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Xu J, Chen H, Sun C, Wei S, Tao J, Jia Z, Chen X, Lv W, Lv H, Tang G, Jiang Y, Zhang M. Epigenome-wide methylation haplotype association analysis identified HLA-DRB1, HLA-DRB5 and HLA-DQB1 as risk factors for rheumatoid arthritis. Int J Immunogenet 2023; 50:291-298. [PMID: 37688529 DOI: 10.1111/iji.12637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/04/2023] [Accepted: 09/02/2023] [Indexed: 09/11/2023]
Abstract
The aim of this study was to compare nonrandom associations between physically adjacent single methylation polymorphism loci among rheumatoid arthritis (RA) and normal subjects for investigating RA-risk methylation haplotypes (meplotype). With 354 ACPA-positive RA patients and 335 normal controls selected from a case-control study based on Swedish population, we conducted the first RA epigenome-wide meplotype association study using our software EWAS2.0, mainly including (i) converted the β value to methylation genotype (menotype) data, (ii) identified methylation disequilibrium (MD) block, (iii) calculated frequent of each meplotypes in MD block and performed case-control association test and (iv) screened for RA-risk meplotypes by odd ratio (OR) and p-values. Ultimately, 545 meplotypes on 334 MD blocks were identified significantly associated with RA (p-value < .05). These meplotypes were mapped to 329 candidate genes related to RA. Subsequently, combined with gene optimization, eight RA-risk meplotypes were identified on three risk genes: HLA-DRB1, HLA-DRB5 and HLA-DQB1. Our results reported the relationship between DNA methylation pattern on HLA-DQB1 and the risk of RA for the first time, demonstrating the co-demethylation of 'cg22984282' and 'cg13423887' on HLA-DQB1 gene (meplotype UU, p-value = 2.90E - 6, OR = 1.68, 95% CI = [1.35, 2.10]) may increase the risk of RA. Our results demonstrates the potential of methylation haplotype analysis to identify RA-related genes from a new perspective and its applicability to the study of other disease.
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Affiliation(s)
- Jing Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haiyan Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chen Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Siyu Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Junxian Tao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhe Jia
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xingyu Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Guoping Tang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Mingming Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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de la Calle-Fabregat C, Niemantsverdriet E, Cañete JD, Li T, van der Helm-van Mil AHM, Rodríguez-Ubreva J, Ballestar E. The DNA methylation Profile of Undifferentiated Arthritis Patients Anticipates their Subsequent Differentiation to Rheumatoid Arthritis. Arthritis Rheumatol 2021; 73:2229-2239. [PMID: 34105306 DOI: 10.1002/art.41885] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/27/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Undifferentiated arthritis (UA) is the term used to cover all the cases of arthritis that do not fit a specific diagnosis. A significant percentage of UA patients progress to rheumatoid arthritis (RA), others to a different definite rheumatic disease, and the rest undergo spontaneous remission. Therapeutic intervention in patients with UA can delay or halt disease progression and its long-term consequences. It is therefore of inherent interest to identify those UA patients with a high probability of progressing to RA who would benefit from early appropriate therapy. We hypothesized that alterations in the DNA methylation profiles of immune cells may inform on the genetically- or environmentally-determined status of patients and potentially discriminate between disease subtypes. METHODS In this study, we performed DNA methylation profiling of a UA patient cohort, in which progression into RA occurs for a significant proportion of the patients. RESULTS We find differential DNA methylation in UA patients compared to healthy controls. Most importantly, our analysis identifies a DNA methylation signature characteristic of those UA cases that differentiate to RA. We demonstrate that the methylome of peripheral mononuclear cells can be used to anticipate the evolution of UA to RA, and that this methylome is associated with a number of inflammatory pathways and transcription factors. Finally, we design a machine-learning strategy for DNA methylation-based classification that predicts the differentiation of UA patients towards RA. CONCLUSION DNA methylation profiling provides a good predictor of UA-to-RA progression to anticipate targeted treatments and improve clinical management.
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Affiliation(s)
| | - Ellis Niemantsverdriet
- Department of Rheumatology, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, the Netherlands
| | - Juan D Cañete
- Rheumatology Service, Hospital Clinic and Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | | | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
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Qiu W, Liu Y. DNA Methylation of the MHC Region in Rheumatoid Arthritis: Perspectives and Challenges. J Rheumatol 2020; 47:1597-1599. [PMID: 33139520 DOI: 10.3899/jrheum.191404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Wenqing Qiu
- W. Qiu, MS, Y. Liu, PhD, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Yun Liu
- W. Qiu, MS, Y. Liu, PhD, MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Zhongshan Hospital, Fudan University, Shanghai, China.
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Guo S, Xu L, Chang C, Zhang R, Jin Y, He D. Epigenetic Regulation Mediated by Methylation in the Pathogenesis and Precision Medicine of Rheumatoid Arthritis. Front Genet 2020; 11:811. [PMID: 32849810 PMCID: PMC7417338 DOI: 10.3389/fgene.2020.00811] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/06/2020] [Indexed: 12/11/2022] Open
Abstract
Rheumatoid arthritis (RA) is a complex disease triggered by the interaction between genetics and the environment, especially through the shared epitope (SE) and cell surface calreticulin (CSC) theory. However, the available evidence shows that genetic diversity and environmental exposure cannot explain all the clinical characteristics and heterogeneity of RA. In contrast, recent studies demonstrate that epigenetics play important roles in the pathogenesis of RA, especially DNA methylation and histone modification. DNA methylation and histone methylation are involved in innate and adaptive immune cell differentiation and migration, proliferation, apoptosis, and mesenchymal characteristics of fibroblast-like synoviocytes (FLS). Epigenetic-mediated regulation of immune-related genes and inflammation pathways explains the dynamic expression network of RA. In this review, we summarize the comprehensive evidence to show that methylation of DNA and histones is significantly involved in the pathogenesis of RA and could be applied as a promising biomarker in the disease progression and drug-response prediction. We also explain the advantages and challenges of the current epigenetics research in RA. In summary, epigenetic modules provide a possible interface through which genetic and environmental risk factors connect to contribute to the susceptibility and pathogenesis of RA. Additionally, epigenetic regulators provide promising drug targets to develop novel therapeutic drugs for RA. Finally, DNA methylation and histone modifications could be important features for providing a better RA subtype identification to accelerate personalized treatment and precision medicine.
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Affiliation(s)
- Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.,Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States
| | - Lingxia Xu
- Department of Rheumatology, Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Cen Chang
- Department of Rheumatology, Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Runrun Zhang
- Department of Rheumatology, Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yehua Jin
- Department of Rheumatology, Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Dongyi He
- Department of Rheumatology, Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
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Anaparti V, Agarwal P, Smolik I, Mookherjee N, El-Gabalawy H. Whole Blood Targeted Bisulfite Sequencing and Differential Methylation in the C6ORF10 Gene of Patients with Rheumatoid Arthritis. J Rheumatol 2019; 47:1614-1623. [DOI: 10.3899/jrheum.190376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2019] [Indexed: 12/25/2022]
Abstract
Objective.Polymorphisms in human major histocompatibility complex (MHC) are the strongest genetic associations with rheumatoid arthritis (RA). Epigenome-wide methylation studies suggest DNA methylation changes within MHC may contribute to disease susceptibility. We profiled MHC-specific methylated CpG (5′–C–phosphate–G–3′) in autoantibody-positive patients with RA and matched unaffected anticitrullinated protein antibodies–negative first-degree relatives (ACPA−/FDR) from an indigenous North American (INA) population that is known to have prevalent RA.Methods.DNA was isolated from whole blood and targeted bisulfite sequencing was used to profile methylated CpG in patients with RA and ACPA−/FDR. Differentially methylated CpG loci (DML) were mapped and gene annotated. Ingenuity pathway analysis (IPA) was used for curating biomolecular networks of mapped genes. Transcript abundance was determined by quantitative (q)PCR.Results.We identified 74 uniquely methylated CpG sites within the MHC region that were differentially methylated in patients with RA (p < 0.05), compared to ACPA−/FDR. Of these, 32 DML were located on 22 genes. IPA showed these genes are involved in regulating the nuclear factor–κB complex and processes involved in antigen presentation, and immune cell crosstalk in autoimmunity. Pearson correlation analysis demonstrated a negative association between differentially methylated CpG in the C6ORF10 gene and risk factors associated with RA. Analysis by qPCR confirmed differential abundance of C6ORF10, TNXB, and HCG18 mRNA in patients with RA compared to ACPA−/FDR.Conclusion.Our results confirm the presence of differential methylation at specific gene loci within the MHC region of INA patients with RA. These epigenetic signatures may precede disease onset, or alternatively, may be a result of developing RA.
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Nemtsova MV, Zaletaev DV, Bure IV, Mikhaylenko DS, Kuznetsova EB, Alekseeva EA, Beloukhova MI, Deviatkin AA, Lukashev AN, Zamyatnin AA. Epigenetic Changes in the Pathogenesis of Rheumatoid Arthritis. Front Genet 2019; 10:570. [PMID: 31258550 PMCID: PMC6587113 DOI: 10.3389/fgene.2019.00570] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/31/2019] [Indexed: 01/06/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease that affects about 1% of the world’s population. The etiology of RA remains unknown. It is considered to occur in the presence of genetic and environmental factors. An increasing body of evidence pinpoints that epigenetic modifications play an important role in the regulation of RA pathogenesis. Epigenetics causes heritable phenotype changes that are not determined by changes in the DNA sequence. The major epigenetic mechanisms include DNA methylation, histone proteins modifications and changes in gene expression caused by microRNAs and other non-coding RNAs. These modifications are reversible and could be modulated by diet, drugs, and other environmental factors. Specific changes in DNA methylation, histone modifications and abnormal expression of non-coding RNAs associated with RA have already been identified. This review focuses on the role of these multiple epigenetic factors in the pathogenesis and progression of the disease, not only in synovial fibroblasts, immune cells, but also in the peripheral blood of patients with RA, which clearly shows their high diagnostic potential and promising targets for therapy in the future.
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Affiliation(s)
- Marina V Nemtsova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Dmitry V Zaletaev
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Irina V Bure
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Dmitry S Mikhaylenko
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina A Alekseeva
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Marina I Beloukhova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrei A Deviatkin
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Alexander N Lukashev
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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Ramos PS, Zimmerman KD, Haddad S, Langefeld CD, Medsger TA, Feghali-Bostwick CA. Integrative analysis of DNA methylation in discordant twins unveils distinct architectures of systemic sclerosis subsets. Clin Epigenetics 2019; 11:58. [PMID: 30947741 PMCID: PMC6449959 DOI: 10.1186/s13148-019-0652-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/11/2019] [Indexed: 02/08/2023] Open
Abstract
Background Systemic sclerosis (SSc) is a rare autoimmune fibrosing disease with an incompletely understood genetic and non-genetic etiology. Defining its etiology is important to allow the development of effective predictive, preventative, and therapeutic strategies. We conducted this epigenomic study to investigate the contributions of DNA methylation to the etiology of SSc while minimizing confounding due to genetic heterogeneity. Methods Genomic methylation in whole blood from 27 twin pairs discordant for SSc was assayed over 450 K CpG sites. In silico integration with reported differentially methylated cytosines, differentially expressed genes, and regulatory annotation was conducted to validate and interpret the results. Results A total of 153 unique cytosines in limited cutaneous SSc (lcSSc) and 266 distinct sites in diffuse cutaneous SSc (dcSSc) showed suggestive differential methylation levels in affected twins. Integration with available data revealed 76 CpGs that were also differentially methylated in blood cells from lupus patients, suggesting their role as potential epigenetic blood biomarkers of autoimmunity. It also revealed 27 genes with concomitant differential expression in blood from SSc patients, including IFI44L and RSAD2. Regulatory annotation revealed that dcSSc-associated CpGs (but not lcSSc) are enriched at Encyclopedia of DNA Elements-, Roadmap-, and BLUEPRINT-derived regulatory regions, supporting their potential role in disease presentation. Notably, the predominant enrichment of regulatory regions in monocytes and macrophages is consistent with the role of these cells in fibrosis, suggesting that the observed cellular dysregulation might be, at least partly, due to altered epigenetic mechanisms of these cells in dcSSc. Conclusions These data implicate epigenetic changes in the pathogenesis of SSc and suggest functional mechanisms in SSc etiology. Electronic supplementary material The online version of this article (10.1186/s13148-019-0652-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.,Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Kip D Zimmerman
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Thomas A Medsger
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carol A Feghali-Bostwick
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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Webster AP, Plant D, Ecker S, Zufferey F, Bell JT, Feber A, Paul DS, Beck S, Barton A, Williams FMK, Worthington J. Increased DNA methylation variability in rheumatoid arthritis-discordant monozygotic twins. Genome Med 2018; 10:64. [PMID: 30176915 PMCID: PMC6122744 DOI: 10.1186/s13073-018-0575-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis is a common autoimmune disorder influenced by both genetic and environmental factors. Epigenome-wide association studies can identify environmentally mediated epigenetic changes such as altered DNA methylation, which may also be influenced by genetic factors. To investigate possible contributions of DNA methylation to the aetiology of rheumatoid arthritis with minimum confounding genetic heterogeneity, we investigated genome-wide DNA methylation in disease-discordant monozygotic twin pairs. METHODS Genome-wide DNA methylation was assessed in 79 monozygotic twin pairs discordant for rheumatoid arthritis using the HumanMethylation450 BeadChip array (Illumina). Discordant twins were tested for both differential DNA methylation and methylation variability between rheumatoid arthritis and healthy twins. The methylation variability signature was then compared with methylation variants from studies of other autoimmune diseases and with an independent healthy population. RESULTS We have identified a differentially variable DNA methylation signature that suggests multiple stress response pathways may be involved in the aetiology of the disease. This methylation variability signature also highlighted potential epigenetic disruption of multiple RUNX3 transcription factor binding sites as being associated with disease development. Comparison with previously performed epigenome-wide association studies of rheumatoid arthritis and type 1 diabetes identified shared pathways for autoimmune disorders, suggesting that epigenetics plays a role in autoimmunity and offering the possibility of identifying new targets for intervention. CONCLUSIONS Through genome-wide analysis of DNA methylation in disease-discordant monozygotic twins, we have identified a differentially variable DNA methylation signature, in the absence of differential methylation in rheumatoid arthritis. This finding supports the importance of epigenetic variability as an emerging component in autoimmune disorders.
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Affiliation(s)
- Amy P Webster
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK. .,Department of Cancer Biology, UCL Cancer Institute, University College London, London, UK.
| | - Darren Plant
- NIHR Manchester Biomedical Research Centre, Manchester Academy of Health Sciences, Manchester University Foundation Trust, Manchester, UK
| | - Simone Ecker
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, UK
| | - Flore Zufferey
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Andrew Feber
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, UK.,Division of Surgery and Interventional Science, University College London, London, UK
| | - Dirk S Paul
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Stephan Beck
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, UK
| | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Manchester Academy of Health Sciences, Manchester University Foundation Trust, Manchester, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK. .,NIHR Manchester Biomedical Research Centre, Manchester Academy of Health Sciences, Manchester University Foundation Trust, Manchester, UK.
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Nair N, Wilson AG, Barton A. DNA methylation as a marker of response in rheumatoid arthritis. Pharmacogenomics 2017; 18:1323-1332. [PMID: 28836487 DOI: 10.2217/pgs-2016-0195] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Rheumatoid arthritis (RA) is a complex disease affecting approximately 0.5-1% of the population. While there are effective biologic therapies, in up to 40% of patients, disease activity remains inadequately controlled. Therefore, identifying factors that predict, prior to the initiation of therapy, which patients are likely to respond best to which treatment is a research priority and DNA methylation is increasingly being explored as a potential theranostic biomarker. DNA methylation is thought to play a role in RA disease pathogenesis and in mediating the relationship between genetic variants and patient outcomes. The role of DNA methylation has been most extensively explored in cancer medicine, where it has been shown to be predictive of treatment response. Studies in RA, however, are in their infancy and, while showing promise, further investigation in well-powered studies is warranted.
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Affiliation(s)
- Nisha Nair
- Arthritis Research UK Centre for Genetics & Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK
| | - Anthony G Wilson
- University College Dublin School of Medicine & Medical Science & Conway Institute, Dublin, Ireland
| | - Anne Barton
- Arthritis Research UK Centre for Genetics & Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK.,NIHR Manchester Musculoskeletal BRU, Central Manchester Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
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Guo S, Zhu Q, Jiang T, Wang R, Shen Y, Zhu X, Wang Y, Bai F, Ding Q, Zhou X, Chen G, He DY. Genome-wide DNA methylation patterns in CD4+ T cells from Chinese Han patients with rheumatoid arthritis. Mod Rheumatol 2016; 27:441-447. [PMID: 27585642 DOI: 10.1080/14397595.2016.1218595] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Rheumatoid arthritis (RA) is an autoimmune disease that causes chronic inflammation of the joints. Recent evidence indicated the epigenetic changes may contribute to the pathogenesis of RA. METHOD To understand the extent and nature of dysregulated DNA methylation in RA CD4T cells, we performed a genome-wide DNA methylation study in CD4 + T cells in 12 RA patients compared to 12 matched normal healthy controls. Cytosine methylation status was quantified with Illumina methylation 450K microarray. RESULT The DNA methylation profiling showed 383 hyper- and 785 hypo-methylated genes in the CD4 + T cells of the RA patients (p < 3.4 × 10-7). Gene ontology analysis indicated transcript alternative splicing and protein modification mediated by DNA methylation might play an important role in the pathogenesis of RA. In addition, the result showed that human leukocyte antigen (HLA) region including HLA-DRB6, HLA-DQA1 and HLA-E was frequently hypomethylated, but HLA-DQB1 hypermethylated in CpG island region and hypomethylated in CpG shelf region in RA patients. Outside the MHC region, HDAC4, NXN, TBCD and TMEM61 were the most hypermethylated genes, while ITIH3, TCN2, PRDM16, SLC1A5 and GALNT9 are the most hypomethylated genes. CONCLUSION Genome-wide DNA methylation profile revealed significant DNA methylation change in CD4 + T cells from patients with RA.
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Affiliation(s)
- Shicheng Guo
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China
| | - Qi Zhu
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China
| | - Ting Jiang
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Rongsheng Wang
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Yi Shen
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Xiao Zhu
- c Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics , Dongguan Scientific Research Center, Guangdong Medical University , Dongguan , China
| | - Yan Wang
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China
| | - Fengmin Bai
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Qin Ding
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Xiaodong Zhou
- d University of Texas Medical School at Houston , Houston , TX , USA , and
| | - Guangjie Chen
- e Department of Immunology and Microbiology , Shanghai JiaoTong University School of Medicine , Shanghai , China
| | - Dong Yi He
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
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