, physically interacts with the intracellular phosphatase Lyp (PTPN22) and can modify the activation state of downstream Src kinases, such as Lyn, in lymphocytes. We identified an association of Csk with systemic lupus erythematosus (SLE) and refined its location to an intronic polymorphism rs34933034 (OR 1.32, p = 1.04 × 10−9). The risk allele is associated with increased CSK expression and augments inhibitory phosphorylation of Lyn. In carriers of the risk allele, B cell receptor (BCR)-mediated activation of mature B cells, as well as plasma IgM, are increased. Moreover, the fraction of transitional B cells is doubled in the cord blood of carriers of the risk allele compared to non-risk haplotypes due to an expansion of the late transitional cells, a stage targeted by selection mechanisms. This suggests that the Lyp-Csk complex increases susceptibility to lupus at multiple maturation and activation points of B cells.
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Affiliation(s)
- Nataly Manjarrez-Orduño
- Center for Autoimmune and Musculoskeletal Disorders, The Feinstein Institute for Medical Research, North Shore-Long Island Jewish, Manhasset, New York, USA
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15
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Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component and is characterized by chronic inflammation and the production of anti-nuclear auto-antibodies. In the era of genome-wide association studies (GWASs), elucidating the genetic factors present in SLE has been a very successful endeavor; 28 confirmed disease susceptibility loci have been mapped. In this review, we summarize the current understanding of the genetics of lupus and focus on the strongest associated risk loci found to date (P <1.0 × 10−8). Although these loci account for less than 10% of the genetic heritability and therefore do not account for the bulk of the disease heritability, they do implicate important pathways, which contribute to SLE pathogenesis. Consequently, the main focus of the review is to outline the genetic variants in the known associated loci and then to explore the potential functional consequences of the associated variants. We also highlight the genetic overlap of these loci with other autoimmune diseases, which indicates common pathogenic mechanisms. The importance of developing functional assays will be discussed and each of them will be instrumental in furthering our understanding of these associated variants and loci. Finally, we indicate that performing a larger SLE GWAS and applying a more targeted set of methods, such as the ImmunoChip and next generation sequencing methodology, are important for identifying additional loci and enhancing our understanding of the pathogenesis of SLE.
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Affiliation(s)
- Sandra G Guerra
- Department of Medical and Molecular Genetics, Division of Genetics and Molecular Medicine, King's College London, Great Maze Pond, London, SE1 9RT, UK
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16
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Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease which behaves as a complex genetic trait. At least 20 SLE risk susceptibility loci have been mapped using both candidate gene and genome-wide association strategies. The gene encoding the pro-inflammatory cytokine, IL18, has been reported as a candidate gene showing an association with SLE. This pleiotropic cytokine is expressed in a range of immune cells and has been shown to induce interferon-γ and tumour necrosis factor-α. Serum interleukin-18 has been reported to be elevated in patients with SLE. Here we aimed to densely map single nucleotide polymorphisms (SNPs) across IL18 to investigate the association across this locus. We genotyped 36 across IL18 by Illumina bead express in 372 UK SLE trios. We also genotyped these SNPs in a further 508 non-trio UK cases and were able to accurately impute a dense marker set across IL18 in WTCCC2 controls with a total of 258 SNPs. To improve the study's power, we also imputed a total of 158 SNPs across the IL18 locus using data from an SLE genome-wide association study and performed association testing. In total, we analysed 1818 cases and 10 770 controls in this study. Our large well-powered study (98% to detect odds ratio = 1.5, with respect to rs360719) showed that no individual SNP or haplotype was associated with SLE in any of the cohorts studied. We conclude that we were unable to replicate the SLE association with rs360719 located upstream of IL18. No evidence for association with any other common variant at IL18 with SLE was found.
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17
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Abstract
Genome-wide association studies (GWAS) have been shown to be a powerful way of identifying novel susceptibility genes in systemic lupus erythematosus (SLE), as demonstrated by a series of publications in the past year. Lupus has been a late-comer to the GWAS community, being preceded by success stories for the GWAS approach in other autoimmune diseases, including type I diabetes, ankylosing spondylitis, rheumatoid arthritis, Crohn's disease and ulcerative colitis. The paper by Suarez-Gestal and colleagues seeks to exploit the wealth of data available from a total of four GWAS in SLE, three in European-American populations and one in a Swedish population. The authors describe replication of ten lupus susceptibility alleles in a Spanish SLE case-control study.
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18
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Manku H, Graham DSC, Vyse TJ. Association of the co-stimulator OX40L with systemic lupus erythematosus. J Mol Med (Berl) 2008; 87:229-34. [PMID: 19083191 DOI: 10.1007/s00109-008-0431-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 10/14/2008] [Accepted: 12/04/2008] [Indexed: 10/21/2022]
Abstract
The archetypal systemic autoimmune disease systemic lupus erythematosus (SLE) has incompletely understood pathogenesis, although evidence suggests a strong genetic component. Unlike organ-specific autoimmune diseases such as type 1 diabetes, the genetics of lupus are not as dominated by the effect of a single locus. Undoubtedly, the major histocompatibility complex is the greatest and most consistent genetic risk factor in SLE susceptibility; however, recent candidate gene and whole genome association (WGA) studies have identified several other genes that are likely to advance our understanding of this complex disease. One of these, the TNF superfamily member OX40L, interacts with its unique receptor OX40, to maintain T cell memory by providing a late-stage co-stimulatory signal to sustain the survival of activated T cells. The precise immunological consequences are yet to be determined; however, signalling through OX40-OX40L is bidirectional and the reverse signalling pathway via OX40L may quantitatively enhance B cell proliferation to augment the B cell hyperactivity found in SLE. Like OX40L, several genes recently identified in WGA studies are components of B cell pathways. Collectively, these genes will help us to unravel the mechanisms by which aberrant B cell signalling results in lupus pathogenesis.
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Fanciulli M, Norsworthy PJ, Petretto E, Dong R, Harper L, Kamesh L, Heward JM, Gough SCL, de Smith A, Blakemore AIF, Froguel P, Owen CJ, Pearce SHS, Teixeira L, Guillevin L, Graham DSC, Pusey CD, Cook HT, Vyse TJ, Aitman TJ. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat Genet 2007; 39:721-3. [PMID: 17529978 PMCID: PMC2742197 DOI: 10.1038/ng2046] [Citation(s) in RCA: 372] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 04/20/2007] [Indexed: 01/17/2023]
Abstract
Naturally occurring variation in gene copy number is increasingly recognized as a heritable source of susceptibility to genetically complex diseases. Here we report strong association between FCGR3B copy number and risk of systemic lupus erythematosus (P = 2.7 x 10(-8)), microscopic polyangiitis (P = 2.9 x 10(-4)) and Wegener's granulomatosis in two independent cohorts from the UK (P = 3 x 10(-3)) and France (P = 1.1 x 10(-4)). We did not observe this association in the organ-specific Graves' disease or Addison's disease. Our findings suggest that low FCGR3B copy number, and in particular complete FCGR3B deficiency, has a key role in the development of systemic autoimmunity.
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Affiliation(s)
- Manuela Fanciulli
- Physiological Genomics and Medicine Group, UK Medical Research Council (MRC) Clinical Sciences Centre, Imperial College, London W12 0NN, UK
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20
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Graham RR, Kyogoku C, Sigurdsson S, Vlasova IA, Davies LRL, Baechler EC, Plenge RM, Koeuth T, Ortmann WA, Hom G, Bauer JW, Gillett C, Burtt N, Cunninghame Graham DS, Onofrio R, Petri M, Gunnarsson I, Svenungsson E, Rönnblom L, Nordmark G, Gregersen PK, Moser K, Gaffney PM, Criswell LA, Vyse TJ, Syvänen AC, Bohjanen PR, Daly MJ, Behrens TW, Altshuler D. Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc Natl Acad Sci U S A 2007; 104:6758-63. [PMID: 17412832 PMCID: PMC1847749 DOI: 10.1073/pnas.0701266104] [Citation(s) in RCA: 364] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Systematic genome-wide studies to map genomic regions associated with human diseases are becoming more practical. Increasingly, efforts will be focused on the identification of the specific functional variants responsible for the disease. The challenges of identifying causal variants include the need for complete ascertainment of genetic variants and the need to consider the possibility of multiple causal alleles. We recently reported that risk of systemic lupus erythematosus (SLE) is strongly associated with a common SNP in IFN regulatory factor 5 (IRF5), and that this variant altered spicing in a way that might provide a functional explanation for the reproducible association to SLE risk. Here, by resequencing and genotyping in patients with SLE, we find evidence for three functional alleles of IRF5: the previously described exon 1B splice site variant, a 30-bp in-frame insertion/deletion variant of exon 6 that alters a proline-, glutamic acid-, serine- and threonine-rich domain region, and a variant in a conserved polyA+ signal sequence that alters the length of the 3' UTR and stability of IRF5 mRNAs. Haplotypes of these three variants define at least three distinct levels of risk to SLE. Understanding how combinations of variants influence IRF5 function may offer etiological and therapeutic insights in SLE; more generally, IRF5 and SLE illustrates how multiple common variants of the same gene can together influence risk of common disease.
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Affiliation(s)
- Robert R. Graham
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Chieko Kyogoku
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Snaevar Sigurdsson
- Molecular Medicine, Department of Medical Sciences, Uppsala University, SE-751 Uppsala, Sweden
| | - Irina A. Vlasova
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Leela R. L. Davies
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Emily C. Baechler
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Robert M. Plenge
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Thearith Koeuth
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Ward A. Ortmann
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Geoffrey Hom
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Jason W. Bauer
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Clarence Gillett
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Noel Burtt
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | | | - Robert Onofrio
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Michelle Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Iva Gunnarsson
- Department of Medicine, Rheumatology Unit, Karolinska Institutet/Karolinska University Hospital, SE-771 Stockholm, Sweden
| | - Elisabet Svenungsson
- Department of Medicine, Rheumatology Unit, Karolinska Institutet/Karolinska University Hospital, SE-771 Stockholm, Sweden
| | - Lars Rönnblom
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, SE-751 Uppsala, Sweden
| | - Gunnel Nordmark
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, SE-751 Uppsala, Sweden
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, NY 11030
| | - Kathy Moser
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Patrick M. Gaffney
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Lindsey A. Criswell
- Department of Medicine, University of California, San Francisco, CA 94143; and
| | - Timothy J. Vyse
- Rheumatology Section, Imperial College, Hammersmith Hospital, London W12 0NN, United Kingdom
| | - Ann-Christine Syvänen
- Molecular Medicine, Department of Medical Sciences, Uppsala University, SE-751 Uppsala, Sweden
| | - Paul R. Bohjanen
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Mark J. Daly
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
| | - Timothy W. Behrens
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - David Altshuler
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- Departments of Genetics and Medicine, Harvard Medical School, and Center for Human Genetics Research and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA 02114
- To whom correspondence should be addressed. E-mail:
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Graham DSC, Manku H, Wagner S, Reid J, Timms K, Gutin A, Lanchbury JS, Vyse TJ. Association of IRF5 in UK SLE families identifies a variant involved in polyadenylation. Hum Mol Genet 2006; 16:579-91. [PMID: 17189288 PMCID: PMC3706933 DOI: 10.1093/hmg/ddl469] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Results from two studies have implicated the interferon regulatory gene IRF5 as a susceptibility gene in systemic lupus erythematosus (SLE). In this study, we conducted a family-based association analysis in 380 UK SLE nuclear families. Using a higher density of markers than has hitherto been screened, we show that there is association with two SNPs in the first intron, rs2004640 (P = 3.4 x 10(-4)) and rs3807306 (P = 4.9 x 10(-4)), and the association extends into the 3'-untranslated region (UTR). There is a single haplotype block encompassing IRF5 and we show for the first time that the gene comprises two over-transmitted haplotypes and a single under-transmitted haplotype. The strongest association is with a TCTAACT haplotype (T:U = 1.92, P = 5.8 x 10(-5)), which carries all the over-transmitted alleles from this study. Haplotypes carrying the T alleles of rs2004640 and rs2280714 and the A allele of rs10954213 are over-transmitted in SLE families. The TAT haplotype shows a dose-dependent relationship with mRNA expression. A differential expression pattern was seen between two expression probes located each side of rs10954213 in the 3'-UTR. rs10954213 shows the strongest association with RNA expression levels (P = 1 x 10(-14)). The A allele of rs10954213 creates a functional polyadenylation site and the A genotype correlates with increased expression of a transcript variant containing a shorter 3'-UTR. Expression levels of transcript variants with the shorter or longer 3'-UTRs are inversely correlated. Our data support a new mechanism by which an IRF5 polymorphism controls the expression of alternate transcript variants which may have different effects on interferon signalling.
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Affiliation(s)
- Deborah S. Cunninghame Graham
- Imperial College, Faculty of Medicine, Molecular Genetics and Rheumatology Section, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Harinder Manku
- Imperial College, Faculty of Medicine, Molecular Genetics and Rheumatology Section, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Susanne Wagner
- Myriad Genetics Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Julia Reid
- Myriad Genetics Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Kirsten Timms
- Myriad Genetics Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Alexander Gutin
- Myriad Genetics Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | | | - Tim J. Vyse
- Imperial College, Faculty of Medicine, Molecular Genetics and Rheumatology Section, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
- To whom correspondence should be addressed. Tel: +44 2083832339; Fax: +44 2087433109;
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22
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Wu H, Cantor RM, Graham DSC, Lingren CM, Farwell L, Jager PLD, Bottini N, Grossman JM, Wallace DJ, Hahn BH, Julkunen H, Hebert LA, Rovin BH, Birmingham DJ, Rioux JD, Yu CY, Kere J, Vyse TJ, Tsao BP. Association analysis of the R620W polymorphism of protein tyrosine phosphatase PTPN22 in systemic lupus erythematosus families: increased T allele frequency in systemic lupus erythematosus patients with autoimmune thyroid disease. ACTA ACUST UNITED AC 2005; 52:2396-402. [PMID: 16052563 DOI: 10.1002/art.21223] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVE Recent case-control studies show associations of the minor T allele (of the C1858T single-nucleotide polymorphism corresponding to the R620W amino acid substitution) of PTPN22 with multiple autoimmune diseases, including systemic lupus erythematosus (SLE). We performed family-based association studies of this polymorphism in 4 independent cohorts containing SLE patients and their parents and/or other family members. METHODS A total of 2,689 individuals from 902 independent Caucasian families with SLE were genotyped using polymerase chain reaction pyrosequencing (cohorts 1 and 2) and the Sequenom MassArray system (cohorts 3 and 4). The transmission disequilibrium test (TDT) and the pedigree disequilibrium test (PDT) were conducted to assess the evidence of association. RESULTS The 1858 C > T allele frequencies of the parents showed no deviation from Hardy-Weinberg equilibrium within each cohort. No evidence of preferential transmission of the T allele from heterozygous parents to their affected offspring was observed in each of the 4 cohorts or in the combined sample. Consistent with the TDT result, the PDT analysis revealed no significant association between the T allele and SLE. In 54 of the 661 SLE patients (cohorts 1 and 3) with documented autoimmune thyroid disease, the T allele frequency was higher than in individuals with SLE alone (16.7% versus 8.5%; P = 0.008, odds ratio 2.16 [95% confidence interval 1.25-3.72]). CONCLUSION The R620W polymorphism of the PTPN22 gene is not a major risk allele for SLE susceptibility in our sample of Caucasian individuals from northern America, the UK, or Finland, but it appears to be a risk factor for the concurrent autoimmune diseases of autoimmune thyroid disease and SLE.
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Affiliation(s)
- Hui Wu
- David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
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23
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Russell AI, Graham DSC, Shepherd C, Roberton CA, Whittaker J, Meeks J, Powell RJ, Isenberg DA, Walport MJ, Vyse TJ. Polymorphism at the C-reactive protein locus influences gene expression and predisposes to systemic lupus erythematosus. Hum Mol Genet 2003; 13:137-47. [PMID: 14645206 PMCID: PMC3707088 DOI: 10.1093/hmg/ddh021] [Citation(s) in RCA: 222] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Relative deficiency of pentraxin proteins is implicated in the pathogenesis of systemic lupus erythematosus. The C-reactive protein (CRP) response is defective in patients with acute flares of disease, and mice with targeted deletions of the serum amyloid P component gene (Sap) develop a lupus-like illness. In humans, the genes for CRP (CRP) and SAP (APCS) map to 1q23.2 within an interval linked with SLE. We have investigated the candidate genes CRP and APCS in two cohorts totalling 586 UK simplex SLE families. The inheritance of an intronic dinucleotide repeat and seven single nucleotide polymorphisms in the CRP and APCS genes was examined by application of family-based tests of association and linkage. Basal levels of CRP were influenced independently by two polymorphisms at the CRP locus, CRP 2 and CRP 4. Furthermore, the latter polymorphism was linked/associated with SLE and antinuclear autoantibody production. Thus, the polymorphism associated with reduced basal CRP was also associated with the development of SLE. These data support the hypothesis that defective disposal of potentially immunogenic material is a contributory factor in lupus pathogenesis. The identification of polymorphisms that determine basal CRP levels has implications in ischaemic heart disease, where CRP level is an important predictor of risk.
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Affiliation(s)
- Andrew I. Russell
- Rheumatology Section, Imperial College Faculty of Medicine, Hammersmith Hospital, London W12 0NN, UK
| | | | - Christopher Shepherd
- Rheumatology Section, Imperial College Faculty of Medicine, Hammersmith Hospital, London W12 0NN, UK
| | - Cheri A. Roberton
- Rheumatology Section, Imperial College Faculty of Medicine, Hammersmith Hospital, London W12 0NN, UK
| | - John Whittaker
- Department of Epidemiology and Public Health, Imperial College Faculty of Medicine, St Mary’s Campus, Norfolk Place, London W2 1PG, UK
| | - John Meeks
- Department of Pathology, Imperial College Faculty of Medicine, Hammersmith Hospital, London W12 0NN, UK
| | - Richard J. Powell
- Clinical Immunology Unit, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - David A. Isenberg
- The Middlesex Hospital, University College London, Arthur Stanley House, Tottenham Street, London W1T 4NJ, UK
| | - Mark J. Walport
- Rheumatology Section, Imperial College Faculty of Medicine, Hammersmith Hospital, London W12 0NN, UK
| | - Timothy J. Vyse
- Rheumatology Section, Imperial College Faculty of Medicine, Hammersmith Hospital, London W12 0NN, UK
- To whom correspondence should be addressed. Tel: +44 2083832339; Fax: +44 2087433109;
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