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Bakutenko IY, Haurylchyk ID, Sechko EV, Tchitchko AM, Batyan GM, Sukalo AV, Ryabokon NI. AGER gene variant as a risk factor for juvenile idiopathic arthritis. J Gene Med 2021; 24:e3399. [PMID: 34806241 DOI: 10.1002/jgm.3399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The AGER gene encodes a cell surface multiligand receptor of advanced glycation end-products that is also capable of binding other molecules and is involved in numerous pathways related to inflammation, apoptosis, immunity and so on. In the present study, we aimed to investigate whether the AGER rs1035798 (G>A) intronic polymorphism, showing an association with multiple sclerosis and rheumatoid arthritis in adults, is related to juvenile idiopathic arthritis (JIA). METHODS Caucasian children from the Belarusian population were enrolled in the study. In total, there were 201 cases with JIA, 37 with juvenile systemic lupus erythematosus, 222 children with the articular syndrome of non-autoimmune etiology (positive control for JIA) and 365 negative controls (children without any autoimmune or inflammatory diseases). Genomic DNA samples from the patients and controls were genotyped by a real-time polymerase chain reaction. RESULTS A marked association of the homozygous AA rs1035798 genotype with JIA (p = 5 × 10-4 ) was found. Allele A was also associated with JIA (p = 0.0058), as well as with the articular syndrome of non-autoimmune etiology (p = 0.0264). The highest frequencies of the AA genotype were found in the subgroups of JIA patients with polyarthritis or severe oligoarthritis. The AA genotype patients also had the smallest mean age of the JIA onset. CONCLUSIONS Our results demonstrate that the AGER rs1035798 AA genotype is a risk factor for JIA in Belarusian children. They also suggest a link between the AGER AA genotype and the risk of JIA early onset and severity. However, the functional relevance of the rs1035798 polymorphism is still unclear.
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Affiliation(s)
- Ivan Yurievich Bakutenko
- Laboratory of Molecular Basis of Genome Stability, Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Irena Dmitrievna Haurylchyk
- Laboratory of Molecular Basis of Genome Stability, Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Elena Vladimirovna Sechko
- 1st Department of Childhood Diseases, Belarusian State Medical University, Minsk, Republic of Belarus
| | | | - Galina Mihajlovna Batyan
- 1st Department of Childhood Diseases, Belarusian State Medical University, Minsk, Republic of Belarus
| | | | - Nadezhda Ivanovna Ryabokon
- Laboratory of Molecular Basis of Genome Stability, Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
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2
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Genetic approaches for the diagnosis and treatment of rheumatoid arthritis through personalized medicine. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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3
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Al Khabouri S, Benson RA, Prendergast CT, Gray JI, Otto TD, Brewer JM, Garside P. TCRβ Sequencing Reveals Spatial and Temporal Evolution of Clonal CD4 T Cell Responses in a Breach of Tolerance Model of Inflammatory Arthritis. Front Immunol 2021; 12:669856. [PMID: 33986757 PMCID: PMC8110912 DOI: 10.3389/fimmu.2021.669856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/07/2021] [Indexed: 11/13/2022] Open
Abstract
Effective tolerogenic intervention in Rheumatoid Arthritis (RA) will rely upon understanding the evolution of articular antigen specific CD4 T cell responses. TCR clonality of endogenous CD4 T cell infiltrates in early inflammatory arthritis was assessed to monitor evolution of the TCR repertoire in the inflamed joint and associated lymph node (LN). Mouse models of antigen-induced breach of self-tolerance and chronic polyarthritis were used to recapitulate early and late phases of RA. The infiltrating endogenous, antigen experienced CD4 T cells in inflamed joints and LNs were analysed using flow cytometry and TCRβ sequencing. TCR repertoires from inflamed late phase LNs displayed increased clonality and diversity compared to early phase LNs, while inflamed joints remained similar with time. Repertoires from late phase LNs accumulated clones with a diverse range of TRBV genes, while inflamed joints at both phases contained clones expressing similar TRBV genes. Repertoires from LNs and joints at the late phase displayed reduced CDR3β sequence overlap compared to the early disease phase, however the most abundant clones in LNs accumulate in the joint at the later phase. The results indicate CD4 T cell repertoire clonality and diversity broadens with progression of inflammatory arthritis and is first reflected in LNs before mirroring in the joint. These observations imply that antigen specific tolerogenic therapies could be more effective if targeted at earlier phases of disease when CD4 T cell clonality is least diverse.
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Affiliation(s)
| | | | | | | | | | | | - Paul Garside
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Polymorphisms in Processing and Antigen Presentation-Related Genes and Their Association with Host Susceptibility to Influenza A/H1N1 2009 Pandemic in a Mexican Mestizo Population. Viruses 2020; 12:v12111224. [PMID: 33138079 PMCID: PMC7692058 DOI: 10.3390/v12111224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
(1) Background: The influenza A/H1N1 pdm09 virus rapidly spread throughout the world. Despite the inflammatory and virus-degradation pathways described in the pathogenesis of influenza A virus (IAV) infection, little is known about the role of the single nucleotide polymorphisms (SNPs) in the genes involved in the processing and antigenic presentation-related mechanisms. (2) Methods: In this case-control study, we evaluated 17 SNPs in five genes (TAP1, TAP2, TAPBP, PSMB8, and PSMB9). One hundred and twenty-eight patients with influenza A/H1N1 infection (INF-P) and 111 healthy contacts (HC) were included; all of them are Mexican mestizo. (3) Results: In allele and genotype comparison, the rs241433/C allele (TAP2), as well as AG haplotype (rs3763365 and rs4148882), are associated with reduced risk for influenza A/H1N1 infection (p < 0.05). On the other hand, the rs2071888G allele (TAPBP) and GG haplotype (rs3763365 and rs9276810) are associated with a higher risk for influenza A/H1N1 infection. In addition, after adjustment for covariates, the association to a reduced risk for influenza A/H1N1 infection remains with rs241433/C allele (p < 0.0001, OR = 0.24, 95% CI = 0.13-0.43), and the association with TAPBP is also maintained with the G allele (p = 0.0095, OR = 1.89, 95% CI = 1.17-3.06) and GG genotype models (p < 0.05, OR = 2.18, 95% CI = 1.27-3.74). (4) Conclusion: The rs241433/C allele and AC genotype (TAP2) and the AG haplotype are associated with a reduced risk for influenza A/H1N1 infection. In addition, the rs2071888/G allele and GG genotype (TAPBP) and the GG haplotype are associated with a higher risk for developing influenza A/H1N1 infection in a Mexican mestizo population.
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5
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Farré A, Tirado J, Spataro N, Alías-Ferri M, Torrens M, Fonseca F. Alcohol Induced Depression: Clinical, Biological and Genetic Features. J Clin Med 2020; 9:jcm9082668. [PMID: 32824737 PMCID: PMC7465278 DOI: 10.3390/jcm9082668] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background: In clinical practice, there is the need to have clinical and biological markers to identify induced depression. The objective was to investigate clinical, biological and genetic differences between Primary Major Depression (Primary MD) and Alcohol Induced MD (AI-MD). Methods: Patients, of both genders, were recruited from psychiatric hospitalisation units. The PRISM instrument was used to establish the diagnoses. Data on socio-demographic/family history, clinical scales for depression, anxiety, personality and stressful life events were recorded. A blood test was performed analysing biochemical parameters and a Genome Wide Association Study (GWAS) to identify genetic markers associated with AI-MD. Results: A total of 80 patients were included (47 Primary MD and 33 AI-MD). The AI-MD group presented more medical comorbidities and less family history of depression. There were differences in traumatic life events, with higher scores in the AI-MD (14.21 ± 11.35 vs. 9.30 ± 7.38; p = 0.021). DSM-5 criteria were different between groups with higher prevalence of weight changes and less anhedonia, difficulties in concentration and suicidal thoughts in the AI-MD. None of the genetic variants reached significance beyond multiple testing thresholds; however, some suggestive variants were observed. Conclusions: This study has found clinical and biological features that may help physicians to identify AI-MD and improve its therapeutic approach.
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Affiliation(s)
- Adriana Farré
- Institut de Neuropsiquiatria i Addiccions (INAD), Hospital del Mar, 08003 Barcelona, Spain; (A.F.); (M.T.)
- Grup de Recerca en Addiccions, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain; (J.T.); (M.A.-F.)
- Psychiatry Department, Universitat Autònoma de Barcelona, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Judit Tirado
- Grup de Recerca en Addiccions, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain; (J.T.); (M.A.-F.)
| | - Nino Spataro
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, 08208 Sabadell, Spain;
| | - María Alías-Ferri
- Grup de Recerca en Addiccions, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain; (J.T.); (M.A.-F.)
- Psychiatry Department, Universitat Autònoma de Barcelona, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Marta Torrens
- Institut de Neuropsiquiatria i Addiccions (INAD), Hospital del Mar, 08003 Barcelona, Spain; (A.F.); (M.T.)
- Grup de Recerca en Addiccions, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain; (J.T.); (M.A.-F.)
- Psychiatry Department, Universitat Autònoma de Barcelona, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Francina Fonseca
- Institut de Neuropsiquiatria i Addiccions (INAD), Hospital del Mar, 08003 Barcelona, Spain; (A.F.); (M.T.)
- Grup de Recerca en Addiccions, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain; (J.T.); (M.A.-F.)
- Psychiatry Department, Universitat Autònoma de Barcelona, Cerdanyola del Valles, 08193 Barcelona, Spain
- Correspondence:
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Amariuta T, Luo Y, Knevel R, Okada Y, Raychaudhuri S. Advances in genetics toward identifying pathogenic cell states of rheumatoid arthritis. Immunol Rev 2019; 294:188-204. [PMID: 31782165 DOI: 10.1111/imr.12827] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
Rheumatoid arthritis (RA) risk has a large genetic component (~60%) that is still not fully understood. This has hampered the design of effective treatments that could promise lifelong remission. RA is a polygenic disease with 106 known genome-wide significant associated loci and thousands of small effect causal variants. Our current understanding of RA risk has suggested cell-type-specific contexts for causal variants, implicating CD4 + effector memory T cells, as well as monocytes, B cells and stromal fibroblasts. While these cellular states and categories are still mechanistically broad, future studies may identify causal cell subpopulations. These efforts are propelled by advances in single cell profiling. Identification of causal cell subpopulations may accelerate therapeutic intervention to achieve lifelong remission.
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Affiliation(s)
- Tiffany Amariuta
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Graduate School of Arts and Sciences, Harvard University, Boston, MA, USA
| | - Yang Luo
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Rachel Knevel
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Yukinori Okada
- Division of Medicine, Osaka University, Osaka, Japan.,Osaka University Graduate School of Medicine, Osaka, Japan
| | - Soumya Raychaudhuri
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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7
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Siegel RJ, Bridges SL, Ahmed S. HLA-C: An Accomplice in Rheumatic Diseases. ACR Open Rheumatol 2019; 1:571-579. [PMID: 31777841 PMCID: PMC6858028 DOI: 10.1002/acr2.11065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/08/2019] [Indexed: 01/14/2023] Open
Abstract
Human leukocyte antigen c (HLA-C) is a polymorphic membrane protein encoded by the HLA-C gene in the class I major histocompatibility complex. HLA-C plays an essential role in protection against cancer and viruses but has also been implicated in allograft rejection, preeclampsia, and autoimmune disease. This review summarizes reports and proposed mechanisms for the accessory role of HLA-C in rheumatic diseases. Historically, contributions of HLA-C to rheumatic diseases were eclipsed by the stronger association with HLA-DRB1 alleles containing the "shared epitope" with rheumatoid arthritis. Larger genetic association studies and more powerful analytical approaches have revealed independent associations of HLA-C with rheumatic disease-associated phenotypes, including development of anticitrullinated peptide antibodies. HLA-C functions by presenting antigens to T cells and by binding activatory and inhibitory receptors on natural killer (NK) cells, but the exact mechanisms by which the HLA-C locus contributes to autoimmunity are largely undefined. Studies have suggested that HLA-C and NK cell receptor polymorphisms may predict responsiveness to pharmacotherapy. Understanding the mechanisms of the role of HLA-C in rheumatic disease could uncover therapeutic targets or guide precision pharmacologic treatments.
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Affiliation(s)
- Ruby J. Siegel
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
| | - S. Louis Bridges
- Division of Clinical Immunology and RheumatologyUniversity of Alabama at BirminghamBirminghamAlabama
| | - Salahuddin Ahmed
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
- Division of RheumatologyUniversity of Washington School of MedicineSeattleWashington
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Pathological Implications of Receptor for Advanced Glycation End-Product ( AGER) Gene Polymorphism. DISEASE MARKERS 2019; 2019:2067353. [PMID: 30863465 PMCID: PMC6378764 DOI: 10.1155/2019/2067353] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/01/2019] [Accepted: 01/15/2019] [Indexed: 12/12/2022]
Abstract
The receptor for advanced glycation end-products (RAGE) is a cell surface transmembrane multiligand receptor, encoded by the AGER gene. RAGE presents many transcripts, is expressed mainly in the lung, and involves multiple pathways (such as NFκB, Akt, p38, and MAP kinases) that initiate and perpetuate an unfavorable proinflammatory state. Due to these numerous functional activities, RAGE is implicated in multiple diseases. AGER is a highly polymorphic gene, with polymorphisms or SNP (single-nucleotide polymorphism) that could be responsible or co-responsible for disease development. This review was designed to shed light on the pathological implications of AGER polymorphisms. Five polymorphisms are described: rs2070600, rs1800624, rs1800625, rs184003, and a 63 bp deletion. The rs2070600 SNP may be associated with the development of human autoimmune disease, diabetes complications, cancer, and lung diseases such as chronic obstructive pulmonary disease and acute respiratory distress syndrome. The rs1800624 SNP involves AGER gene regulation and may be related to reduced risk of heart disease, cancer, Crohn's disease, and type 1 diabetes complications. The rs1800625 SNP may be associated with the development of diabetic retinopathy, cancer, and lupus but may be protective against cardiovascular risk. The rs184003 SNP seems related to coronary artery disease, breast cancer, and diabetes. The 63 bp deletion may be associated with reduced survival from heart diseases during diabetic nephropathy. Here, these potential associations between AGER polymorphisms and the development of diseases are discussed, as there have been conflicting findings on the pathological impact of AGER SNPs in the literature. These contradictory results might be explained by distinct AGER SNP frequencies depending on ethnicity.
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Yang Y, Dai M, Huang J, Lin X, Yang C, Chen M, Liu J. LPG: A four-group probabilistic approach to leveraging pleiotropy in genome-wide association studies. BMC Genomics 2018; 19:503. [PMID: 29954342 PMCID: PMC6022345 DOI: 10.1186/s12864-018-4851-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 06/04/2018] [Indexed: 01/30/2023] Open
Abstract
Background To date, genome-wide association studies (GWAS) have successfully identified tens of thousands of genetic variants among a variety of traits/diseases, shedding light on the genetic architecture of complex disease. The polygenicity of complex diseases is a widely accepted phenomenon through which a vast number of risk variants, each with a modest individual effect, collectively contribute to the heritability of complex diseases. This imposes a major challenge on fully characterizing the genetic bases of complex diseases. An immediate implication of polygenicity is that a much larger sample size is required to detect individual risk variants with weak/moderate effects. Meanwhile, accumulating evidence suggests that different complex diseases can share genetic risk variants, a phenomenon known as pleiotropy. Results In this study, we propose a statistical framework for Leveraging Pleiotropic effects in large-scale GWAS data (LPG). LPG utilizes a variational Bayesian expectation-maximization (VBEM) algorithm, making it computationally efficient and scalable for genome-wide-scale analysis. To demonstrate the advantages of LPG over existing methods that do not leverage pleiotropy, we conducted extensive simulation studies and applied LPG to analyze two pairs of disorders (Crohn’s disease and Type 1 diabetes, as well as rheumatoid arthritis and Type 1 diabetes). The results indicate that by levelaging pleiotropy, LPG can improve the power of prioritization of risk variants and the accuracy of risk prediction. Conclusions Our methodology provides a novel and efficient tool to detect pleiotropy among GWAS data for multiple traits/diseases collected from different studies. The software is available at https://github.com/Shufeyangyi2015310117/LPG. Electronic supplementary material The online version of this article (10.1186/s12864-018-4851-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi Yang
- School of Statistics and Management, The Shanghai University of Finance and Economics, Guoding Road, Shanghai, China.,Centre for Quantitative Medicine, Duke-NUS Medical School, 8 College Road, Singapore, Singapore
| | - Mingwei Dai
- Institute for Information and System Sciences, Xian Jiaotong University, No.28, Xianning West Road, Xi'an, China.,Department of Mathematics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jian Huang
- Department of Applied Mathematics, Hong Kong Polytechnics University, Hung Hom, Hong Kong, China
| | - Xinyi Lin
- Centre for Quantitative Medicine, Duke-NUS Medical School, 8 College Road, Singapore, Singapore
| | - Can Yang
- Department of Mathematics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Min Chen
- School of Statistics and Management, The Shanghai University of Finance and Economics, Guoding Road, Shanghai, China
| | - Jin Liu
- Centre for Quantitative Medicine, Duke-NUS Medical School, 8 College Road, Singapore, Singapore.
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10
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Genetic markers as therapeutic target in rheumatoid arthritis: A game changer in clinical therapy? Rheumatol Int 2016; 36:1601-1607. [PMID: 27638722 DOI: 10.1007/s00296-016-3563-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/01/2016] [Indexed: 12/19/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic, inflammatory, multi-systemic autoimmune disease unremitted by genetic and environmental factors. The factors are crucial but inadequate in the development of disease; however, these factors can be representative of potential therapeutic targets and response to clinical therapy. Insights into the contribution of genetic risk factors are currently in progress with studies querying the genetic variation, their role in gene expression of coding and non-coding genes and other mechanisms of disease. In this review, we describe the significance of genetic markers architecture of RA through genome-wide association studies and meta-analysis studies. Further, it also reveals the mechanism of disease pathogenesis investigated through the mutual findings of functional and genetic studies of individual RA-associated genes, which includes HLA-DRB1, HLA-DQB1, HLA-DPB1, PADI4, PTPN22, TRAF1-C5, STAT4 and C5orf30. However, the genetic background of RA remains to be clearly depicted. Prospective efforts of the post-genomic and functional genomic period can travel toward real possible assessment of the genetic effect on RA. The discovery of novel genes associated with the disease can be appropriate in identifying potential biomarkers, which could assist in early diagnosis and aggressive treatment.
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11
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Xiao X, Hao J, Wen Y, Wang W, Guo X, Zhang F. Genome-wide association studies and gene expression profiles of rheumatoid arthritis: An analysis. Bone Joint Res 2016; 5:314-9. [PMID: 27445359 PMCID: PMC5005471 DOI: 10.1302/2046-3758.57.2000502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 06/07/2016] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVES The molecular mechanism of rheumatoid arthritis (RA) remains elusive. We conducted a protein-protein interaction network-based integrative analysis of genome-wide association studies (GWAS) and gene expression profiles of RA. METHODS We first performed a dense search of RA-associated gene modules by integrating a large GWAS meta-analysis dataset (containing 5539 RA patients and 20 169 healthy controls), protein interaction network and gene expression profiles of RA synovium and peripheral blood mononuclear cells (PBMCs). Gene ontology (GO) enrichment analysis was conducted by DAVID. The protein association networks of gene modules were generated by STRING. RESULTS For RA synovium, the top-ranked gene module is HLA-A, containing TAP2, HLA-A, HLA-C, TAPBP and LILRB1 genes. For RA PBMCs, the top-ranked gene module is GRB7, consisting of HLA-DRB5, HLA-DRA, GRB7, CD63 and KIT genes. Functional enrichment analysis identified three significant GO terms for RA synovium, including antigen processing and presentation of peptide antigen via major histocompatibility complex class I (false discovery rate (FDR) = 4.86 × 10 - 4), antigen processing and presentation of peptide antigen (FDR = 2.33 × 10 - 3) and eukaryotic translation initiation factor 4F complex (FDR = 2.52 × 10 - 2). CONCLUSION This study reported several RA-associated gene modules and their functional association networks.Cite this article: X. Xiao, J. Hao, Y. Wen, W. Wang, X. Guo, F. Zhang. Genome-wide association studies and gene expression profiles of rheumatoid arthritis: an analysis. Bone Joint Res 2016;5:314-319. DOI: 10.1302/2046-3758.57.2000502.
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Affiliation(s)
- X Xiao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China
| | - J Hao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China
| | - Y Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China
| | - W Wang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China
| | - X Guo
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China
| | - F Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China
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Genética da artrite reumatoide: é necessário um novo impulso em populações latino‐americanas. REVISTA BRASILEIRA DE REUMATOLOGIA 2016. [DOI: 10.1016/j.rbr.2015.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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Castro-Santos P, Díaz-Peña R. Genetics of rheumatoid arthritis: a new boost is needed in Latin American populations. REVISTA BRASILEIRA DE REUMATOLOGIA 2015; 56:171-7. [PMID: 27267531 DOI: 10.1016/j.rbre.2015.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 08/30/2015] [Indexed: 01/17/2023] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune inflammatory rheumatic disease which affects several organs and tissue, predominantly the synovial joints. Like many other autoimmune diseases, RA is a complex disease, where genetic variants, environmental factors and random events interact to trigger pathological pathways. Genetic implication in RA is evident, and recent advances have expanded our knowledge about the genetic factors that contribute to RA. An exponential increment in the number of genes associated with the disease has been described, mainly through gene wide screen studies (GWAS) involving international consortia with large patient cohorts. However, there are a few studies on Latin American populations. This article describes what is known about the RA genetics, the future that is emerging, and how this will develop a more personalized approach for the treatment of the disease. Latin American RA patients cannot be excluded from this final aim, and a higher collaboration with the international consortia may be needed for a better knowledge of the genetic profile of patients from this origin.
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Affiliation(s)
| | - Roberto Díaz-Peña
- Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile; Department of Immunology, Hospital Universitario Central de Asturias, Oviedo, Spain.
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Saad MN, Mabrouk MS, Eldeib AM, Shaker OG. Identification of rheumatoid arthritis biomarkers based on single nucleotide polymorphisms and haplotype blocks: A systematic review and meta-analysis. J Adv Res 2015; 7:1-16. [PMID: 26843965 PMCID: PMC4703421 DOI: 10.1016/j.jare.2015.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 01/13/2015] [Accepted: 01/20/2015] [Indexed: 12/30/2022] Open
Abstract
Genetics of autoimmune diseases represent a growing domain with surpassing biomarker results with rapid progress. The exact cause of Rheumatoid Arthritis (RA) is unknown, but it is thought to have both a genetic and an environmental bases. Genetic biomarkers are capable of changing the supervision of RA by allowing not only the detection of susceptible individuals, but also early diagnosis, evaluation of disease severity, selection of therapy, and monitoring of response to therapy. This review is concerned with not only the genetic biomarkers of RA but also the methods of identifying them. Many of the identified genetic biomarkers of RA were identified in populations of European and Asian ancestries. The study of additional human populations may yield novel results. Most of the researchers in the field of identifying RA biomarkers use single nucleotide polymorphism (SNP) approaches to express the significance of their results. Although, haplotype block methods are expected to play a complementary role in the future of that field.
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Affiliation(s)
- Mohamed N Saad
- Biomedical Engineering Department, Faculty of Engineering, Misr University for Science and Technology, 6th of October City, Egypt
| | - Mai S Mabrouk
- Biomedical Engineering Department, Faculty of Engineering, Misr University for Science and Technology, 6th of October City, Egypt
| | - Ayman M Eldeib
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Olfat G Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
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Govind N, Choudhury A, Hodkinson B, Ickinger C, Frost J, Lee A, Gregersen PK, Reynolds RJ, Bridges SL, Hazelhurst S, Ramsay M, Tikly M. Immunochip identifies novel, and replicates known, genetic risk loci for rheumatoid arthritis in black South Africans. Mol Med 2014; 20:341-9. [PMID: 25014791 DOI: 10.2119/molmed.2014.00097] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 07/03/2014] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to identify genetic variants associated with rheumatoid arthritis (RA) risk in black South Africans. Black South African RA patients (n = 263) were compared with healthy controls (n = 374). Genotyping was performed using the Immunochip, and four-digit high-resolution human leukocyte antigen (HLA) typing was performed by DNA sequencing of exon 2. Standard quality control measures were implemented on the data. The strongest associations were in the intergenic region between the HLA-DRB1 and HLA-DQA1 loci. After conditioning on HLA-DRB1 alleles, the effect in the rest of the extended major histocompatibility (MHC) diminished. Non-HLA single nucleotide polymorphisms (SNPs) in the intergenic regions LOC389203|RBPJ, LOC100131131|IL1R1, KIAA1919|REV3L, LOC643749|TRAF3IP2, and SNPs in the intron and untranslated regions (UTR) of IRF1 and the intronic region of ICOS and KIAA1542 showed association with RA (p < 5 × 10(-5)). Of the SNPs previously associated with RA in Caucasians, one SNP, rs874040, locating to the intergenic region LOC389203|RBPJ was replicated in this study. None of the variants in the PTPN22 gene was significantly associated. The seropositive subgroups showed similar results to the overall cohort. The effects observed across the HLA region are most likely due to HLA-DRB1, and secondary effects in the extended MHC cannot be detected. Seven non-HLA loci are associated with RA in black South Africans. Similar to Caucasians, the intergenic region between LOC38920 and RBPJ is associated with RA in this population. The strong association of the R620W variant of the PTPN22 gene with RA in Caucasians was not replicated since this variant was monomorphic in our study, but other SNP variants of the PTPN22 gene were also not associated with RA in black South Africans, suggesting that this locus does not play a major role in RA in this population.
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Affiliation(s)
- Nimmisha Govind
- Division of Rheumatology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Bridget Hodkinson
- Division of Rheumatology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Claudia Ickinger
- Division of Rheumatology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jacqueline Frost
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Annette Lee
- Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Peter K Gregersen
- Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Richard J Reynolds
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - S Louis Bridges
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohammed Tikly
- Division of Rheumatology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
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Genome-wide association studies to advance our understanding of critical cell types and pathways in rheumatoid arthritis: recent findings and challenges. Curr Opin Rheumatol 2014; 26:85-92. [PMID: 24276088 DOI: 10.1097/bor.0000000000000012] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW A significant number of loci implicated in rheumatoid arthritis (RA) susceptibility have been highlighted by genome-wide association studies (GWAS). Here, we review the recent advances of GWAS in understanding the genetic architecture of RA, and place these findings in the context of RA pathogenesis. RECENT FINDINGS Although the interpretation of GWAS findings in the context of the disease biology remains challenging, interesting observations can be highlighted. Integration of GWAS results with cell-type specific gene expression or epigenetic marks have highlighted regulatory T cells and CD4 memory T cells as critical cell types in RA. In addition, many genes in RA loci are involved in the nuclear factor-kappaB signaling pathway or the Janus kinase (JAK)-signal transducers and activators of transcription (STAT) signaling pathway. The observation that these pathways are targeted by several approved drugs used to treat the symptoms of RA highlights the promises of human genetics to provide insights in the disease biology, and help identify new therapeutic targets. SUMMARY These findings highlight the promises and need of future studies investigating causal genes and underlined mechanisms in GWAS loci to advance our understanding of RA.
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Dai D, Chen Y, Ru P, Zhou X, Tao J, Ye H, Hong Q, Tang L, Pan G, Lin D, Gong Q, Lv Y, Xu L, Duan S. Significant association between TAP2 polymorphisms and rheumatoid arthritis: a meta-analysis. Diagn Pathol 2014; 9:129. [PMID: 24972609 PMCID: PMC4090395 DOI: 10.1186/1746-1596-9-129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/23/2014] [Indexed: 12/19/2022] Open
Abstract
Background Rheumatoid arthritis (RA) is a severe chronic immune mediated inflammatory disease that has been shown to be associated with human leukocyte antigen (HLA) loci. The transporter associated with antigen processing 2 (TAP2) has been identified to play an important role in the HLA-associated diseases and immune response. The goal of our meta-analysis was to summarize the contribution of TAP2 polymorphisms to the risk of RA. Methods Meta-analyses were performed between RA and 3 TAP2 coding polymorphisms that comprised TAP2-379Ile > Val (rs1800454), TAP2-565Ala > Thr (rs2228396) and TAP2-665Thr > Ala (rs241447). The meta-analyses were involved with 9 studies (24 individual studies) among 973 cases and 965 controls. Results Meta-analyses showed that TAP2-379Ile allele was significantly associated with an increased risk of RA (p = 0.0002, odds ratio (OR) = 1.44, 95% confidence interval (CI) = 1.18-1.74). This association was further shown only in the dominant model (p = 0.006, OR = 1.59, 95% CI = 1.14-2.22). Subgroup analyses by ethnicity revealed that the association of TAP2-379Ile was significant in Asians (p = 0.03, OR = 1.38, 95% CI = 1.04-1.83). In addition, another significant association of TAP2-565Thr allele with RA was observed in Europeans (p = 0.002, OR = 1.62, 95% CI = 1.20-2.20). Conclusions Our meta-analyses suggested that TAP2-379Ile allele was significantly associated with a 59% increased risk in the dominant effect model. Subgroup analyses by ethnicity showed that TAP2-379-Ile increased the risk of RA by 38% in Asians and TAP2-565Thr increased the risk of RA by 38% in Europeans. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2097080313124700
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
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HLA-C alleles confer risk for anti-citrullinated peptide antibody-positive rheumatoid arthritis independent of HLA-DRB1 alleles. Rheumatology (Oxford) 2013; 52:1973-82. [DOI: 10.1093/rheumatology/ket252] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Hay M, Patricios J, Collins R, Branfield A, Cook J, Handley CJ, September AV, Posthumus M, Collins M. Association of type XI collagen genes with chronic Achilles tendinopathy in independent populations from South Africa and Australia. Br J Sports Med 2013; 47:569-74. [PMID: 23624467 DOI: 10.1136/bjsports-2013-092379] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Type XI collagen, which is expressed in developing tendons and is encoded by the COL11A1, COL11A2 and COL2A1 genes, shares structural and functional homology with type V collagen, which plays an important role in collagen fibril assembly. We investigated the association of these three polymorphisms with Achilles tendinopathy (AT) and whether these polymorphisms interact with COL5A1 to modulate the risk of AT. METHODS 184 participants diagnosed with chronic AT (TEN) and 338 appropriately matched asymptomatic controls (CON) were genotyped for the three polymorphisms. RESULTS Although there were no independent associations with AT, the TCT pseudohaplotype constructed from rs3753841 (T/C), rs1676486 (C/T) and rs1799907 (T/A) was significantly over-represented (p=0.006) in the TEN (25.9%) compared with the CON (17.1%) group. The TCT(AGGG) pseudohaplotypes constructed using these type XI collagen polymorphisms and the functional COL5A1 rs71746744 (-/AGGG) polymorphism were also significantly over-represented (p<0.001) in the TEN (25.2%) compared with the CON (9.1%) group. DISCUSSION The genes encoding structural and functionally related type XI (COL11A1 and COL11A2) and type V (COL5A1) collagens interact with one another to collectively modulate the risk for AT. Although there are no immediate clinical applications, the results of this study provide additional evidence that interindividual variations in collagen fibril assembly might be an important molecular mechanism in the aetiology of chronic AT.
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Affiliation(s)
- Melanie Hay
- MRC/UCT Research Unit for Exercise Science and Sports Medicine, Department of Human Biology, University of Cape Town, Cape Town, South Africa
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Fabris M, Quartuccio L, Vital E, Pontarini E, Salvin S, Fabro C, Zabotti A, Benucci M, Manfredi M, Ravagnani V, Biasi D, Atzeni F, Sarzi-Puttini P, Morassi P, Fischetti F, Bazzicchi L, Saracco M, Pellerito R, Cimmino M, Carraro V, Semeraro A, Schiavon F, Caporali R, Bortolotti R, Govoni M, Fogolari F, Tonutti E, Bombardieri S, Emery P, De Vita S. The TTTT B lymphocyte stimulator promoter haplotype is associated with good response to rituximab therapy in seropositive rheumatoid arthritis resistant to tumor necrosis factor blockers. ACTA ACUST UNITED AC 2013; 65:88-97. [PMID: 23001900 DOI: 10.1002/art.37707] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 09/11/2012] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To investigate the polymorphisms in the promoter region of the B lymphocyte stimulator (BLyS) gene as markers of response to rituximab (RTX) in rheumatoid arthritis (RA). METHODS The study was first conducted in 152 Italian RA patients and then replicated in an additional 117 RA patients (73 Italian, 44 British). The European League Against Rheumatism response criteria were used to evaluate the response rate at months 4 and 6 after the first cycle of RTX, by means of the Disease Activity Score in 28 joints using the erythrocyte sedimentation rate; patients were classified according to the best response shown between months 4 and 6. BLyS promoter polymorphisms were analyzed by polymerase chain reaction followed by the analysis of the restriction fragments, BLyS promoter haplotypes were analyzed using the expectation-maximization algorithm, and BLyS serum levels were analyzed using enzyme-linked immunosorbent assay. Odds ratios (ORs) were calculated with 95% confidence intervals (95% CIs). RESULTS The TTTT BLyS promoter haplotype appeared to be significantly associated with response to RTX only in the subset of seropositive patients (those positive for rheumatoid factor and/or anti-cyclic citrullinated peptide). The replication study confirmed that this association was limited to seropositive RA patients in whom treatment with anti-tumor necrosis factor (anti-TNF) agents had previously failed. In the whole series of seropositive patients in whom anti-TNF agents had previously failed, patients carrying the TTTT BLyS promoter haplotype were more prevalent in good responders (18 of 43 [41.9%]) than in moderate responders (20 of 83 [24.1%]) or in nonresponders (1 of 21 [4.8%]) (for good responders versus nonresponders, OR 14.4 [95% CI 1.77-117.39], P=0.0028). Furthermore, multivariate analysis selected the TTTT BLyS promoter haplotype as an independent marker of good response to RTX (for good responders versus nonresponders, OR 16.2 [95% CI 1.7-152.5], P=0.01; for good responders versus moderate responders and nonresponders combined, OR 3.1 [95% CI 1.2-7.8], P=0.02). The relationship between BLyS polymorphisms and BLyS serum levels remained unclear. CONCLUSION BLyS promoter genotyping may be suitable for identifying seropositive RA patients who may have a good response to RTX after anti-TNF agents have failed.
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Affiliation(s)
- Martina Fabris
- DSMB, Azienda Ospedaliero Universitaria of Udine, Udine, Italy
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Abstract
Investigators have made key advances in rheumatoid arthritis (RA) genetics in the past 10 years. Although genetic studies have had limited influence on clinical practice and drug discovery, they are currently generating testable hypotheses to explain disease pathogenesis. Firstly, we review here the major advances in identifying RA genetic susceptibility markers both within and outside of the MHC. Understanding how genetic variants translate into pathogenic mechanisms and ultimately into phenotypes remains a mystery for most of the polymorphisms that confer susceptibility to RA, but functional data are emerging. Interplay between environmental and genetic factors is poorly understood and in need of further investigation. Secondly, we review current knowledge of the role of epigenetics in RA susceptibility. Differences in the epigenome could represent one of the ways in which environmental exposures translate into phenotypic outcomes. The best understood epigenetic phenomena include post-translational histone modifications and DNA methylation events, both of which have critical roles in gene regulation. Epigenetic studies in RA represent a new area of research with the potential to answer unsolved questions.
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Affiliation(s)
- Sebastien Viatte
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, The University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
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23
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Kim SK, Bae J, Lee H, Kim JH, Park SH, Choe JY. Greater prevalence of seropositivity for anti-cyclic citrullinated peptide antibody in unaffected first-degree relatives in multicase rheumatoid arthritis-affected families. Korean J Intern Med 2013; 28:45-53. [PMID: 23345996 PMCID: PMC3543960 DOI: 10.3904/kjim.2013.28.1.45] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 05/02/2012] [Accepted: 06/20/2012] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND/AIMS This study determined the prevalence and determinants of seropositivity for rheumatoid factor (RF), anti-cyclic citrullinated peptide (anti-CCP) antibody, and anti-mutated citrullinated vimentin (anti-MCV) antibody in unaffected first-degree relatives (FDRs) of rheumatoid arthritis (RA) patients. METHODS A total of 337 subjects (135 with RA and 202 FDRs) were enrolled in this case-control study. Serum RF, anti-CCP antibody, and anti-MCV antibody were assayed. Subjects in multicase families (≥ 2 affected FDRs within the same family) were identified. Multivariate logistic regression analysis was used to identify risk factors associated with RA-related autoantibodies. RESULTS Seropositivity for RF, anti-CCP antibody, or anti-MCV antibody was detected in 14.4%, 5.0%, or 13.4% of unaffected FDRs, respectively. Anti-CCP antibody seropositivity was more prevalent in FDRs in multicase families (17.8%) than in those not in multicase families (1.3%, p < 0.0001). Significant correlations between RA-associated autoantibodies were detected in the FDR group (between RF and anti-CCP antibody: r = 0.366, p < 0.0001; between RF and anti-MCV antibody: r = 0.343, p < 0.0001; and between anti-CCP antibody and anti-MCV antibody: r = 0.849, p < 0.0001). After adjustment for age and sex, anti-CCP antibody seropositivity in FDRs was significantly associated with being in a multicase family (odds ratio, 49.8; 95% confidence interval, 5.6 to 441.6). CONCLUSIONS The association between anti-CCP antibody seropositivity in unaffected FDRs and being in a multicase family suggests that genetic and/or environmental factors may increase the risk for RA development in unaffected FDRs.
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Affiliation(s)
- Seong-Kyu Kim
- Department of Internal Medicine, Arthritis and Autoimmunity Research Center, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Jisuk Bae
- Department of Preventive Medicine, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Hwajeong Lee
- Department of Internal Medicine, Arthritis and Autoimmunity Research Center, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Ji Hun Kim
- Department of Internal Medicine, Arthritis and Autoimmunity Research Center, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Sung-Hoon Park
- Department of Internal Medicine, Arthritis and Autoimmunity Research Center, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Jung-Yoon Choe
- Department of Internal Medicine, Arthritis and Autoimmunity Research Center, Catholic University of Daegu School of Medicine, Daegu, Korea
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Scheinman R. NF-κB and Rheumatoid Arthritis: Will Understanding Genetic Risk Lead to a Therapeutic Reward? ACTA ACUST UNITED AC 2013; 4:93-110. [PMID: 24678426 DOI: 10.1615/forumimmundisther.2013008408] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
NF-κB has long been known to play an important role in autoimmune diseases such as rheumatoid arthritis (RA). Indeed, as our understanding of how NF-κB is utilized has increased, we have been hard put to find a process not associated with this transcription factor family in some way. However, new data originating, in part, from genome-wide association studies have demonstrated that very specific alterations in components of the NF-κB pathway are sufficient to confer increased risk of developing disease. Here we review the data which have identified specific components of the NF-κB pathway, and consider what is known of their mechanisms of action and how these mechanisms might play into the disease process. In addition, the use of genetic information to predict RA is considered.
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Affiliation(s)
- Robert Scheinman
- University of Colorado Denver, School of Pharmacy, Department of Pharmaceutical Sciences, Aurora, CO 80045;
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25
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Xie G, Lu Y, Sun Y, Zhang SS, Keystone EC, Gregersen PK, Plenge RM, Amos CI, Siminovitch KA. Identification of the NF-κB activating protein-like locus as a risk locus for rheumatoid arthritis. Ann Rheum Dis 2012; 72:1249-54. [PMID: 23223422 PMCID: PMC3686260 DOI: 10.1136/annrheumdis-2012-202076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Objective To fine-map the NF-κB activating protein-like (NKAPL) locus identified in a prior genome-wide study as a possible rheumatoid arthritis (RA) risk locus and thereby delineate additional variants with stronger and/or independent disease association. Methods Genotypes for 101 SNPs across the NKAPL locus on chromosome 6p22.1 were obtained on 1368 Canadian RA cases and 1471 controls. Single marker associations were examined using logistic regression and the most strongly associated NKAPL locus SNPs then typed in another Canadian and a US-based RA case/control cohort. Results Fine-mapping analyses identified six NKAPL locus variants in a single haplotype block showing association with p≤5.6×10−8 in the combined Canadian cohort. Among these SNPs, rs35656932 in the zinc finger 193 gene and rs13208096 in the NKAPL gene remained significant after conditional logistic regression, contributed independently to risk for disease, and were replicated in the US cohort (Pcomb=4.24×10−10 and 2.44×10−9, respectively). These associations remained significant after conditioning on SNPs tagging the HLA-shared epitope (SE) DRB1*0401 allele and were significantly stronger in the HLA-SE negative versus positive subgroup, with a significant negative interaction apparent between HLA-DRB1 SE and NKAPL risk alleles. Conclusions By illuminating additional NKAPL variants with highly significant effects on risk that are distinct from, but interactive with those arising from the HLA-DRB1 locus, our data conclusively identify NKAPL as an RA susceptibility locus.
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Affiliation(s)
- Gang Xie
- Mount Sinai Hospital Samuel Lunenfeld Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
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On the perils of poor editing: regulation of peptide loading by HLA-DQ and H2-A molecules associated with celiac disease and type 1 diabetes. Expert Rev Mol Med 2012; 14:e15. [PMID: 22805744 DOI: 10.1017/erm.2012.9] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review discusses mechanisms that link allelic variants of major histocompatibility complex (MHC) class II molecules (MHCII) to immune pathology. We focus on HLA (human leukocyte antigen)-DQ (DQ) alleles associated with celiac disease (CD) and type 1 diabetes (T1D) and the role of the murine DQ-like allele, H2-Ag7 (I-Ag7 or Ag7), in murine T1D. MHCII molecules bind peptides, and alleles vary in their peptide-binding specificity. Disease-associated alleles permit binding of disease-inducing peptides, such as gluten-derived, Glu-/Pro-rich gliadin peptides in CD and peptides from islet autoantigens, including insulin, in T1D. In addition, the CD-associated DQ2.5 and DQ8 alleles are unusual in their interactions with factors that regulate their peptide loading, invariant chain (Ii) and HLA-DM (DM). The same alleles, as well as other T1D DQ risk alleles (and Ag7), share nonpolar residues in place of Asp at β57 and prefer peptides that place acidic side chains in a pocket in the MHCII groove (P9). Antigen-presenting cells from T1D-susceptible mice and humans retain CLIP because of poor DM editing, although underlying mechanisms differ between species. We propose that these effects on peptide presentation make key contributions to CD and T1D pathogenesis.
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Jacob N, Jacob CO. Genetics of rheumatoid arthritis: an impressionist perspective. Rheum Dis Clin North Am 2012; 38:243-57. [PMID: 22819082 DOI: 10.1016/j.rdc.2012.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rheumatoid arthritis (RA) is the most common rheumatic disease. The genetic basis of RA is supported through the identification of more than 30 susceptibility genetic variants. Each of these genes individually makes only a slight contribution to the risk of disease. Moreover, there is significant disparity in the genetic variants associated with different RA subgroups and patient ethnicities, which emphasizes the intricate nature of the disease's pathogenesis, and the complexities involved in large-scale genetic studies. This review evaluates critically the recent literature on the genetic contribution to RA and assesses the methodology used to identify these risk alleles.
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Affiliation(s)
- Noam Jacob
- Department of Medicine, Keck School of Medicine, University of Southern California, 2011 Zonal Avenue HMR 703, Los Angeles, CA 90033, USA.
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29
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Abstract
Cataloging the association of transcripts to genetic variants in recent years holds the promise for functional dissection of regulatory structure of human transcription. Here, we present a novel approach, which aims at elucidating the joint relationships between transcripts and single-nucleotide polymorphisms (SNPs). This entails detection and analysis of modules of transcripts, each weakly associated to a single genetic variant, together exposing a high-confidence association signal between the module and this 'main' SNP. To explore how transcripts in a module are related to causative loci for that module, we represent such dependencies by a graphical model. We applied our method to the existing data on genetics of gene expression in the liver. The modules are significantly more, larger and denser than found in permuted data. Quantification of the confidence in a module as a likelihood score, allows us to detect transcripts that do not reach genome-wide significance level. Topological analysis of each module identifies novel insights regarding the flow of causality between the main SNP and transcripts. We observe similar annotations of modules from two sources of information: the enrichment of a module in gene subsets and locus annotation of the genetic variants. This and further phenotypic analysis provide a validation for our methodology.
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Affiliation(s)
- Anat Kreimer
- Department of Biomedical Informatics, Columbia University, New York 10032, USA.
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Raychaudhuri S, Sandor C, Stahl EA, Freudenberg J, Lee HS, Jia X, Alfredsson L, Padyukov L, Klareskog L, Worthington J, Siminovitch KA, Bae SC, Plenge RM, Gregersen PK, de Bakker PI. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nat Genet 2012; 44:291-6. [PMID: 22286218 PMCID: PMC3288335 DOI: 10.1038/ng.1076] [Citation(s) in RCA: 659] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 12/12/2011] [Indexed: 12/16/2022]
Abstract
The genetic association of the major histocompatibility complex (MHC) to rheumatoid arthritis risk has commonly been attributed to alleles in HLA-DRB1. However, debate persists about the identity of the causal variants in HLA-DRB1 and the presence of independent effects elsewhere in the MHC. Using existing genome-wide SNP data in 5,018 individuals with seropositive rheumatoid arthritis (cases) and 14,974 unaffected controls, we imputed and tested classical alleles and amino acid polymorphisms in HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1 and HLA-DRB1, as well as 3,117 SNPs across the MHC. Conditional and haplotype analyses identified that three amino acid positions (11, 71 and 74) in HLA-DRβ1 and single-amino-acid polymorphisms in HLA-B (at position 9) and HLA-DPβ1 (at position 9), which are all located in peptide-binding grooves, almost completely explain the MHC association to rheumatoid arthritis risk. This study shows how imputation of functional variation from large reference panels can help fine map association signals in the MHC.
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Affiliation(s)
- Soumya Raychaudhuri
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Cynthia Sandor
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eli A. Stahl
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jan Freudenberg
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, NY USA
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Xiaoming Jia
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet at Karolinska University Hospital Solna, Stockholm, Sweden
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet at Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Katherine A. Siminovitch
- Department of Medicine, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, Ontario, Canada
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Robert M. Plenge
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Peter K. Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, NY USA
| | - Paul I.W. de Bakker
- Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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31
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Aláez C, Flores-A H, Concha del Río LE, Munguía A, Rodríguez A, García D, Arellanes L, Gorodezky C. Major histocompatibility complex and strong human leukocyte antigen–DRB1 and gender association with Vogt–Koyanagi–Harada syndrome in Mexican Mestizos. Hum Immunol 2011; 72:1198-203. [DOI: 10.1016/j.humimm.2011.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 09/08/2011] [Accepted: 09/15/2011] [Indexed: 10/17/2022]
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32
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Vignal CM, Bansal AT, Balding DJ. Using Penalised Logistic Regression to Fine Map HLA Variants for Rheumatoid Arthritis. Ann Hum Genet 2011; 75:655-64. [DOI: 10.1111/j.1469-1809.2011.00670.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Wang N, Shen N, Vyse TJ, Anand V, Gunnarson I, Sturfelt G, Rantapää-Dahlqvist S, Elvin K, Truedsson L, Andersson BA, Dahle C, Örtqvist E, Gregersen PK, Behrens TW, Hammarström L. Selective IgA deficiency in autoimmune diseases. Mol Med 2011; 17:1383-96. [PMID: 21826374 PMCID: PMC3321806 DOI: 10.2119/molmed.2011.00195] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/02/2011] [Indexed: 12/12/2022] Open
Abstract
Selective immunoglobulin A deficiency (IgAD) is the most common primary immunodeficiency in Caucasians. It has previously been suggested to be associated with a variety of concomitant autoimmune diseases. In this review, we present data on the prevalence of IgAD in patients with Graves disease (GD), systemic lupus erythematosus (SLE), type 1 diabetes (T1D), celiac disease (CD), myasthenia gravis (MG) and rheumatoid arthritis (RA) on the basis of both our own recent large-scale screening results and literature data. Genetic factors are important for the development of both IgAD and various autoimmune disorders, including GD, SLE, T1D, CD, MG and RA, and a strong association with the major histocompatibility complex (MHC) region has been reported. In addition, non-MHC genes, such as interferon-induced helicase 1 (IFIH1) and c-type lectin domain family 16, member A (CLEC16A), are also associated with the development of IgAD and some of the above diseases. This indicates a possible common genetic background. In this review, we present suggestive evidence for a shared genetic predisposition between these disorders.
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Affiliation(s)
- Ning Wang
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Nan Shen
- Department of Rheumatology, Renji Hospital, JiaoTong University School of Medicine, Shanghai, China
| | - Timothy J Vyse
- Section of Molecular Genetics and Rheumatology, Hammersmith Hospital, London, United Kingdom
| | - Vidya Anand
- Section of Molecular Genetics and Rheumatology, Hammersmith Hospital, London, United Kingdom
| | - Iva Gunnarson
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Gunnar Sturfelt
- Department of Rheumatology, Lund University Hospital, Lund, Sweden
| | | | - Kerstin Elvin
- Unit of Clinical Immunology, Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lennart Truedsson
- Department of Laboratory Medicine, Section of Microbiology, Immunology and Glycobiology, Lund University, Sweden
| | | | - Charlotte Dahle
- Clinical Immunology Unit, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Eva Örtqvist
- Department of Woman and Child Health, Astrid Lindgren Children’s Hospital, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Timothy W Behrens
- Division of Immunology, Tissue Growth & Repair, Biomarker Discovery and Human Genetics, Genentech, South San Francisco, California, United States of America
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
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Abstract
The study of complex genetics in autoimmune diseases has progressed at a tremendous pace over the last 4 years, as a direct result of the enormous gains made by genome wide association studies (GWAS). Novel genetic findings are continuously being reported alongside the rapid development of genetic technologies, sophisticated statistical analysis, and larger sample collections. It is now becoming clear that multiple genes contribute to disease risk in many complex genetic disorders including rheumatoid arthritis (RA) and that there are common genetic risk factors that underlie a spectrum of autoimmune diseases. This review details the current genetic landscape of RA, and describes what GWAS has taught us in terms of missing heritability, subsets of disease, existence of genetic heterogeneity, and shared autoimmune risk loci. Finally, this review addresses the initial challenges faced in translating the wealth of genetic findings into determining the biological mechanisms that contribute to the relationship between genotype and phenotype. Unraveling the mechanism of how genes directly influence the cause of RA will lead to a better understanding of the disease and will ultimately have a direct clinical impact, informing the development of new therapies that can be utilized in the treatment of RA.
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Affiliation(s)
- Kate McAllister
- Arthritis Research United Kingdom Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, UK
| | - Stephen Eyre
- Arthritis Research United Kingdom Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, UK
| | - Gisela Orozco
- Arthritis Research United Kingdom Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, UK
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35
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Perricone C, Ceccarelli F, Valesini G. An overview on the genetic of rheumatoid arthritis: a never-ending story. Autoimmun Rev 2011; 10:599-608. [PMID: 21545847 DOI: 10.1016/j.autrev.2011.04.021] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic, systemic, inflammatory, multi-factorial disease sustained by environmental and genetic factors. These seem to be necessary but not sufficient in the disease development, nonetheless they can be responsible of different clinical pictures and response to therapy, and they can represent potential therapeutic targets. Several genes have been indicated so far in the pathogenesis of RA. The most important region is the Human Leukocyte Antigen (HLA) that contributes to approximately half of the genetic susceptibility for RA. The association seems to be stronger or specific for anti-citrullinated protein antibodies positive disease. Several alleles in the epitope-recognition part of the HLA molecule that show the highest association with RA susceptibility, also share a common string of amminoacid residues (the so-called shared-epitope hypothesis). Other variants in potentially pathogenic genes located in non-MHC regions have been implicated by recently performed genome wide analysis studies. These genes include PTPN22, TRAF1-C5, PADI4, STAT4. Other polymorphisms seem to be responsible for more aggressive disease phenotype such as those located at TNF, IL-1, IL-6, IL-4, IL-5, OPN, PRF1. However, still nowadays, the genetic background of RA remains to be clearly depicted, and the efforts in the post-genomic era can bring to an estimation of the real likelihood of the genetic effect on RA. Finally, the discovery of new genes associated with the disease can be relevant in finding potential biomarkers, potentially useful in disease diagnosis and treatment.
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Affiliation(s)
- Carlo Perricone
- Reumatologia, Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy.
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Bronson PG, Ramsay PP, Seldin MF, Gregersen PK, Criswell LA, Barcellos LF. CIITA is not associated with risk of developing rheumatoid arthritis. Genes Immun 2011; 12:235-8. [PMID: 21248776 PMCID: PMC3449225 DOI: 10.1038/gene.2010.67] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) class II transactivator gene (CIITA) encodes an important transcription factor regulating genes required for human leukocyte antigen (HLA) class II MHC-restricted antigen presentation. MHC genes, particularly HLA class II, are strongly associated with risk of developing rheumatoid arthritis (RA). Given the strong biological relationship between CIITA and HLA class II genes, a comprehensive investigation of CIITA variation in RA was conducted. This study tested 31 CIITA single-nucleotide polymorphisms in 2542 RA cases and 3690 controls (N=6232). All individuals were of European ancestry, as determined by ancestry informative genetic markers. No evidence for association between CIITA variation and RA was observed after a correction for multiple testing was applied. This is the largest study to fully characterize common genetic variation in CIITA, including an assessment of haplotypes. Results exclude even a modest role for common CIITA polymorphisms in susceptibility to RA.
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Affiliation(s)
- P G Bronson
- Division of Epidemiology, Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, CA 94720-7356, USA
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Klareskog L, Malmström V, Lundberg K, Padyukov L, Alfredsson L. Smoking, citrullination and genetic variability in the immunopathogenesis of rheumatoid arthritis. Semin Immunol 2011; 23:92-8. [PMID: 21376627 DOI: 10.1016/j.smim.2011.01.014] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 01/10/2011] [Indexed: 11/17/2022]
Abstract
This review describes how studies on interactions between genetic variants, and environmental factors, mainly smoking, contribute to the understanding of how autoimmunity to post-translationally (citrullinated) proteins/peptides may occur and potentially contribute to certain subsets of rheumatoid arthritis. A main message is that studies on specific immune mechanisms in a complex and heterogeneous disease like RA should be undertaken with the help of results from genetic epidemiology. By those means, it may be possible to identify subsets of RA in a way that in the end allows development and testing of precise and subset-specific interventions against environment as well as genetically defined molecular pathways, in particular those that regulate specific immune responses.
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Affiliation(s)
- Lars Klareskog
- Department of Medicine, Karolinska Institutet/Karolinska University Hospital, Solna, Stockholm, Sweden.
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38
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Orozco G, Barton A, Eyre S, Ding B, Worthington J, Ke X, Thomson W. HLA-DPB1-COL11A2 and three additional xMHC loci are independently associated with RA in a UK cohort. Genes Immun 2011; 12:169-75. [PMID: 21293383 DOI: 10.1038/gene.2010.57] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The aim of this study was to investigate the complex association pattern of the extended major histocompatibility complex (xMHC) region with rheumatoid arthritis (RA) susceptibility to identify effects independent of HLA-DRB1. A total of 1804 RA cases and 1474 controls were included. High-resolution HLA-DRB1 typing was performed. Subjects were genotyped for 1546 single-nucleotide polymorphisms (SNPs) using Affymetrix GeneChip 500 K (Santa Clara, CA, USA) as part of the Wellcome Trust Case Control Consortium Study. Statistical analysis was carried out using PLINK. To avoid confounding by RA-associated HLA-DRB1 alleles, we analyzed xMHC SNPs using a data set with pairwise matching of cases and controls on DRB1 genotypes. A total of 594 case-control pairs with identical DRB1 genotypes were identified. After this adjustment, 104 SNPs remained significantly associated with RA (P<0.05), suggesting that additional RA loci independent of HLA-DRB1 can be found in the xMHC region. Of these, four loci showed the strongest associations with RA (P<0.005): ZNF391, the olfactory receptor (OR) gene cluster, C6orf26-RDBP and HLA-DPB1-COL11A2. An additional locus mapping to the BTN (butyrophilin) cluster showed independent association with RA in anti-cyclic citrullinated peptide-positive patients exclusively. We have validated the previously described independent association of the HLA-DPB1-COL11A2 locus with RA. In addition, association with three novel independent RA loci in the xMHC region (ZNF391, OR2H1 and C6orf26-RDBP) has been detected.
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Affiliation(s)
- G Orozco
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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39
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Liu C, Ackerman HH, Carulli JP. A genome-wide screen of gene-gene interactions for rheumatoid arthritis susceptibility. Hum Genet 2011; 129:473-85. [PMID: 21210282 DOI: 10.1007/s00439-010-0943-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Accepted: 12/22/2010] [Indexed: 12/16/2022]
Abstract
The objective of the study was to identify interacting genes contributing to rheumatoid arthritis (RA) susceptibility and identify SNPs that discriminate between RA patients who were anti-cyclic citrullinated protein positive and healthy controls. We analyzed two independent cohorts from the North American Rheumatoid Arthritis Consortium. A cohort of 908 RA cases and 1,260 controls was used to discover pairwise interactions among SNPs and to identify a set of single nucleotide polymorphisms (SNPs) that predict RA status, and a second cohort of 952 cases and 1,760 controls was used to validate the findings. After adjusting for HLA-shared epitope alleles, we identified and replicated seven SNP pairs within the HLA class II locus with significant interaction effects. We failed to replicate significant pairwise interactions among non-HLA SNPs. The machine learning approach "random forest" applied to a set of SNPs selected from single-SNP and pairwise interaction tests identified 93 SNPs that distinguish RA cases from controls with 70% accuracy. HLA SNPs provide the most classification information, and inclusion of non-HLA SNPs improved classification. While specific gene-gene interactions are difficult to validate using genome-wide SNP data, a stepwise approach combining association and classification methods identifies candidate interacting SNPs that distinguish RA cases from healthy controls.
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Affiliation(s)
- Chunyu Liu
- Center for Population Studies and the Framingham Heart Study, National Heart, Lung, and Blood Institute/NIH, 73 Mt. Wayte Avenue, Framingham, MA 01702, USA.
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40
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The contribution of genetic factors to rheumatoid arthritis. Rheumatology (Oxford) 2011. [DOI: 10.1016/b978-0-323-06551-1.00086-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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41
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Padyukov L, Seielstad M, Ong RTH, Ding B, Rönnelid J, Seddighzadeh M, Alfredsson L, Klareskog L. A genome-wide association study suggests contrasting associations in ACPA-positive versus ACPA-negative rheumatoid arthritis. Ann Rheum Dis 2010; 70:259-65. [PMID: 21156761 PMCID: PMC3015094 DOI: 10.1136/ard.2009.126821] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Rheumatoid arthritis (RA) can be divided into two major subsets based on the presence or absence of antibodies to citrullinated peptide antigens (ACPA). Until now, data from genome-wide association studies (GWAS) have only been published from ACPA-positive subsets of RA or from studies that have not separated the two subsets. The aim of the current study is to provide and compare GWAS data for both subsets. METHODS AND RESULTS GWAS using the Illumina 300K chip was performed for 774 ACPA-negative patients with RA, 1147 ACPA-positive patients with RA and 1079 controls from the Swedish population-based case-control study EIRA. Imputation was performed which allowed comparisons using 1,723,056 single nucleotide polymorphisms (SNPs). No SNP achieved genome-wide significance (2.9 × 10⁻⁸) in the comparison between ACPA-negative RA and controls. A case-case association study was then performed between ACPA-negative and ACPA-positive RA groups. The major difference in this analysis was in the HLA region where 768 HLA SNPs passed the threshold for genome-wide significance whereas additional contrasting SNPs did not reach genome-wide significance. However, one SNP close to the RPS12P4 locus in chromosome 2 reached a p value of 2 × 10⁶ and this locus can thus be considered as a tentative candidate locus for ACPA-negative RA. CONCLUSIONS ACPA-positive and ACPA-negative RA display significant risk allele frequency differences which are mainly confined to the HLA region. The data provide further support for distinct genetic aetiologies of RA subsets and emphasise the need to consider them separately in genetic as well as functional studies of this disease.
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Affiliation(s)
- Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
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42
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Anticitrullinated protein antibody (ACPA) in rheumatoid arthritis: influence of an interaction between HLA-DRB1 shared epitope and a deletion polymorphism in glutathione S-transferase in a cross-sectional study. Arthritis Res Ther 2010; 12:R213. [PMID: 21087494 PMCID: PMC3046521 DOI: 10.1186/ar3190] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 11/10/2010] [Accepted: 11/18/2010] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION A deletion polymorphism in glutathione S-transferase Mu-1 (GSTM1-null) has previously been implicated to play a role in rheumatoid arthritis (RA) risk and progression, although no prior investigations have examined its associations with anticitrullinated protein antibody (ACPA) positivity. The purpose of this study was to examine the associations of GSTM1-null with ACPA positivity in RA and to assess for evidence of interaction between GSTM1 and HLA-DRB1 shared epitope (SE). METHODS Associations of GSTM1-null with ACPA positivity were examined separately in two RA cohorts, the Veterans Affairs Rheumatoid Arthritis (VARA) registry (n = 703) and the Study of New-Onset RA (SONORA; n = 610). Interactions were examined by calculating an attributable proportion (AP) due to interaction. RESULTS A majority of patients in the VARA registry (76%) and SONORA (69%) were positive for ACPA with a similar frequency of GSTM1-null (53% and 52%, respectively) and HLA-DRB1 SE positivity (76% and 71%, respectively). The parameter of patients who had ever smoked was more common in the VARA registry (80%) than in SONORA (65%). GSTM1-null was significantly associated with ACPA positivity in the VARA registry (odds ratio (OR), 1.45; 95% confidence interval (CI), 1.02 to 2.05), but not in SONORA (OR, 1.00; 95% CI, 0.71 to 1.42). There were significant additive interactions between GSTM1 and HLA-DRB1 SE in the VARA registry (AP, 0.49; 95% CI, 0.21 to 0.77; P < 0.001) in ACPA positivity, an interaction replicated in SONORA (AP, 0.38; 95% CI, 0.00 to 0.76; P = 0.050). CONCLUSIONS This study is the first to show that the GSTM1-null genotype, a common genetic variant, exerts significant additive interaction with HLA-DRB1 SE on the risk of ACPA positivity in RA. Since GSTM1 has known antioxidant functions, these data suggest that oxidative stress may be important in the development of RA-specific autoimmunity in genetically susceptible individuals.
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43
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Delgado-Vega A, Sánchez E, Löfgren S, Castillejo-López C, Alarcón-Riquelme ME. Recent findings on genetics of systemic autoimmune diseases. Curr Opin Immunol 2010; 22:698-705. [PMID: 20933377 DOI: 10.1016/j.coi.2010.09.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 08/26/2010] [Accepted: 09/07/2010] [Indexed: 12/11/2022]
Abstract
Association studies of over 1 million SNPs capturing most of the human genome common variation became possible thanks to the information provided by the HapMap International project and the development of high-throughput genotyping technologies at accessible prices. Genome-wide scans analyzing thousands of individuals have now identified most if not all of the major genes involved in susceptibility for several systemic autoimmune diseases. In particular, results for rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic sclerosis (SSc) are reviewed here. While most genes are shared between diseases, few seem to be unique reflecting that we still are long before knowing all genes, their interactions with other genes and the environment and their impact on biological functions.
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Affiliation(s)
- Angélica Delgado-Vega
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarsjölds väg 20, 751 85 Uppsala, Sweden
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44
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Cui J, Saevarsdottir S, Thomson B, Padyukov L, van der Helm-van Mil AHM, Nititham J, Hughes LB, de Vries N, Raychaudhuri S, Alfredsson L, Askling J, Wedrén S, Ding B, Guiducci C, Wolbink GJ, Crusius JBA, van der Horst-Bruinsma IE, Herenius M, Weinblatt ME, Shadick NA, Worthington J, Batliwalla F, Kern M, Morgan AW, Wilson AG, Isaacs JD, Hyrich K, Seldin MF, Moreland LW, Behrens TW, Allaart CF, Criswell LA, Huizinga TWJ, Tak PP, Bridges SL, Toes REM, Barton A, Klareskog L, Gregersen PK, Karlson EW, Plenge RM. Rheumatoid arthritis risk allele PTPRC is also associated with response to anti-tumor necrosis factor alpha therapy. ACTA ACUST UNITED AC 2010; 62:1849-61. [PMID: 20309874 DOI: 10.1002/art.27457] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE Anti-tumor necrosis factor alpha (anti-TNF) therapy is a mainstay of treatment in rheumatoid arthritis (RA). The aim of the present study was to test established RA genetic risk factors to determine whether the same alleles also influence the response to anti-TNF therapy. METHODS A total of 1,283 RA patients receiving etanercept, infliximab, or adalimumab therapy were studied from among an international collaborative consortium of 9 different RA cohorts. The primary end point compared RA patients with a good treatment response according to the European League Against Rheumatism (EULAR) response criteria (n = 505) with RA patients considered to be nonresponders (n = 316). The secondary end point was the change from baseline in the level of disease activity according to the Disease Activity Score in 28 joints (triangle upDAS28). Clinical factors such as age, sex, and concomitant medications were tested as possible correlates of treatment response. Thirty-one single-nucleotide polymorphisms (SNPs) associated with the risk of RA were genotyped and tested for any association with treatment response, using univariate and multivariate logistic regression models. RESULTS Of the 31 RA-associated risk alleles, a SNP at the PTPRC (also known as CD45) gene locus (rs10919563) was associated with the primary end point, a EULAR good response versus no response (odds ratio [OR] 0.55, P = 0.0001 in the multivariate model). Similar results were obtained using the secondary end point, the triangle upDAS28 (P = 0.0002). There was suggestive evidence of a stronger association in autoantibody-positive patients with RA (OR 0.55, 95% confidence interval [95% CI] 0.39-0.76) as compared with autoantibody-negative patients (OR 0.90, 95% CI 0.41-1.99). CONCLUSION Statistically significant associations were observed between the response to anti-TNF therapy and an RA risk allele at the PTPRC gene locus. Additional studies will be required to replicate this finding in additional patient collections.
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Affiliation(s)
- Jing Cui
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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Sheu JJ, Lin YJ, Chang JS, Wan L, Chen SY, Huang YC, Chan C, Chiu IW, Tsai FJ. Association of COL11A2 polymorphism with susceptibility to Kawasaki disease and development of coronary artery lesions. Int J Immunogenet 2010; 37:487-92. [DOI: 10.1111/j.1744-313x.2010.00952.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Criswell LA. Gene discovery in rheumatoid arthritis highlights the CD40/NF-kappaB signaling pathway in disease pathogenesis. Immunol Rev 2010; 233:55-61. [PMID: 20192992 DOI: 10.1111/j.0105-2896.2009.00862.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
During the past several years, substantial progress has been made in the identification of genetic variants that predispose to rheumatoid arthritis (RA) and other autoimmune disorders. Progress in this area has been facilitated by the availability of new technology that allows for a much more comprehensive screen of the genome than was possible before, in conjunction with large samples of RA patients with well-characterized disease. Recent RA genetic studies have identified genes with important functions related to intracellular signaling mechanisms, transcription factors, cytokines, membrane receptors, costimulatory molecules, and enzymes. In particular, recent discoveries highlight the importance of the CD40/NF-kappaB signaling pathway in RA, based on genetic association with several genes relevant to this pathway, including CD40, TRAF1, TNFAIP3, and REL. Progress in the identification of genes that contribute to RA is proceeding at a very rapid pace. These genetic discoveries shed light on underlying disease mechanisms in RA and provide targets for the development of novel diagnostic and therapeutic tools for future use in this chronic inflammatory disorder.
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Affiliation(s)
- Lindsey A Criswell
- Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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Orozco G, Barton A. Update on the genetic risk factors for rheumatoid arthritis. Expert Rev Clin Immunol 2010; 6:61-75. [PMID: 20383892 DOI: 10.1586/eci.09.72] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Rheumatoid arthritis (RA) is a complex disease, meaning that multiple genetic variants, environmental factors and random events interact to trigger pathological pathways. Although many of these etiological factors have not yet been identified, recent groundbreaking advances have expanded our knowledge about the genetic factors that contribute to RA. Here, we review the most recent findings on the genetic risk factors for RA. First, we give an overview of the genetics of RA and briefly describe the susceptibility loci discovered prior to the availability of genome-wide association studies (GWAS). Second, we focus on the newly discovered RA loci that have arisen from GWAS in populations of European ancestry. Through these studies, the number of established RA susceptibility loci has now grown to 13. Third, we discuss several important issues emerging from GWAS, such as ethnic heterogeneity and shared autoimmunity risk loci. Finally, we discuss what still needs to be accomplished before a more complete picture of the genetic risk to RA can be attained.
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Affiliation(s)
- Gisela Orozco
- Arthritis Research Campaign Epidemiology Unit, The University of Manchester, Manchester Academic Health Science Centre, Stopford Building, Oxford Road, Manchester M13 9PT, UK.
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O'Rielly DD, Rahman P. Pharmacogenetics of rheumatoid arthritis: Potential targets from susceptibility genes and present therapies. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2010; 3:15-31. [PMID: 23226040 PMCID: PMC3513198 DOI: 10.2147/pgpm.s5012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Indexed: 01/29/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic heterogeneous autoimmune disorder of unknown etiology resulting in inflammation in the synovium, cartilage, and bone. Genetic factors play an important role in susceptibility to RA as the heritability of RA is between 50% and 60%, with the human leukocyte antigen (HLA) locus accounting for at least 30% of overall genetic risk. Outside the major histocompatibility complex (MHC) region, six additional risk loci have been identified and validated including PTPN22, STAT4, PADI4, CTLA4, TNFAIP3-OLIG3, and TRAF1/C5. Genetic factors are also important in RA pharmacotherapy due to the gene-dependent activity of enzymes involved in the pharmacokinetics and/or pharmacodynamics of RA medications. Indeed, there is great variability in drug efficacy as well as adverse events associated with any anti-rheumatic therapy and genetics is thought to contribute significantly to this inter-individual variability in response. This review will summarize the genetic factors that have been implicated in the pathogenesis of RA, and how these determinants may factor into the potential pharmacogenetics of this disease. We will also review the therapeutic agents that are currently being utilized or presently being evaluated in the treatment of RA, along with potential pharmacogenetic markers that have been proposed for such medications.
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Affiliation(s)
- Darren D O'Rielly
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
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Current World Literature. Curr Opin Rheumatol 2010; 22:229-34. [DOI: 10.1097/bor.0b013e32833755c4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
PURPOSE OF REVIEW To review the recently discovered genetic risk loci in rheumatoid arthritis (RA), the pathways they implicate, and the genetic architecture of RA. RECENT FINDINGS Since 2008 investigators have identified many common genetic variants that confer disease risk through single nucleotide polymorphism genotyping studies; the list of variants will no doubt continue to expand at a rapid rate as genotyping technologies evolve and case-control sample collections continue to grow. In aggregate, these variants implicate pathways leading to NF-kappaB (nuclear factor kappa-light-chain-enhancer of activated B cells) activation, the interluekin-2 signaling pathway, and T-cell activation. SUMMARY Although the effect of any individual variant is modest and even in aggregate considerably less than that of the major histocompatability complex, discovery of recent risk variants suggests immunological processes that are involved in disease pathogenesis.
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Affiliation(s)
- Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.
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