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Shi Y, Ma J, Li S, Liu C, Liu Y, Chen J, Liu N, Liu S, Huang H. Sex difference in human diseases: mechanistic insights and clinical implications. Signal Transduct Target Ther 2024; 9:238. [PMID: 39256355 PMCID: PMC11387494 DOI: 10.1038/s41392-024-01929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/26/2024] [Accepted: 07/23/2024] [Indexed: 09/12/2024] Open
Abstract
Sex characteristics exhibit significant disparities in various human diseases, including prevalent cardiovascular diseases, cancers, metabolic disorders, autoimmune diseases, and neurodegenerative diseases. Risk profiles and pathological manifestations of these diseases exhibit notable variations between sexes. The underlying reasons for these sex disparities encompass multifactorial elements, such as physiology, genetics, and environment. Recent studies have shown that human body systems demonstrate sex-specific gene expression during critical developmental stages and gene editing processes. These genes, differentially expressed based on different sex, may be regulated by androgen or estrogen-responsive elements, thereby influencing the incidence and presentation of cardiovascular, oncological, metabolic, immune, and neurological diseases across sexes. However, despite the existence of sex differences in patients with human diseases, treatment guidelines predominantly rely on male data due to the underrepresentation of women in clinical trials. At present, there exists a substantial knowledge gap concerning sex-specific mechanisms and clinical treatments for diverse diseases. Therefore, this review aims to elucidate the advances of sex differences on human diseases by examining epidemiological factors, pathogenesis, and innovative progress of clinical treatments in accordance with the distinctive risk characteristics of each disease and provide a new theoretical and practical basis for further optimizing individualized treatment and improving patient prognosis.
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Affiliation(s)
- Yuncong Shi
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Jianshuai Ma
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Sijin Li
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Chao Liu
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Yuning Liu
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Jie Chen
- Department of Radiotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ningning Liu
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shiming Liu
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Hui Huang
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China.
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
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Ye C, Zhao Z, Lai P, Chen C, Jian F, Liang H, Guo Q. Strategies for the detection of site-specific DNA methylation and its application, opportunities and challenges in the field of electrochemical biosensors. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5496-5508. [PMID: 39051422 DOI: 10.1039/d4ay00779d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in various biological processes. Aberrant DNA methylation is closely associated with the onset of diseases, and the specific localization of methylation sites in the genome offers further insight into the connection between methylation and diseases. Currently, there are numerous methods available for site-specific methylation detection. Electrochemical biosensors have garnered significant attention due to their distinct advantages, such as rapidity, simplicity, high sensitivity, low cost, and the potential for miniaturization. In this paper, we present a systematic review of the primary sensing strategies utilized in the past decade for analyzing site-specific methylation and their applications in electrochemical sensors, from a novel perspective focusing on the localization analysis of site-specific methylation. These strategies include bisulfite treatment, restriction endonuclease treatment, other sensing strategies, and deamination without direct bisulfite treatment. We hope that this paper can offer ideas and references for establishing site-specific methylation electrochemical analysis in clinical practice.
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Affiliation(s)
- Chenliu Ye
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Zhibin Zhao
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Penghui Lai
- The Second Hospital of Longyan, Longyan 364000, China
| | - Chunmei Chen
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Fumei Jian
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Haiying Liang
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Qiongying Guo
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
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Deng T, Wang Z, Geng Q, Wang Z, Jiao Y, Diao W, Xu J, Deng T, Luo J, Tao Q, Xiao C. Methylation of T and B Lymphocytes in Autoimmune Rheumatic Diseases. Clin Rev Allergy Immunol 2024; 66:401-422. [PMID: 39207646 DOI: 10.1007/s12016-024-09003-4] [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] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
The role of abnormal epigenetic modifications, particularly DNA methylation, in the pathogenesis of autoimmune rheumatic diseases (ARDs) has garnered increasing attention. Lymphocyte dysfunction is a significant contributor to the pathogenesis of ARDs. Methylation is crucial for maintaining normal immune system function, and aberrant methylation can hinder lymphocyte differentiation, resulting in functional abnormalities that disrupt immune tolerance, leading to the excessive expression of inflammatory cytokines, thereby exacerbating the onset and progression of ARDs. Recent studies suggest that methylation-related factors have the potential to serve as biomarkers for monitoring the activity of ARDs. This review summarizes the current state of research on the impact of DNA and RNA methylation on the development, differentiation, and function of T and B cells and examines the progress of these epigenetic modifications in studies of six specific ARDs: systemic lupus erythematosus, rheumatoid arthritis, Sjögren's syndrome, systemic sclerosis, juvenile idiopathic arthritis, and ankylosing spondylitis. Additionally, we propose that exploring the interplay between RNA methylation and DNA methylation may represent a novel direction for understanding the pathogenesis of ARDs and developing novel treatment strategies.
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Affiliation(s)
- Tiantian Deng
- Beijing University of Chinese Medicine, School of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Zihan Wang
- Beijing University of Chinese Medicine, School of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Qishun Geng
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Zhaoran Wang
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yi Jiao
- Beijing University of Chinese Medicine, School of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Wenya Diao
- Beijing University of Chinese Medicine, School of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jiahe Xu
- China-Japan Friendship Hospital, Peking University, Beijing, 100029, China
| | - Tingting Deng
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jing Luo
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Qingwen Tao
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Cheng Xiao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China.
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Wang Y, Riaz F, Wang W, Pu J, Liang Y, Wu Z, Pan S, Song J, Yang L, Zhang Y, Wu H, Han F, Tang J, Wang X. Functional significance of DNA methylation: epigenetic insights into Sjögren's syndrome. Front Immunol 2024; 15:1289492. [PMID: 38510251 PMCID: PMC10950951 DOI: 10.3389/fimmu.2024.1289492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024] Open
Abstract
Sjögren's syndrome (SjS) is a systemic, highly diverse, and chronic autoimmune disease with a significant global prevalence. It is a complex condition that requires careful management and monitoring. Recent research indicates that epigenetic mechanisms contribute to the pathophysiology of SjS by modulating gene expression and genome stability. DNA methylation, a form of epigenetic modification, is the fundamental mechanism that modifies the expression of various genes by modifying the transcriptional availability of regulatory regions within the genome. In general, adding a methyl group to DNA is linked with the inhibition of genes because it changes the chromatin structure. DNA methylation changes the fate of multiple immune cells, such as it leads to the transition of naïve lymphocytes to effector lymphocytes. A lack of central epigenetic enzymes frequently results in abnormal immune activation. Alterations in epigenetic modifications within immune cells or salivary gland epithelial cells are frequently detected during the pathogenesis of SjS, representing a robust association with autoimmune responses. The analysis of genome methylation is a beneficial tool for establishing connections between epigenetic changes within different cell types and their association with SjS. In various studies related to SjS, most differentially methylated regions are in the human leukocyte antigen (HLA) locus. Notably, the demethylation of various sites in the genome is often observed in SjS patients. The most strongly linked differentially methylated regions in SjS patients are found within genes regulated by type I interferon. This demethylation process is partly related to B-cell infiltration and disease progression. In addition, DNA demethylation of the runt-related transcription factor (RUNX1) gene, lymphotoxin-α (LTA), and myxovirus resistance protein A (MxA) is associated with SjS. It may assist the early diagnosis of SjS by serving as a potential biomarker. Therefore, this review offers a detailed insight into the function of DNA methylation in SjS and helps researchers to identify potential biomarkers in diagnosis, prognosis, and therapeutic targets.
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Affiliation(s)
- Yanqing Wang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Farooq Riaz
- Center for Cancer Immunology, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Wei Wang
- Department of Radiology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jincheng Pu
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuanyuan Liang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhenzhen Wu
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shengnan Pan
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiamin Song
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lufei Yang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Youwei Zhang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Huihong Wu
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fang Han
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jianping Tang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xuan Wang
- Department of Rheumatology and Immunology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
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Yu Y, Lu C, Yu W, Lei Y, Sun S, Liu P, Bai F, Chen Y, Chen J. B Cells Dynamic in Aging and the Implications of Nutritional Regulation. Nutrients 2024; 16:487. [PMID: 38398810 PMCID: PMC10893126 DOI: 10.3390/nu16040487] [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: 01/07/2024] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Aging negatively affects B cell production, resulting in a decrease in B-1 and B-2 cells and impaired antibody responses. Age-related B cell subsets contribute to inflammation. Investigating age-related alterations in the B-cell pool and developing targeted therapies are crucial for combating autoimmune diseases in the elderly. Additionally, optimal nutrition, including carbohydrates, amino acids, vitamins, and especially lipids, play a vital role in supporting immune function and mitigating the age-related decline in B cell activity. Research on the influence of lipids on B cells shows promise for improving autoimmune diseases. Understanding the aging B-cell pool and considering nutritional interventions can inform strategies for promoting healthy aging and reducing the age-related disease burden.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Juan Chen
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; (Y.Y.)
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Banerjee S, Paradkar MU, Ponde CK, Rajani RM, Pillai S, Ashavaid TF. Does epigenetic markers of HLA gene show association with coronary artery disease in Indian subjects? Mol Biol Rep 2024; 51:173. [PMID: 38252175 DOI: 10.1007/s11033-023-08974-5] [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: 09/04/2023] [Accepted: 10/23/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND DNA methylation, one of the most stable forms of epigenetic modification is associated with the development and progression of coronary artery disease (CAD). Our previously reported study on epigenome-wide microarray analysis showed significantly methylated CpG sites. Top 5 significant CpGs from HLA gene were selected and analysed by Pyrosequencing (PSQ) to determine their association with severity of CAD. METHODS Blood samples of 50-age matched angiographically CAD positive male cases with 50 angiographically CAD negative male controls were subjected to lipid profile estimation and PSQ for methylation level analysis. Findings and subgroup analysis were evaluated by Mann-Whitney U; Kruskal-Wallis' rank test and two-way ANOVA by MedCalc (v19.6). RESULTS Methylation levels in HLA-DQA1 for cg10217052 was 78.5 (37-85) and 76.5 (24-84); cg09411910 was 81 (72.0 to 93.0) and 81.5 (50.0 to 89.0) in cases and controls respectively. Levels in HLA-DQB1-cg03344051, were 28.88 + 9.41 for cases and 30.36 + 9.37 in controls. For HLA-DRB1-cg07889003, levels in cases and controls were 15.5 (5.00-39.00) and 10.5 (5.00-29.0); while in cg08269402 were 52 (16-65) and 42.5 (17-61) respectively. No association was observed between methylation levels and lipid profile. cg03344051, cg07889003 and cg08269402 were significantly differentiated in double or triple vessel disease (DVD or TVD) as compared to single vessel disease (SVD) suggesting an increase in the extent of methylation with the increase in CAD severity. CONCLUSION The present study shows significant increase in the extent of methylation in 3 CpG sites in DVD/TVD cases as compared to SVD cases. Additionally, a novel site, cg07889003 identified in our discovery phase has shown association with the severity of CAD.
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Affiliation(s)
- Shyamashree Banerjee
- Research Laboratories, P.D Hinduja Hospital & Medical Research Centre, Mumbai, India
| | - Minal U Paradkar
- Research Laboratories, P.D Hinduja Hospital & Medical Research Centre, Mumbai, India
- Department of Biochemistry, P.D Hinduja Hospital & Medical Research Centre, Mumbai, India
| | | | - Rajesh M Rajani
- Department of Cardiology, P.D Hinduja Hospital & Medical Research Centre, Mumbai, India
| | - Sudhir Pillai
- Department of Cardiology, P.D Hinduja Hospital & Medical Research Centre, Mumbai, India
| | - Tester F Ashavaid
- Research Laboratories, P.D Hinduja Hospital & Medical Research Centre, Mumbai, India.
- Department of Biochemistry, P.D Hinduja Hospital & Medical Research Centre, Mumbai, India.
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He W, Lu Y, Shi R, An Q, Zhao J, Gao X, Zhang L, Ma D. Application of omics in Sjögren's syndrome. Inflamm Res 2023; 72:2089-2109. [PMID: 37878024 DOI: 10.1007/s00011-023-01797-x] [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: 08/07/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 10/26/2023] Open
Abstract
OBJECTIVE The pathogenesis, diagnosis, and treatment of Sjögren's syndrome (SS) face many challenges, and there is an urgent need to develop new technologies to improve our understanding of SS. METHODS By searching the literature published domestically and internationally in the past 20 years, this artical reviewed the research of various omics techniques in SS. RESULTS Omics technology provided valuable insights into the pathogenesis, early diagnosis, condition and efficacy evaluation of SS. It is helpful to reveal the pathogenesis of the disease and explore new treatment schemes, which will open a new era for the study of SS. CONCLUSION At present, omics research has made some gratifying achievements, but there are still many uncertainties. Therefore, in the future, we should improve research techniques, standardize the collection of samples, and adopt a combination of multi-omics techniques to jointly study the pathogenesis of SS and provide new schemes for its treatment.
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Affiliation(s)
- Wenqin He
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Taiyuan, China
- Shanxi Province Clinical Theranostics Technology Innovation Center for Immunologic and Rheumatic Diseases, Taiyuan, China
| | - Yangyang Lu
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Taiyuan, China
- Shanxi Province Clinical Theranostics Technology Innovation Center for Immunologic and Rheumatic Diseases, Taiyuan, China
| | - Rongjing Shi
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Taiyuan, China
- Shanxi Province Clinical Theranostics Technology Innovation Center for Immunologic and Rheumatic Diseases, Taiyuan, China
| | - Qi An
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Taiyuan, China
- Shanxi Province Clinical Theranostics Technology Innovation Center for Immunologic and Rheumatic Diseases, Taiyuan, China
| | - Jingwen Zhao
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Taiyuan, China
- Shanxi Province Clinical Theranostics Technology Innovation Center for Immunologic and Rheumatic Diseases, Taiyuan, China
| | - Xinnan Gao
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Taiyuan, China
- Shanxi Province Clinical Theranostics Technology Innovation Center for Immunologic and Rheumatic Diseases, Taiyuan, China
| | - Liyun Zhang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Taiyuan, China
- Shanxi Province Clinical Theranostics Technology Innovation Center for Immunologic and Rheumatic Diseases, Taiyuan, China
| | - Dan Ma
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China.
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Taiyuan, China.
- Shanxi Province Clinical Theranostics Technology Innovation Center for Immunologic and Rheumatic Diseases, Taiyuan, China.
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China.
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Lu DQ, Yao XY, Ren YT, Zhang KY, Zhu XC, Hong T, Yu X, Xie ZM, Chen LY, Wang XC. Genome-wide DNA methylation sequencing reveals epigenetic features and potential biomarkers of Sjögren syndrome. Int J Rheum Dis 2023; 26:2223-2232. [PMID: 37740638 DOI: 10.1111/1756-185x.14918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/08/2023] [Accepted: 09/03/2023] [Indexed: 09/24/2023]
Abstract
AIM Sjögren syndrome (SS) is a slowly progressive, inflammatory, autoimmune disease. The aim of this study was to construct the DNA methylation profiles of whole blood of SS patients and healthy controls (HC), and to explore the role of differentially methylated genes in the pathogenesis of the disease. METHODS Whole-genome bisulfite sequencing was performed on three SS patients and four HC. The biological function of genes associated with differentially methylated regions (DMRs) was investigated using Gene Ontology functional analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis, using network-based key driver analysis (KDA) to find KDA genes. In clinical samples of SS patients and controls, the expression levels of KDA genes were validated by quantitative real-time polymerase chain reaction and immunohistochemical analysis. Moreover, the diagnostic value of KDA genes for SS was confirmed using receiver operating characteristic curves. RESULTS We identified 322 DMRs, annotated as 162 associated genes. Six genes were selected via the number of networks of KDA genes. Differential expression of genes such as human leukocyte antigen (HLA) class I, ADAR, and OAS2 was observed in patients' peripheral blood mononuclear cells and the minor salivary glands, which can be used as potential diagnostic biomarkers for SS. CONCLUSION Clinical sample validation suggested that HLA class I, ADAR, and OAS2 might play a role in the development of SS. Our study shows epigenetic regulatory mechanisms and potential disease markers associated with SS, which in turn will enable us to identify new therapeutic targets.
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Affiliation(s)
- Ding-Qi Lu
- Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xin-Yi Yao
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Ya-Ting Ren
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Kai-Yuan Zhang
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xin-Chao Zhu
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Tao Hong
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xue Yu
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Zhi-Min Xie
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Li-Ying Chen
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xin-Chang Wang
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
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Jia Y, Yao P, Li J, Wei X, Liu X, Wu H, Wang W, Feng C, Li C, Zhang Y, Cai Y, Zhang S, Ma X. Causal associations of Sjögren's syndrome with cancers: a two-sample Mendelian randomization study. Arthritis Res Ther 2023; 25:171. [PMID: 37715206 PMCID: PMC10503000 DOI: 10.1186/s13075-023-03157-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Several observational studies have explored the associations between Sjögren's syndrome (SS) and certain cancers. Nevertheless, the causal relationships remain unclear. Mendelian randomization (MR) method was used to investigate the causality between SS and different types of cancers. METHODS We conducted the two-sample Mendelian randomization with the public genome-wide association studies (GWASs) summary statistics in European population to evaluate the causality between SS and nine types of cancers. The sample size varies from 1080 to 372,373. The inverse variance weighted (IVW) method was used to estimate the causal effects. A Bonferroni-corrected threshold of P < 0.0031 was considered significant, and P value between 0.0031 and 0.05 was considered to be suggestive of an association. Sensitivity analysis was performed to validate the causality. Moreover, additional analysis was used to assess the associations between SS and well-accepted risk factors of cancers. RESULTS After correcting the heterogeneity and horizontal pleiotropy, the results indicated that patients with SS were significantly associated with an increased risk of lymphomas (odds ratio [OR] = 1.0010, 95% confidence interval [CI]: 1.0005-1.0015, P = 0.0002) and reduced risks of prostate cancer (OR = 0.9972, 95% CI: 0.9960-0.9985, P = 2.45 × 10-5) and endometrial cancer (OR = 0.9414, 95% CI: 0.9158-0.9676, P = 1.65 × 10-5). Suggestive associations were found in liver and bile duct cancer (OR = 0.9999, 95% CI: 0.9997-1.0000, P = 0.0291) and cancer of urinary tract (OR = 0.9996, 95% CI: 0.9992-1.0000, P = 0.0281). No causal effect of SS on other cancer types was detected. Additional MR analysis indicated that causal effects between SS and cancers were not mediated by the well-accepted risk factors of cancers. No evidence of the causal relationship was observed for cancers on SS. CONCLUSIONS SS had significant causal relationships with lymphomas, prostate cancer, and endometrial cancer, and suggestive evidence of association was found in liver and bile duct cancer and cancer of urinary tract, indicating that SS may play a vital role in the incidence of these malignancies.
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Affiliation(s)
- Yiwei Jia
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Peizhuo Yao
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Jia Li
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Xinyu Wei
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Xuanyu Liu
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Huizi Wu
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Weiwei Wang
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Cong Feng
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Chaofan Li
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Yu Zhang
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Yifan Cai
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Shuqun Zhang
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China.
| | - Xingcong Ma
- Department of Oncology, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China.
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Natoli V, Charras A, Hofmann SR, Northey S, Russ S, Schulze F, McCann L, Abraham S, Hedrich CM. DNA methylation patterns in CD4 + T-cells separate psoriasis patients from healthy controls, and skin psoriasis from psoriatic arthritis. Front Immunol 2023; 14:1245876. [PMID: 37662940 PMCID: PMC10472451 DOI: 10.3389/fimmu.2023.1245876] [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: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 09/05/2023] Open
Abstract
Background Psoriasis is an autoimmune/inflammatory disorder primarily affecting the skin. Chronic joint inflammation triggers the diagnosis of psoriatic arthritis (PsA) in approximately one-third of psoriasis patients. Although joint disease typically follows the onset of skin psoriasis, in around 15% of cases it is the initial presentation, which can result in diagnostic delays. The pathophysiological mechanisms underlying psoriasis and PsA are not yet fully understood, but there is evidence pointing towards epigenetic dysregulation involving CD4+ and CD8+ T-cells. Objectives The aim of this study was to investigate disease-associated DNA methylation patterns in CD4+ T-cells from psoriasis and PsA patients that may represent potential diagnostic and/or prognostic biomarkers. Methods PBMCs were collected from 12 patients with chronic plaque psoriasis and 8 PsA patients, and 8 healthy controls. CD4+ T-cells were separated through FACS sorting, and DNA methylation profiling was performed (Illumina EPIC850K arrays). Bioinformatic analyses, including gene ontology (GO) and KEGG pathway analysis, were performed using R. To identify genes under the control of interferon (IFN), the Interferome database was consulted, and DNA Methylation Scores were calculated. Results Numbers and proportions of CD4+ T-cell subsets (naïve, central memory, effector memory, CD45RA re-expressing effector memory cells) did not vary between controls, skin psoriasis and PsA patients. 883 differentially methylated positions (DMPs) affecting 548 genes were identified between controls and "all" psoriasis patients. Principal component and partial least-squares discriminant analysis separated controls from skin psoriasis and PsA patients. GO analysis considering promoter DMPs delivered hypermethylation of genes involved in "regulation of wound healing, spreading of epidermal cells", "negative regulation of cell-substrate junction organization" and "negative regulation of focal adhesion assembly". Comparing controls and "all" psoriasis, a majority of DMPs mapped to IFN-related genes (69.2%). Notably, DNA methylation profiles also distinguished skin psoriasis from PsA patients (2,949 DMPs/1,084 genes) through genes affecting "cAMP-dependent protein kinase inhibitor activity" and "cAMP-dependent protein kinase regulator activity". Treatment with cytokine inhibitors (IL-17/TNF) corrected DNA methylation patterns of IL-17/TNF-associated genes, and methylation scores correlated with skin disease activity scores (PASI). Conclusion DNA methylation profiles in CD4+ T-cells discriminate between skin psoriasis and PsA. DNA methylation signatures may be applied for quantification of disease activity and patient stratification towards individualized treatment.
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Affiliation(s)
- Valentina Natoli
- Department of Women’s & Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- Università degli Studi di Genova, Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-infantili (DINOGMI), Genoa, Italy
| | - Amandine Charras
- Department of Women’s & Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Sigrun R. Hofmann
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Sarah Northey
- Department of Women’s & Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Susanne Russ
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Felix Schulze
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Liza McCann
- Department of Paediatric Rheumatology, Alder Hey Children’s NHS Foundation Trust Hospital, Liverpool, United Kingdom
| | - Susanne Abraham
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Christian M. Hedrich
- Department of Women’s & Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Paediatric Rheumatology, Alder Hey Children’s NHS Foundation Trust Hospital, Liverpool, United Kingdom
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Thorlacius GE, Björk A, Wahren-Herlenius M. Genetics and epigenetics of primary Sjögren syndrome: implications for future therapies. Nat Rev Rheumatol 2023; 19:288-306. [PMID: 36914790 PMCID: PMC10010657 DOI: 10.1038/s41584-023-00932-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2023] [Indexed: 03/14/2023]
Abstract
In primary Sjögren syndrome (pSS), chronic inflammation of exocrine glands results in tissue destruction and sicca symptoms, primarily of the mouth and eyes. Fatigue, arthralgia and myalgia are also common symptoms, whereas extraglandular manifestations that involve the respiratory, nervous and vascular systems occur in a subset of patients. The disease predominantly affects women, with an estimated female to male ratio of 14 to 1. The aetiology of pSS, however, remains incompletely understood, and effective treatment is lacking. Large-scale genetic and epigenetic investigations have revealed associations between pSS and genes in both innate and adaptive immune pathways. The genetic variants mediate context-dependent effects, and both sex and environmental factors can influence the outcome. As such, genetic and epigenetic studies can provide insight into the dysregulated molecular mechanisms, which in turn might reveal new therapeutic possibilities. This Review discusses the genetic and epigenetic features that have been robustly connected with pSS, putting them into the context of cellular function, carrier sex and environmental challenges. In all, the observations point to several novel opportunities for early detection, treatment development and the pathway towards personalized medicine.
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Affiliation(s)
- Gudny Ella Thorlacius
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Albin Björk
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Rheumatology, Academic Specialist Center, Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.
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Chi C, Solomon O, Shiboski C, Taylor KE, Quach H, Quach D, Barcellos LF, Criswell LA. Identification of Sjögren's syndrome patient subgroups by clustering of labial salivary gland DNA methylation profiles. PLoS One 2023; 18:e0281891. [PMID: 36862625 PMCID: PMC9980741 DOI: 10.1371/journal.pone.0281891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
Heterogeneity in Sjögren's syndrome (SS), increasingly called Sjögren's disease, suggests the presence of disease subtypes, which poses a major challenge for the diagnosis, management, and treatment of this autoimmune disorder. Previous work distinguished patient subgroups based on clinical symptoms, but it is not clear to what extent symptoms reflect underlying pathobiology. The purpose of this study was to discover clinical meaningful subtypes of SS based on genome-wide DNA methylation data. We performed a cluster analysis of genome-wide DNA methylation data from labial salivary gland (LSG) tissue collected from 64 SS cases and 67 non-cases. Specifically, hierarchical clustering was performed on low dimensional embeddings of DNA methylation data extracted from a variational autoencoder to uncover unknown heterogeneity. Clustering revealed clinically severe and mild subgroups of SS. Differential methylation analysis revealed that hypomethylation at the MHC and hypermethylation at other genome regions characterize the epigenetic differences between these SS subgroups. Epigenetic profiling of LSGs in SS yields new insights into mechanisms underlying disease heterogeneity. The methylation patterns at differentially methylated CpGs are different in SS subgroups and support the role of epigenetic contributions to the heterogeneity in SS. Biomarker data derived from epigenetic profiling could be explored in future iterations of the classification criteria for defining SS subgroups.
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Affiliation(s)
- Calvin Chi
- Division of Computing, Center for Computational Biology, Data Science and Society, University of California Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Olivia Solomon
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Caroline Shiboski
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, United States of America
| | - Kimberly E. Taylor
- Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California, United States of America
| | - Hong Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Diana Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Lisa F. Barcellos
- Division of Computing, Center for Computational Biology, Data Science and Society, University of California Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Lindsey A. Criswell
- Genomics of Autoimmune Rheumatic Disease Section, National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland, United States of America
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Differential CpG DNA methylation of peripheral B cells, CD4 + T cells, and salivary gland tissues in IgG4-related disease. Arthritis Res Ther 2023; 25:4. [PMID: 36609529 PMCID: PMC9824958 DOI: 10.1186/s13075-022-02978-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVES Immunoglobulin-G4-related disease (IgG4-RD) is a distinct systemic autoimmune-mediated disease manifesting as chronic inflammation and tissue fibrosis. Since the role of DNA methylation in the pathogenesis of IgG4-RD is still unclear, we conduct this study to investigate epigenetic modifications in IgG4-RD. METHODS A genome-wide DNA methylation study was conducted with B cells, CD4+ T cells, and salivary gland tissues from IgG4-RD patients and matched controls by using the Illumina HumanMethylation 850K BeadChip. We further performed pyrosequencing and immunohistochemistry assays to validate the methylation status of some targets of interest. RESULTS We identified differentially methylated CpG sites including 44 hypomethylated and 166 hypermethylated differentially methylated probes (DMPs) in B cells and 260 hypomethylated and 112 hypermethylated DMPs in CD4+ T cells from 10 IgG4-RD patients compared with 10 healthy controls. We also identified 36945 hypomethylated and 78380 hypermethylated DMPs in salivary gland tissues of 4 IgG4-RD patients compared with 4 controls. DPM2 (cg21181453), IQCK (cg10266221), and ABCC13 (cg05699681, cg04985582) were hypermethylated and MBP (cg18455083) was hypomethylated in B cells, CD4+ T cells, and salivary gland tissues of IgG4-RD patients. We also observed the hypomethylated HLA-DQB2 in CD4+ T cells from IgG4-RD patients. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DMPs in salivary gland tissues of IgG4-RD patients revealed enrichment of pathways involved in the regulation of immune cell responses and fibrosis. CONCLUSION This is the first DNA methylation study in peripheral B cells, CD4+ T cells, and salivary gland tissues from IgG4-RD patients. Our findings highlighted the role of epigenetic modification of DNA methylation and identified several genes and pathways possibly involved in IgG4-RD pathogenesis.
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Nocturne G, Mariette X. Interferon signature in systemic autoimmune diseases: what does it mean? RMD Open 2022; 8:rmdopen-2022-002687. [PMID: 36597991 PMCID: PMC9723951 DOI: 10.1136/rmdopen-2022-002687] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Gaetane Nocturne
- Department of Rheumatology, Université Paris-Saclay, INSERM UMR1184 : Center for immunology of viral infections and autoimmune diseases, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Xavier Mariette
- Department of Rheumatology, Université Paris-Saclay, INSERM UMR1184 : Center for immunology of viral infections and autoimmune diseases, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Le Kremlin-Bicêtre, France
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15
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Epigenetic regulation of B cells and its role in autoimmune pathogenesis. Cell Mol Immunol 2022; 19:1215-1234. [PMID: 36220996 PMCID: PMC9622816 DOI: 10.1038/s41423-022-00933-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/19/2022] [Indexed: 11/05/2022] Open
Abstract
B cells play a pivotal role in the pathogenesis of autoimmune diseases. Although previous studies have shown many genetic polymorphisms associated with B-cell activation in patients with various autoimmune disorders, progress in epigenetic research has revealed new mechanisms leading to B-cell hyperactivation. Epigenetic mechanisms, including those involving histone modifications, DNA methylation, and noncoding RNAs, regulate B-cell responses, and their dysregulation can contribute to the pathogenesis of autoimmune diseases. Patients with autoimmune diseases show epigenetic alterations that lead to the initiation and perpetuation of autoimmune inflammation. Moreover, many clinical and animal model studies have shown the promising potential of epigenetic therapies for patients. In this review, we present an up-to-date overview of epigenetic mechanisms with a focus on their roles in regulating functional B-cell subsets. Furthermore, we discuss epigenetic dysregulation in B cells and highlight its contribution to the development of autoimmune diseases. Based on clinical and preclinical evidence, we discuss novel epigenetic biomarkers and therapies for patients with autoimmune disorders.
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Li P, Han M, Zhao X, Ren G, Mei S, Zhong C. Abnormal Epigenetic Regulations in the Immunocytes of Sjögren's Syndrome Patients and Therapeutic Potentials. Cells 2022; 11:1767. [PMID: 35681462 PMCID: PMC9179300 DOI: 10.3390/cells11111767] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023] Open
Abstract
Sjögren's syndrome (SjS), characterized by keratoconjunctivitis sicca and dry mouth, is a common autoimmune disease, especially in middle-aged women. The immunopathogenesis of SjS is caused by the sequential infiltration of T and B cells into exocrine glands, including salivary and lacrimal glands. Effector cytokines produced by these immunocytes, such as interferons (IFNs), IL-17, IL-22, IL-21, IL-4, TNF-α, BAFF and APRIL, play critical roles in promoting autoimmune responses and inducing tissue damages. Epigenetic regulations, including DNA methylation, histone modification and non-coding RNAs, have recently been comprehensively studied during the activation of various immunocytes. The deficiency of key epigenetic enzymes usually leads to aberrant immune activation. Epigenetic modifications in T and B cells are usually found to be altered during the immunopathogenesis of SjS, and they are closely correlated with autoimmune responses. In particular, the important role of methylation in activating IFN pathways during SjS progression has been revealed. Thus, according to the involvement of epigenetic regulations in SjS, target therapies to reverse the altered epigenetic modifications in auto-responsive T and B cells are worthy of being considered as a potential therapeutic strategy for SjS.
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Affiliation(s)
- Peng Li
- Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China; (P.L.); (M.H.); (X.Z.); (G.R.); (S.M.)
| | - Mengwei Han
- Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China; (P.L.); (M.H.); (X.Z.); (G.R.); (S.M.)
| | - Xingyu Zhao
- Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China; (P.L.); (M.H.); (X.Z.); (G.R.); (S.M.)
| | - Guanqun Ren
- Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China; (P.L.); (M.H.); (X.Z.); (G.R.); (S.M.)
| | - Si Mei
- Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China; (P.L.); (M.H.); (X.Z.); (G.R.); (S.M.)
| | - Chao Zhong
- Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, China; (P.L.); (M.H.); (X.Z.); (G.R.); (S.M.)
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing 100191, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing 100191, China
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Exploration of the pathogenesis of Sjögren's syndrome via DNA methylation and transcriptome analyses. Clin Rheumatol 2022; 41:2765-2777. [PMID: 35562622 DOI: 10.1007/s10067-022-06200-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/07/2022] [Accepted: 05/03/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Sjögren's syndrome (SS), a systemic autoimmune disorder, is characterized by dry mouth and eyes. However, SS pathogenesis is poorly understood. We performed bioinformatics analysis to investigate the potential targets and molecular pathogenesis of SS. METHODS Gene expression profiles (GSE157159) and methylation data (GSE110007) associated with SS patients were obtained from the Gene Expression Omnibus (GEO) database. Differentially methylated positions (DMPs) and differentially expressed genes (DEGs) were identified by the R package limma. The potential biological functions of DEGs were determined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Key DMPs were selected by overlap and the shrunken centroid algorithm, and corresponding genes were identified as hub genes, with their diagnostic value assessed by receiver operating characteristic (ROC) curves. The potential molecular mechanisms of hub genes were analyzed by protein-protein interaction (PPI) networks and single-gene gene set enrichment analysis (GSEA). Peripheral blood mononuclear cells (PBMCs) were collected from control and SS patients at The Affiliated Hospital of Southwest Medical University and Dazhou Central Hospital. The mRNA levels of hub genes were verified by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS We identified 788 DMPs and 2457 DEGs between the two groups. Functional enrichment analysis suggested that the DEGs were significantly enriched in T cell activation, leukocyte cell-cell adhesion, and cytokine-cytokine receptor interaction. TSS200, TSS1500, and 1stExon were identified as highly enriched areas of differentially methylated promoter CpG islands (DMCIs). In total, 61 differentially methylated genes (DMGs) were identified by the overlap of 2457 DEGs and 507 genes related to DMPs (DMPGs), of which 21 genes located near TSS200, TSS1500, and 1stExon were selected. Then, three key DMPs and the corresponding hub genes (RUNX3, HLA-DPA1, and CD6) were screened by the shrunken centroid algorithm and calculated to have areas under the ROC curve of 1.000, 0.931, and 0.986, respectively, indicating good diagnostic value. The GSEA results suggested that all three hub genes were highly associated with the immune response. Finally, positive mRNA expression of the three hub genes in clinical SS samples was verified by qRT-PCR, consistent with the GSE157159 data. CONCLUSIONS The identification of three hub genes provides novel insight into molecular mechanisms and therapeutic targets for SS. Key Points • Hub genes were screened by DNA methylation and transcriptome analyses. • The relative expression of hub genes in peripheral blood samples was verified by qRT-PCR. • HLA-DPA1 was correlated with the pathogenic mechanism of SS.
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Guimarães JR, Coêlho MDC, de Oliveira NFP. Contribution of DNA methylation to the pathogenesis of Sjögren's syndrome: A review. Autoimmunity 2022; 55:215-222. [DOI: 10.1080/08916934.2022.2062593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Juliana Ramalho Guimarães
- Graduate Program in Dentistry, Centre of Health Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
| | - Marina de Castro Coêlho
- Graduate Program in Dentistry, Centre of Health Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
| | - Naila Francis Paulo de Oliveira
- Graduate Program in Dentistry, Centre of Health Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
- Molecular Biology Department, Centre of Exact and Natural Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
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19
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Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Teruel M, Barturen G, Martínez-Bueno M, Castellini-Pérez O, Barroso-Gil M, Povedano E, Kerick M, Català-Moll F, Makowska Z, Buttgereit A, Pers JO, Marañón C, Ballestar E, Martin J, Carnero-Montoro E, Alarcón-Riquelme ME. Integrative epigenomics in Sjögren´s syndrome reveals novel pathways and a strong interaction between the HLA, autoantibodies and the interferon signature. Sci Rep 2021; 11:23292. [PMID: 34857786 PMCID: PMC8640069 DOI: 10.1038/s41598-021-01324-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022] Open
Abstract
Primary Sjögren's syndrome (SS) is a systemic autoimmune disease characterized by lymphocytic infiltration and damage of exocrine salivary and lacrimal glands. The etiology of SS is complex with environmental triggers and genetic factors involved. By conducting an integrated multi-omics study, we confirmed a vast coordinated hypomethylation and overexpression effects in IFN-related genes, what is known as the IFN signature. Stratified and conditional analyses suggest a strong interaction between SS-associated HLA genetic variation and the presence of Anti-Ro/SSA autoantibodies in driving the IFN epigenetic signature and determining SS. We report a novel epigenetic signature characterized by increased DNA methylation levels in a large number of genes enriched in pathways such as collagen metabolism and extracellular matrix organization. We identified potential new genetic variants associated with SS that might mediate their risk by altering DNA methylation or gene expression patterns, as well as disease-interacting genetic variants that exhibit regulatory function only in the SS population. Our study sheds new light on the interaction between genetics, autoantibody profiles, DNA methylation and gene expression in SS, and contributes to elucidate the genetic architecture of gene regulation in an autoimmune population.
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Affiliation(s)
- María Teruel
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Guillermo Barturen
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Manuel Martínez-Bueno
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Olivia Castellini-Pérez
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Miguel Barroso-Gil
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Elena Povedano
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Martin Kerick
- IPBLN-CSIC, Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, 18016, Granada, Spain
| | - Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
- IDIBELL, Bellvitge Biomedical Research Institute 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Zuzanna Makowska
- Pharmaceuticals Division, Bayer Pharma Aktiengesellschaft, Berlin, Germany
| | - Anne Buttgereit
- Pharmaceuticals Division, Bayer Pharma Aktiengesellschaft, Berlin, Germany
| | | | - Concepción Marañón
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
- IDIBELL, Bellvitge Biomedical Research Institute 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier Martin
- IPBLN-CSIC, Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, 18016, Granada, Spain
| | - Elena Carnero-Montoro
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain.
| | - Marta E Alarcón-Riquelme
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain.
- Institute for Environmental Medicine, Karolinska Institutet, 171 67, Solna, Sweden.
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Karagianni P, Kapsogeorgou EK, Tzioufas AG, Goules AV. DNA Methylation Studies in Saliva of Patients with Sjögren's Syndrome. Mediterr J Rheumatol 2021; 32:176-178. [PMID: 34447917 PMCID: PMC8369270 DOI: 10.31138/mjr.32.2.176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 12/20/2020] [Indexed: 11/28/2022] Open
Abstract
Sjögren’s syndrome (SS) is a relatively common systemic autoimmune disease of unknown aetiology, although genetic, hormonal, immunologic, and environmental factors are thought to be involved in disease pathogenesis. It is also termed “autoimmune epithelitis”, and afflicts mainly the epithelial structures of salivary and lachrymal glands, through periepithelial lymphocytic infiltration responsible for the occurrence of dryness symptoms. Sjögren’s syndrome (SS) is also characterised by B cell hyperactivity as reflected by the presence of hypergammaglobulinemia and the production of autoantibodies, which seems to be associated with the presence of ectopic germinal centres within the inflamed minor salivary glands. Chronic antigenic stimulation may lead to expansion of B cell autoreactive clones with rheumatoid factor activity, and additional molecular events mediate malignant transformation into non-Hodgkin’s lymphomas of B cell origin. Therefore, the interaction between the immune cells of the inflammatory infiltrate and the salivary epithelium seems to have an important contribution in disease process. Recent histopathologic and molecular studies have shown that DNA methylation levels of SS patients compared to healthy individuals differ in epithelial cells of salivary glands and peripheral blood mononuclear cells. In the present study, we intend to analyse the epigenetic modifications of DNA in the saliva of SS patients compared to healthy controls. More specifically, salivary DNA methylation levels of selected genetic loci previously found to differ in other tissues, will be compared between SS patients and healthy controls. The study includes saliva collection from SS patients and healthy individuals, extraction of genomic DNA and methylation assessment. The epigenetic profile of each genetic locus will be correlated with SS patients’ clinical characteristics and the possibility of genetic loci with differential differences in methylation to be used as potential diagnostic biomarkers will be explored. The current study is anticipated to reveal potential biomarkers for diagnostic and therapeutic purposes, offering the advantage to utilise the easily collected and handled saliva as the main biologic material.
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Affiliation(s)
- Panagiota Karagianni
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Efstathia K Kapsogeorgou
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Athanasios G Tzioufas
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Andreas V Goules
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, Greece
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Yang M, Yi P, Jiang J, Zhao M, Wu H, Lu Q. Dysregulated translational factors and epigenetic regulations orchestrate in B cells contributing to autoimmune diseases. Int Rev Immunol 2021; 42:1-25. [PMID: 34445929 DOI: 10.1080/08830185.2021.1964498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
B cells play a crucial role in antigen presentation, antibody production and pro-/anti-inflammatory cytokine secretion in adaptive immunity. Several translational factors including transcription factors and cytokines participate in the regulation of B cell development, with the cooperation of epigenetic regulations. Autoimmune diseases are generally characterized with autoreactive B cells and high-level pathogenic autoantibodies. The success of B cell depletion therapy in mouse model and clinical trials has proven the role of B cells in pathogenesis of autoimmune diseases. The failure of B cell tolerance in immune checkpoints results in accumulated autoreactive naïve B (BN) cells with aberrant B cell receptor signaling and dysregulated B cell response, contributing to self-antibody-mediated autoimmune reaction. Dysregulation of translational factors and epigenetic alterations in B cells has been demonstrated to correlate with aberrant B cell compartment in autoimmune diseases, such as systemic lupus erythematosus, rheumatoid arthritis, primary Sjögren's syndrome, multiple sclerosis, diabetes mellitus and pemphigus. This review is intended to summarize the interaction of translational factors and epigenetic regulations that are involved with development and differentiation of B cells, and the mechanism of dysregulation in the pathogenesis of autoimmune diseases.
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Affiliation(s)
- Ming Yang
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Ping Yi
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Jiao Jiang
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Ming Zhao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China.,Department of Dermatology, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
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23
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Imgenberg-Kreuz J, Rasmussen A, Sivils K, Nordmark G. Genetics and epigenetics in primary Sjögren's syndrome. Rheumatology (Oxford) 2021; 60:2085-2098. [PMID: 30770922 PMCID: PMC8121440 DOI: 10.1093/rheumatology/key330] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/16/2018] [Indexed: 02/07/2023] Open
Abstract
Primary Sjögren’s syndrome (pSS) is considered to be a multifactorial disease, where underlying genetic predisposition, epigenetic mechanisms and environmental factors contribute to disease development. In the last 5 years, the first genome-wide association studies in pSS have been completed. The strongest signal of association lies within the HLA genes, whereas the non-HLA genes IRF5 and STAT4 show consistent associations in multiple ethnicities but with a smaller effect size. The majority of the genetic risk variants are found at intergenic regions and their functional impact has in most cases not been elucidated. Epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs play a role in the pathogenesis of pSS by their modulating effects on gene expression and may constitute a dynamic link between the genome and phenotypic manifestations. This article reviews the hitherto published genetic studies and our current understanding of epigenetic mechanisms in pSS.
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Affiliation(s)
- Juliana Imgenberg-Kreuz
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden2Arthritis and Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Astrid Rasmussen
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden2Arthritis and Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kathy Sivils
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden2Arthritis and Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Gunnel Nordmark
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden2Arthritis and Clinical Immunology Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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Chi C, Taylor KE, Quach H, Quach D, Criswell LA, Barcellos LF. Hypomethylation mediates genetic association with the major histocompatibility complex genes in Sjögren's syndrome. PLoS One 2021; 16:e0248429. [PMID: 33886574 PMCID: PMC8062105 DOI: 10.1371/journal.pone.0248429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/25/2021] [Indexed: 12/22/2022] Open
Abstract
Differential methylation of immune genes has been a consistent theme observed in Sjögren's syndrome (SS) in CD4+ T cells, CD19+ B cells, whole blood, and labial salivary glands (LSGs). Multiple studies have found associations supporting genetic control of DNA methylation in SS, which in the absence of reverse causation, has positive implications for the potential of epigenetic therapy. However, a formal study of the causal relationship between genetic variation, DNA methylation, and disease status is lacking. We performed a causal mediation analysis of DNA methylation as a mediator of nearby genetic association with SS using LSGs and genotype data collected from 131 female members of the Sjögren's International Collaborative Clinical Alliance registry, comprising of 64 SS cases and 67 non-cases. Bumphunter was used to first identify differentially-methylated regions (DMRs), then the causal inference test (CIT) was applied to identify DMRs mediating the association of nearby methylation quantitative trait loci (MeQTL) with SS. Bumphunter discovered 215 DMRs, with the majority located in the major histocompatibility complex (MHC) on chromosome 6p21.3. Consistent with previous findings, regions hypomethylated in SS cases were enriched for gene sets associated with immune processes. Using the CIT, we observed a total of 19 DMR-MeQTL pairs that exhibited strong evidence for a causal mediation relationship. Close to half of these DMRs reside in the MHC and their corresponding meQTLs are in the region spanning the HLA-DQA1, HLA-DQB1, and HLA-DQA2 loci. The risk of SS conferred by these corresponding MeQTLs in the MHC was further substantiated by previous genome-wide association study results, with modest evidence for independent effects. By validating the presence of causal mediation, our findings suggest both genetic and epigenetic factors contribute to disease susceptibility, and inform the development of targeted epigenetic modification as a therapeutic approach for SS.
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Affiliation(s)
- Calvin Chi
- Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Kimberly E. Taylor
- Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Hong Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Diana Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Lindsey A. Criswell
- Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Lisa F. Barcellos
- Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
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25
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Genome-wide DNA methylation patterns in monocytes derived from patients with primary Sjogren syndrome. Chin Med J (Engl) 2021; 134:1310-1316. [PMID: 33769968 PMCID: PMC8183694 DOI: 10.1097/cm9.0000000000001451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background: Epigenetics, especially DNA methylation, plays an important role in the pathogenesis of primary Sjogren syndrome (pSS). Our study aimed to reveal the role of DNA methylation in peripheral monocytes of pSS patients. Methods: A total of 11 pSS patients and five age-matched healthy controls (HCs) were included in this study. Monocytes were isolated from peripheral blood mononuclear cells using magnetic microbeads. DNA methylation profiles were generated using Human Methylation 850K BeadChips. Results: In monocytes from pSS patients, we identified 2819 differentially methylated positions (DMPs), comprising 1977 hypomethylated- and 842 hypermethylated-DMPs, corresponding to 1313 unique genes when compared with HCs. IFI44L, MX1, PAARP9, and IFITM1, which influence the interferon (IFN) signaling pathway, were among the genes hypomethylated in pSS. Functional analysis of genes with a minimum of two DMPs showed involvement in antigen binding, transcriptional regulation, cell adhesion, IFN-γ pathway, type I IFN pathway, antigen presentation, Epstein-Barr virus infection, human T-lymphotropic virus type 1 virus infection, and metabolic disease-related pathways. In addition, patients with higher serum IgG levels exhibited enrichment in Notch signaling and metabolic-related pathways. Upon comparing monocytes with salivary gland epithelial cells, an important overlap was observed in the cell cycle, cell senescence, and interleukin-17 signaling pathways. The differentially methylated genes were more enriched in the ribosome- and AMP-activated protein kinase signaling pathway in anti-Ro/SSA and anti-La/SSB autoantibodies double-positive patients. Conclusion: Genome-wide DNA methylation profiling revealed significant differences in DNA methylation in monocytes isolated from patients with pSS.
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26
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Jochems SP, Jacquelin B, Tchitchek N, Busato F, Pichon F, Huot N, Liu Y, Ploquin MJ, Roché E, Cheynier R, Dereuddre-Bosquet N, Stahl-Henning C, Le Grand R, Tost J, Müller-Trutwin M. DNA methylation changes in metabolic and immune-regulatory pathways in blood and lymph node CD4 + T cells in response to SIV infections. Clin Epigenetics 2020; 12:188. [PMID: 33298174 PMCID: PMC7724887 DOI: 10.1186/s13148-020-00971-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
The molecular mechanisms underlying HIV-induced inflammation, which persists even during effective long-term treatment, remain incompletely defined. Here, we studied pathogenic and nonpathogenic simian immunodeficiency virus (SIV) infections in macaques and African green monkeys, respectively. We longitudinally analyzed genome-wide DNA methylation changes in CD4 + T cells from lymph node and blood, using arrays. DNA methylation changes after SIV infection were more pronounced in lymph nodes than blood and already detected in primary infection. Differentially methylated genes in pathogenic SIV infection were enriched for Th1-signaling (e.g., RUNX3, STAT4, NFKB1) and metabolic pathways (e.g., PRKCZ). In contrast, nonpathogenic SIVagm infection induced DNA methylation in genes coding for regulatory proteins such as LAG-3, arginase-2, interleukin-21 and interleukin-31. Between 15 and 18% of genes with DNA methylation changes were differentially expressed in CD4 + T cells in vivo. Selected identified sites were validated using bisulfite pyrosequencing in an independent cohort of uninfected, viremic and SIV controller macaques. Altered DNA methylation was confirmed in blood and lymph node CD4 + T cells in viremic macaques but was notably absent from SIV controller macaques. Our study identified key genes differentially methylated already in primary infection and in tissues that could contribute to the persisting metabolic disorders and inflammation in HIV-infected individuals despite effective treatment.
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Affiliation(s)
- Simon P Jochems
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
- Sorbonne Paris Cité, Université Paris Diderot, Paris, France
- Leiden University Medical Center, Leiden, The Netherlands
| | - Beatrice Jacquelin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Nicolas Tchitchek
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Fabien Pichon
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Nicolas Huot
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Yi Liu
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Mickaël J Ploquin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France
| | - Elodie Roché
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Rémi Cheynier
- UMR8104, CNRS, U1016, INSERM, Institut Cochin, Université de Paris, 75014, Paris, France
| | - Nathalie Dereuddre-Bosquet
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | | | - Roger Le Grand
- IDMIT Department/IBFJ, Immunology of Viral Infections and Autoimmune Diseases (IMVA), INSERM U1184, CEA, Université Paris Sud, Fontenay-aux-Roses, France
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Michaela Müller-Trutwin
- HIV Inflammation and Persistence Unit, Institut Pasteur, 28 Rue Didot, 75015, Paris, France.
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27
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Zouali M. DNA methylation signatures of autoimmune diseases in human B lymphocytes. Clin Immunol 2020; 222:108622. [PMID: 33188932 DOI: 10.1016/j.clim.2020.108622] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/28/2020] [Accepted: 11/07/2020] [Indexed: 12/15/2022]
Abstract
B lymphocytes play key roles in adaptive and innate immunity. In autoimmune diseases, their participation in disease instigation and/or progression has been demonstrated in both experimental models and clinical trials. Recent epigenetic investigations of human B lymphocyte subsets revealed the importance of DNA methylation in exquisitely regulating the cellular activation and differentiation programs. This review discusses recent advances on the potential of DNA methylation to shape events that impart generation of plasma cells and memory B cells, providing novel insight into homeostatic regulation of the immune system. In parallel, epigenetic profiling of B cells from patients with systemic or organo-specific autoimmune diseases disclosed distinctive differential methylation regions that, in some cases, could stratify patients from controls. Development of tools for editing DNA methylation in the mammalian genome could be useful for future functional studies of epigenetic regulation by offering the possibility to edit locus-specific methylation, with potential translational applications.
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Affiliation(s)
- Moncef Zouali
- Graduate Institute of Biomedical Sciences, China Medical University, No. 91, Xueshi Road, North District, Taichung City, Taïwan 404, Taichung, Taiwan.
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28
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The multifaceted functional role of DNA methylation in immune-mediated rheumatic diseases. Clin Rheumatol 2020; 40:459-476. [PMID: 32613397 DOI: 10.1007/s10067-020-05255-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
Genomic predisposition cannot explain the onset of complex diseases, as well illustrated by the largely incomplete concordance among monozygotic twins. Epigenetic mechanisms, including DNA methylation, chromatin remodelling and non-coding RNA, are considered to be the link between environmental stimuli and disease onset on a permissive genetic background in autoimmune and chronic inflammatory diseases. The paradigmatic cases of rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), systemic sclerosis (SSc), Sjogren's syndrome (SjS) and type-1 diabetes (T1D) share the loss of immunological tolerance to self-antigen influenced by several factors, with a largely incomplete role of individual genomic susceptibility. The most widely investigated epigenetic mechanism is DNA methylation which is associated with gene silencing and is due to the binding of methyl-CpG binding domain (MBD)-containing proteins, such as MECP2, to 5-methylcytosine (5mC). Indeed, a causal relationship occurs between DNA methylation and transcription factors occupancy and recruitment at specific genomic locus. In most cases, the results obtained in different studies are controversial in terms of DNA methylation comparison while fascinating evidence comes from the comparison of the epigenome in clinically discordant monozygotic twins. In this manuscript, we will review the mechanisms of epigenetics and DNA methylation changes in specific immune-mediated rheumatic diseases to highlight remaining unmet needs and to identify possible shared mechanisms beyond different tissue involvements with common therapeutic opportunities. Key Points • DNA methylation has a crucial role in regulating and tuning the immune system. • Evidences suggest that dysregulation of DNA methylation is pivotal in the context of immune-mediated rheumatic diseases. • DNA methylation dysregulation in FOXP3 and interferons-related genes is shared within several autoimmune diseases. • DNA methylation is an attractive marker for diagnosis and therapy.
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Abstract
Primary Sjögren's syndrome (SjS) is a chronic and systemic autoimmune epithelitis with predominant female incidence, which is characterized by exocrine gland dysfunction. Incompletely understood, the etiology of SjS is multi-factorial and evidence is growing to consider that epigenetic factors are playing a crucial role in its development. Independent from DNA sequence mutations, epigenetics is described as inheritable and reversible processes that modify gene expression. Epigenetic modifications reported in minor salivary gland and lymphocytes from SjS patients are related to (i) an abnormal DNA methylation process inducing in turn defective control of normally repressed genes involving such matters as autoantigens, retrotransposons, and the X chromosome in women; (ii) altered nucleosome positioning associated with autoantibody production; and (iii) altered control of microRNA. Results from epigenome-wide association studies have further revealed the importance of the interferon pathway in disease progression, the calcium signaling pathway for controlling fluid secretions, and a cell-specific cross talk with risk factors associated with SjS. Importantly, epigenetic modifications are reversible thus opening opportunities for therapeutic procedures in this currently incurable disease.
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30
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Arvaniti P, Le Dantec C, Charras A, Arleevskaya MA, Hedrich CM, Zachou K, Dalekos GN, Renaudineau Y. Linking genetic variation with epigenetic profiles in Sjögren's syndrome. Clin Immunol 2019; 210:108314. [PMID: 31765834 DOI: 10.1016/j.clim.2019.108314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/18/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022]
Abstract
DNA methylation represents an important regulatory event governing gene expression that is dysregulated in Sjögren's syndrome (SjS) and a number of autoimmune/inflammatory diseases. As disease-associated single-nucleotide polymorphisms (SNPs) have relevance in controlling DNA methylation, 94 non-HLA SjS-SNPs were investigated, among them 57 (60.6%) with widespread effects on 197 individual DNA methylation quantitative trait loci (meQTL) were selected. Typically, these SNPs are intronic, possess an active promoter histone mark, and control cis-meQTLs located around transcription start sites. Interplay is independent of the physical distance between SNPs and meQTLs. Using epigenome-wide association study datasets, SjS-meQTLs were characterized (41 genes and 13 DNA methylation CpG motifs) and for the most part map to a pro-inflammatory cytokine pathway, which is important for the control of DNA methylation in autoimmune diseases. In conclusion, exploring meQTLs represents a valuable tool to predict and investigate downstream effects of genetic factors in complex diseases such as SjS.
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Affiliation(s)
- Pinelopi Arvaniti
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France; Department of Medicine and Research Laboratory of Internal Medicine, University Hospital of Larissa, Larissa, Greece.
| | - Christelle Le Dantec
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, INSERM, CHU de Brest, Brest, France.
| | - Amandine Charras
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, INSERM, CHU de Brest, Brest, France; Department of Women's & Children's Health, Institute of Translational Medicine, University of Liverpool, UK & Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK.
| | | | - Christian M Hedrich
- Department of Women's & Children's Health, Institute of Translational Medicine, University of Liverpool, UK & Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK.
| | - Kalliopi Zachou
- Department of Medicine and Research Laboratory of Internal Medicine, University Hospital of Larissa, Larissa, Greece.
| | - George N Dalekos
- Department of Medicine and Research Laboratory of Internal Medicine, University Hospital of Larissa, Larissa, Greece.
| | - Yves Renaudineau
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France; UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, INSERM, CHU de Brest, Brest, France.
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31
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Harris VM, Koelsch KA, Kurien BT, Harley ITW, Wren JD, Harley JB, Scofield RH. Characterization of cxorf21 Provides Molecular Insight Into Female-Bias Immune Response in SLE Pathogenesis. Front Immunol 2019; 10:2160. [PMID: 31695690 PMCID: PMC6816314 DOI: 10.3389/fimmu.2019.02160] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/28/2019] [Indexed: 12/30/2022] Open
Abstract
Background: Ninety percent of systemic lupus erythematosus (SLE) patients are women. X chromosome-dosage increases susceptibility to SLE and primary Sjögren's syndrome (pSS). Chromosome X open reading frame 21 (CXorf21) escapes X-inactivation and is an SLE risk gene of previously unknown function. We undertook the present study to delineate the function of CXorf21 in the immune system as well as investigate a potential role in the sex bias of SLE and pSS. Methods: Western blot protein analysis, qPCR, BioPlex cytokine immunoassay, pHrodo™ assays, as well as in vitro CRISPR-Cas9 knockdown experiments were employed to delineate the role of CXorf21 in relevant immunocytes. Results: Expressed in monocytes and B cells, CXorf21 basal Mrna, and protein expression levels are elevated in female primary monocytes, B cells, and EBV-transformed B cells compared to male cells. We also found CXorf21 mRNA and protein expression is higher in both male and female cells from SLE patients compared to control subjects. TLR7 ligation increased CXorf21 protein expression and CXorf21 knockdown abrogated TLR7-driven increased IFNA1 mRNA expression, and reduced secretion of both TNF-alpha and IL-6 in healthy female monocytes. Similarly, we found increased pH in the lysosomes of CXorf21-deficient female monocytes. Conclusion: CXorf21 is more highly expressed in female compared to male cells and is involved in a sexually dimorphic response to TLR7 activation. In addition, CXorf21 expression regulates lysosomal pH in a sexually dimorphic manner. Thus, sexually dimorphic expression of CXorf21 skews cellular immune responses in manner consistent with expected properties of a mediator of the X chromosome dose risk in SLE and pSS.
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Affiliation(s)
- Valerie M Harris
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Departments of Pathology and Medicine, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Kristi A Koelsch
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Departments of Pathology and Medicine, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Biji T Kurien
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Isaac T W Harley
- Division of Rheumatology, School of Medicine, University of Colorado, Aurora, CO, United States.,Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,United States Department of Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - R Hal Scofield
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Departments of Pathology and Medicine, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Medical and Research Services, Oklahoma City Department of Veterans Affairs Health Care Center, Oklahoma City, OK, United States
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32
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Epigenetic Modifications in Generalized Autoimmune Epithelitis: Sjögren's Syndrome and Primary Biliary Cholangitis. EPIGENOMES 2019; 3:epigenomes3030015. [PMID: 34968227 PMCID: PMC8594719 DOI: 10.3390/epigenomes3030015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/25/2019] [Accepted: 08/02/2019] [Indexed: 01/10/2023] Open
Abstract
Sjögren's syndrome (SjS) and primary biliary cholangitis (PBC) can be classified as a model of generalized autoimmune epithelitis based on their frequent coexistence in clinical practice and the highly specific immune mediated injury of target epithelial cells. Both of these autoimmune diseases are characterized by female predominance, highly specific circulating autoantibodies, and immune-mediated destruction of the salivary and lachrymal glands and the biliary epithelial cells, respectively. Although the genetic predisposition has been well described for both diseases, genetic studies have failed to completely elucidate their pathogenesis. The recent integration of epigenetic data, analyzing the different cellular partners, opens new perspectives and allows for better understanding of these complex and still incurable diseases. Epigenetic studies on SjS have elucidated the role of DNA methylation alterations in disease pathogenesis, while epigenetic changes that influence expression of genes on the X chromosome have been implicated in the geo-variability and occurrence of PBC. The aim of this review is to describe the advances in epigenetics in the field of autoimmune epithelitis as well as to highlight how epigenetic changes could contribute to better understanding of disease pathogenesis and progression. These advances could yield insights on novel therapeutic interventions.
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Charras A, Arvaniti P, Le Dantec C, Arleevskaya MI, Zachou K, Dalekos GN, Bordon A, Renaudineau Y. JAK Inhibitors Suppress Innate Epigenetic Reprogramming: a Promise for Patients with Sjögren’s Syndrome. Clin Rev Allergy Immunol 2019; 58:182-193. [DOI: 10.1007/s12016-019-08743-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Mielle J, Tison A, Cornec D, Le Pottier L, Daien C, Pers JO. B cells in Sjögren's syndrome: from pathophysiology to therapeutic target. Rheumatology (Oxford) 2019; 60:2545-2560. [PMID: 30770916 DOI: 10.1093/rheumatology/key332] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
Biological abnormalities associated with B lymphocytes are a hallmark of patients with primary Sjögren's syndrome. Those patients present abnormal distribution of B lymphocytes in peripheral blood and B cells in exocrine glands. B cells produce auto-antibodies, cytokines and present antigens but can also suppressive functions. In this review, we will summarize current knowledge on B cells in primary Sjögren's syndrome patients, demonstrate their critical role in the immunopathology of the disease and describe the past and current trials targeting B cells.
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Affiliation(s)
- Julie Mielle
- Departement of Rheumatology, UMR5535, Inflammation and Cancer, University of Montpellier and Teaching hospital of Montpellier, Montpellier, France
| | - Alice Tison
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, Inserm, France.,Service de Rhumatologie, CHU de Brest, Brest, France
| | - Divi Cornec
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, Inserm, France.,Service de Rhumatologie, CHU de Brest, Brest, France
| | | | - Claire Daien
- Departement of Rheumatology, UMR5535, Inflammation and Cancer, University of Montpellier and Teaching hospital of Montpellier, Montpellier, France
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Morales-Nebreda L, McLafferty FS, Singer BD. DNA methylation as a transcriptional regulator of the immune system. Transl Res 2019; 204:1-18. [PMID: 30170004 PMCID: PMC6331288 DOI: 10.1016/j.trsl.2018.08.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 12/13/2022]
Abstract
DNA methylation is a dynamic epigenetic modification with a prominent role in determining mammalian cell development, lineage identity, and transcriptional regulation. Primarily linked to gene silencing, novel technologies have expanded the ability to measure DNA methylation on a genome-wide scale and uncover context-dependent regulatory roles. The immune system is a prototypic model for studying how DNA methylation patterning modulates cell type- and stimulus-specific transcriptional programs. Preservation of host defense and organ homeostasis depends on fine-tuned epigenetic mechanisms controlling myeloid and lymphoid cell differentiation and function, which shape innate and adaptive immune responses. Dysregulation of these processes can lead to human immune system pathology as seen in blood malignancies, infections, and autoimmune diseases. Identification of distinct epigenotypes linked to pathogenesis carries the potential to validate therapeutic targets in disease prevention and management.
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Affiliation(s)
- Luisa Morales-Nebreda
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Fred S McLafferty
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| | - Benjamin D Singer
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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Abstract
PURPOSE OF REVIEW The purpose of this review is to provide an insight into the pathophysiological mechanisms involved in the pathogenesis of primary Sjögren's Syndrome (pSS), highlighting recent findings with potential therapeutic repercussions. RECENT FINDINGS In the last 2 years, epigenetic analyses provided new insights into pSS pathogenesis. Characterization of DNA methylation patterns, chromatin structures and microRNA confirmed the importance of aberrant interferon and B-cell responses in the development of the disease. The formation of ectopic B-cell follicles with germinal centers is now a well recognized pathogenic mechanism within salivary glands of pSS. In the context of ectopic germinal centers reaction, T/B-cell interactions, that is regarding T-helper 17 and T-follicular helper cells, and their respective counterparts, T-regulatory and T-follicular regulatory cells, appear particularly relevant in pSS pathogenesis as their imbalance is associated with a dysregulation of B-cell dynamics and the production of autoantibodies. SUMMARY Advances in the understanding of pSS pathogenesis have paved the way for clinical trials with novel biologic agents targeting immune pathways regulating T/B-cell interactions and downstream B-cell activation. Reverse translation from these studies provides invaluable novel information of the mechanisms sustaining autoimmunity and chronic inflammation in pSS.
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Microbial Agents as Putative Inducers of B Cell Lymphoma in Sjögren's Syndrome through an Impaired Epigenetic Control: The State-of-The-Art. J Immunol Res 2019; 2019:8567364. [PMID: 30723750 PMCID: PMC6339763 DOI: 10.1155/2019/8567364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/28/2018] [Accepted: 12/09/2018] [Indexed: 12/16/2022] Open
Abstract
Introduction Understanding the mechanisms underlying the pathogenesis of Sjögren's syndrome (SS) is crucially important in order to be able to discriminate the steps that lead to B cell transformation and promptly identify the patients at risk of lymphomagenesis. The aim of this narrative review is to describe the evidence concerning the role that infections or dysbiosis plays in the epigenetic control of gene expression in SS patients and their possible involvement in B cell lymphomagenesis. Materials and Methods We searched the PubMed and Google Scholar databases and selected a total of 92 articles published during the last 25 years that describe experimental and clinical studies of the potential associations of microbiota and epigenetic aberrations with the risk of B cell lymphoma in SS patients. Results and Discussion The genetic background of SS patients is characterized by the hyperexpression of genes that are mainly involved in regulating the innate and adaptive immune responses and oncogenesis. In addition, salivary gland epithelial cells and lymphocytes both have an altered epigenetic background that enhances the activation of proinflammatory and survival pathways. Dysbiosis or chronic latent infections may tune the immune response and modify the cell epigenetic machinery in such a way as to give B lymphocytes an activated or transformed phenotype. It is also worth noting that transposable integrated retroelements may participate in the pathogenesis of SS and B cell lymphomagenesis by inducing DNA breaks, modulating cell gene expression, or generating aberrant transcripts that chronically stimulate the immune system. Conclusions Microorganisms may epigenetically modify target cells and induce their transcriptome to generate an activated or transformed phenotype. The occurrence of lymphoma in more than 15% of SS patients may be the end result of a combination of genetics, epigenetics, and dysbiosis or latent infections.
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Mondoulet L, Dioszeghy V, Busato F, Plaquet C, Dhelft V, Bethune K, Leclere L, Daviaud C, Ligouis M, Sampson H, Dupont C, Tost J. Gata3 hypermethylation and Foxp3 hypomethylation are associated with sustained protection and bystander effect following epicutaneous immunotherapy in peanut-sensitized mice. Allergy 2019; 74:152-164. [PMID: 29779209 PMCID: PMC6585762 DOI: 10.1111/all.13479] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2018] [Indexed: 12/17/2022]
Abstract
Background Epicutaneous immunotherapy (EPIT) is a promising method for treating food allergies. In animal models, EPIT induces sustained unresponsiveness and prevents further sensitization mediated by Tregs. Here, we elucidate the mechanisms underlying the therapeutic effect of EPIT, by characterizing the kinetics of DNA methylation changes in sorted cells from spleen and blood and by evaluating its persistence and bystander effect compared to oral immunotherapy (OIT). Methods BALB/c mice orally sensitized to peanut proteins (PPE) were treated by EPIT using a PPE‐patch or by PPE‐OIT. Another set of peanut‐sensitized mice treated by EPIT or OIT were sacrificed following a protocol of sensitization to OVA. DNA methylation was analyzed during immunotherapy and 8 weeks after the end of treatment in sorted cells from spleen and blood by pyrosequencing. Humoral and cellular responses were measured during and after immunotherapy. Results Analyses showed a significant hypermethylation of the Gata3 promoter detectable only in Th2 cells for EPIT from the 4th week and a significant hypomethylation of the Foxp3 promoter in CD62L+ Tregs, which was sustained only for EPIT. In addition, mice treated with EPIT were protected from subsequent sensitization and maintained the epigenetic signature characteristic for EPIT. Conclusions Our study demonstrates that EPIT leads to a unique and stable epigenetic signature in specific T‐cell compartments with downregulation of Th2 key regulators and upregulation of Treg transcription factors, likely explaining the sustainability of protection and the observed bystander effect.
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Affiliation(s)
| | | | - F. Busato
- Laboratory for Epigenetics & Environment Centre National de Recherche en Génomique Humaine CEA – Institut de Biologie François Jacob Evry France
| | | | | | - K. Bethune
- Laboratory for Epigenetics & Environment Centre National de Recherche en Génomique Humaine CEA – Institut de Biologie François Jacob Evry France
| | - L. Leclere
- Laboratory for Epigenetics & Environment Centre National de Recherche en Génomique Humaine CEA – Institut de Biologie François Jacob Evry France
| | - C. Daviaud
- Laboratory for Epigenetics & Environment Centre National de Recherche en Génomique Humaine CEA – Institut de Biologie François Jacob Evry France
| | | | - H. Sampson
- DBV Technologies Montrouge France
- Icahn School of Medicine at Mont Sinai New York NY USA
| | - C. Dupont
- Université Paris Descartes Hôpital Necker‐Enfants Malades Paris France
| | - J. Tost
- Laboratory for Epigenetics & Environment Centre National de Recherche en Génomique Humaine CEA – Institut de Biologie François Jacob Evry France
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Lagos C, Carvajal P, Castro I, Jara D, González S, Aguilera S, Barrera MJ, Quest AFG, Bahamondes V, Molina C, Urzúa U, Hermoso MA, Leyton C, González MJ. Association of high 5-hydroxymethylcytosine levels with Ten Eleven Translocation 2 overexpression and inflammation in Sjögren's syndrome patients. Clin Immunol 2018; 196:85-96. [PMID: 29894742 DOI: 10.1016/j.clim.2018.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/07/2018] [Accepted: 06/07/2018] [Indexed: 12/17/2022]
Abstract
Here, we determined the 5-hydroxymethylcytosine (5hmC), 5-methylcytosine (5mC), Ten Eleven Translocation (TETs), and DNA methyltransferases (DNMTs) levels in epithelial and inflammatory cells of labial salivary glands (LSG) from Sjögren's syndrome (SS)-patients and the effect of cytokines on HSG cells. LSG from SS-patients, controls and HSG cells incubated with cytokines were analysed. Levels of 5mC, 5hmC, DNMTs, TET2 and MeCP2 were assessed by immunofluorescence. In epithelial cells from SS-patients, an increase in TET2, 5hmC and a decrease in 5mC and MeCP2 were observed, additionally, high levels of 5mC and DNMTs and low levels of 5hmC were detected in inflammatory cells. Cytokines increased TET2 and 5hmC and decreased 5mC levels. Considering that the TET2 gene.promoter contains response elements for transcription factors activated by cytokines, together to in vitro results suggest that changes in DNA hydroxymethylation, resulting from altered levels of TET2 are likely to be relevant in the Sjögren's syndrome etiopathogenesis.
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Affiliation(s)
- Carolina Lagos
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Patricia Carvajal
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Isabel Castro
- Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Daniela Jara
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sergio González
- Escuela de Odontología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Sergio Aguilera
- Departamento de Reumatología, Clínica INDISA, Santiago, Chile
| | - María-José Barrera
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Andrew F G Quest
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Verónica Bahamondes
- Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Claudio Molina
- Escuela de Postgrado, Facultad de Odontología, Universidad San Sebastián, Santiago, Chile
| | - Ulises Urzúa
- Departamento de Oncología Básico-Clínico, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marcela A Hermoso
- Programa de Inmunología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Cecilia Leyton
- Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - María-Julieta González
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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Liu Z, Wang J, Lai J, Wang Q, Zhao J, Huang C, Yang X, Qian J, Wang H, Guo X, Liu Y, Tian Z, Li M, Zhao Y, Zeng X. Is it possible to apply the treat-to-target strategy in primary Sjögren’s syndrome-associated pulmonary arterial hypertension? Clin Rheumatol 2018; 37:2989-2998. [DOI: 10.1007/s10067-018-4184-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/12/2018] [Accepted: 06/19/2018] [Indexed: 02/07/2023]
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Busato F, Dejeux E, El Abdalaoui H, Gut IG, Tost J. Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®. Methods Mol Biol 2018; 1708:427-445. [PMID: 29224157 DOI: 10.1007/978-1-4939-7481-8_22] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many protocols for gene-specific DNA methylation analysis are either labor intensive, not quantitative and/or limited to the measurement of the methylation status of only one or very few CpG positions. Pyrosequencing is a real-time sequencing technology that overcomes these limitations. After bisulfite modification of genomic DNA, a region of interest is amplified by PCR with one of the two primers being biotinylated. The PCR generated template is rendered single-stranded and a pyrosequencing primer is annealed to analyze quantitatively cytosine methylation. In comparative studies, pyrosequencing has been shown to be among the most accurate and reproducible technologies for locus-specific DNA methylation analyses and has become a widely used tool for the validation of DNA methylation changes identified in genome-wide studies as well as for locus-specific analyses with clinical impact such as methylation analysis of the MGMT promoter. Advantages of the Pyrosequencing technology are the ease of its implementation, the high quality and the quantitative nature of the results, and its ability to identify differentially methylated positions in close proximity.
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Affiliation(s)
- Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Emelyne Dejeux
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Hafida El Abdalaoui
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Ivo Glynne Gut
- Biomedical Genomics Group, Centro Nacional de Analisis Genomico, CNAG-CRG, Center for Genomic Regulation, Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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Ulff-Møller CJ, Asmar F, Liu Y, Svendsen AJ, Busato F, Grønbaek K, Tost J, Jacobsen S. Twin DNA Methylation Profiling Reveals Flare-Dependent Interferon Signature and B Cell Promoter Hypermethylation in Systemic Lupus Erythematosus. Arthritis Rheumatol 2018; 70:878-890. [PMID: 29361205 DOI: 10.1002/art.40422] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 01/17/2018] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) has limited monozygotic twin concordance, implying a role for pathogenic factors other than genetic variation, such as epigenetic changes. Using the disease-discordant twin model, we investigated genome-wide DNA methylation changes in sorted CD4+ T cells, monocytes, granulocytes, and B cells in twin pairs with at least 1 SLE-affected twin. METHODS Peripheral blood obtained from 15 SLE-affected twin pairs (6 monozygotic and 9 dizygotic) was processed using density-gradient centrifugation for the granulocyte fraction. CD4+ T cells, monocytes, and B cells were further isolated using magnetic beads. Genome-wide DNA methylation was analyzed using Infinium HumanMethylation450K BeadChips. When comparing probes from SLE-affected twins and co-twins, differential DNA methylation was considered statistically significant when the P value was less than 0.01 and biologically relevant when the median DNA methylation difference was >7%. Findings were validated by pyrosequencing and replicated in an independent case-control sample. RESULTS In paired analyses of twins discordant for SLE restricted to the gene promoter and start region, we identified 55, 327, 247, and 1,628 genes with differentially methylated CpGs in CD4+ T cells, monocytes, granulocytes, and B cells, respectively. All cell types displayed marked hypomethylation in interferon-regulated genes, such as IFI44L, PARP9, and IFITM1, which was more pronounced in twins who experienced a disease flare within the past 2 years. In contrast to what was observed in the other cell types, differentially methylated CpGs in B cells were predominantly hypermethylated, and the most important upstream regulators included TNF and EP300. CONCLUSION Hypomethylation of interferon-regulated genes occurs in all major cellular compartments in SLE-affected twins. The observed B cell promoter hypermethylation is a novel finding with potential significance in SLE pathogenesis.
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Affiliation(s)
- Constance J Ulff-Møller
- Rigshospitalet and University of Copenhagen, Copenhagen, Denmark, and Commissariat à l'énergie atomique et aux énergies alternatives, Institut de Biologie Francois Jacob, Evry, France
| | | | - Yi Liu
- Commissariat à l'énergie atomique et aux énergies alternatives, Institut de Biologie Francois Jacob, Evry, France
| | | | - Florence Busato
- Commissariat à l'énergie atomique et aux énergies alternatives, Institut de Biologie Francois Jacob, Evry, France
| | - Kirsten Grønbaek
- Rigshospitalet and University of Copenhagen, Copenhagen, Denmark
| | - Jörg Tost
- Commissariat à l'énergie atomique et aux énergies alternatives, Institut de Biologie Francois Jacob, Evry, France
| | - Søren Jacobsen
- Rigshospitalet and University of Copenhagen, Copenhagen, Denmark
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Mougeot JL, Noll BD, Bahrani Mougeot FK. Sjögren's syndrome X-chromosome dose effect: An epigenetic perspective. Oral Dis 2018; 25:372-384. [PMID: 29316023 DOI: 10.1111/odi.12825] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/12/2017] [Accepted: 12/20/2017] [Indexed: 02/06/2023]
Abstract
Sjögren's syndrome (SS) is a chronic autoimmune disease affecting exocrine glands leading to mouth and eyes dryness. The extent to which epigenetic DNA methylation changes are responsible for an X-chromosome dose effect has yet to be determined. Our objectives were to (i) describe how epigenetic DNA methylation changes could explain an X-chromosome dose effect in SS for women with normal 46,XX genotype and (ii) determine the relevant relationships to this dose effect, between X-linked genes, genes controlling X-chromosome inactivation (XCI) and genes encoding associated transcription factors, all of which are differentially expressed and/or differentially methylated in the salivary glands of patients with SS. We identified 58 upregulated X-chromosome genes, including 22 genes previously shown to escape XCI, based on the analysis of SS patient salivary gland GEO2R gene expression datasets. Moreover, we found XIST and its cis regulators RLIM, FTX, and CHIC1, and polycomb repressor genes of the PRC1/2 complexes to be upregulated. Many of the X-chromosome genes implicated in SS pathogenesis can be regulated by transcription factors which we found to be overexpressed and/or differentially methylated in patients with SS. Determination of the mechanisms underlying methylation-dependent gene expression and impaired XCI is needed to further elucidate the etiopathogenesis of SS.
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Affiliation(s)
- J-Lc Mougeot
- Department of Oral Medicine-Cannon Research Center, Carolinas HealthCare System, Charlotte, NC, USA.,Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - B D Noll
- Department of Oral Medicine-Cannon Research Center, Carolinas HealthCare System, Charlotte, NC, USA.,Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - F K Bahrani Mougeot
- Department of Oral Medicine-Cannon Research Center, Carolinas HealthCare System, Charlotte, NC, USA.,Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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Epigenetic alterations in primary Sjögren's syndrome - an overview. Clin Immunol 2018; 196:12-20. [PMID: 29649576 DOI: 10.1016/j.clim.2018.04.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/06/2018] [Accepted: 04/06/2018] [Indexed: 12/14/2022]
Abstract
Primary Sjögren's syndrome (pSS) is a chronic autoimmune rheumatic disease characterized by inflammation of exocrine glands, mainly salivary and lacrimal glands. In addition, pSS may affect multiple other organs resulting in systemic manifestations. Although the precise etiology of pSS remains elusive, pSS is considered to be a multi-factorial disease, where underlying genetic predisposition, environmental factors and epigenetic mechanisms contribute to disease development. Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNAs, may constitute a dynamic link between genome, environment and phenotypic manifestation by their modulating effects on gene expression. A growing body of studies reporting altered epigenetic landscapes in pSS suggests that epigenetic mechanisms play a role in the pathogenesis of pSS, and the reversible nature of epigenetic modifications suggests therapeutic strategies targeting epigenetic dysregulation in pSS. This article reviews our current understanding of epigenetic mechanisms in pSS and discusses implications for novel diagnostic and therapeutic approaches.
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Tost J. Epigenetic plasticity of eosinophils and other immune cell subsets in childhood asthma. THE LANCET RESPIRATORY MEDICINE 2018; 6:322-324. [PMID: 29496483 DOI: 10.1016/s2213-2600(18)30051-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 01/15/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, 2 rue Gaston Crémieux, 91000 Evry, France.
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Abstract
Primary Sjögren syndrome (pSS) is a prototypical autoimmune disease. The involvement of B cells in the pathogenesis of pSS has long been suspected on the basis of clinical observations that include the presence of serum autoantibodies, hypergammaglobulinaemia, increased levels of free light chains and increased risk of B cell lymphoma. Moreover, the composition of the B cell subset is altered in pSS. In this Review, we discuss the mechanisms that support the increased activation of B cells in pSS, including genetic and epigenetic factors and environmental triggers that promote B cell activation via the innate immune system. B cell activating factor (BAFF, also known as TNF ligand superfamily member 13B) is at the crossroads of this process. An important role also exists for the target tissue (exocrine glands, namely the salivary and lachrymal glands), which promotes local B cell activation. This continuous stimulation of B cells is the main driver of lymphomatous escape. Identification of the multiple steps that support B cell activation has led to the development of promising targeted therapies that will hopefully lead to the development of an efficient therapeutic strategy for pSS.
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Burbage M, Gasparrini F, Aggarwal S, Gaya M, Arnold J, Nair U, Way M, Bruckbauer A, Batista FD. Tuning of in vivo cognate B-T cell interactions by Intersectin 2 is required for effective anti-viral B cell immunity. eLife 2018; 7. [PMID: 29337666 PMCID: PMC5770159 DOI: 10.7554/elife.26556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 01/01/2018] [Indexed: 12/13/2022] Open
Abstract
Wiskott-Aldrich syndrome (WAS) is an immune pathology associated with mutations in WAS protein (WASp) or in WASp interacting protein (WIP). Together with the small GTPase Cdc42 and other effectors, these proteins participate in the remodelling of the actin network downstream of BCR engagement. Here we show that mice lacking the adaptor protein ITSN2, a G-nucleotide exchange factor (GEF) for Cdc42 that also interacts with WASp and WIP, exhibited increased mortality during primary infection, incomplete protection after Flu vaccination, reduced germinal centre formation and impaired antibody responses to vaccination. These defects were found, at least in part, to be intrinsic to the B cell compartment. In vivo, ITSN2 deficient B cells show a reduction in the expression of SLAM, CD84 or ICOSL that correlates with a diminished ability to form long term conjugates with T cells, to proliferate in vivo, and to differentiate into germinal centre cells. In conclusion, our study not only revealed a key role for ITSN2 as an important regulator of adaptive immune-response during vaccination and viral infection but it is also likely to contribute to a better understanding of human immune pathologies.
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Affiliation(s)
- Marianne Burbage
- Lymphocyte Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Francesca Gasparrini
- Lymphocyte Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Shweta Aggarwal
- Lymphocyte Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Mauro Gaya
- Lymphocyte Biology Laboratory, The Francis Crick Institute, London, United Kingdom.,Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Johan Arnold
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Usha Nair
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Michael Way
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andreas Bruckbauer
- Lymphocyte Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Facundo D Batista
- Lymphocyte Biology Laboratory, The Francis Crick Institute, London, United Kingdom.,Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
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48
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Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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49
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Retamozo S, Flores-Chavez A, Consuegra-Fernández M, Lozano F, Ramos-Casals M, Brito-Zerón P. Cytokines as therapeutic targets in primary Sjögren syndrome. Pharmacol Ther 2017; 184:81-97. [PMID: 29092775 DOI: 10.1016/j.pharmthera.2017.10.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Primary Sjögren syndrome (SjS) is a systemic autoimmune disease that may affect 1 in 1000 people (overwhelmingly women) and that can be a serious disease with excess mortality due to severe organ-specific involvements and the development of B cell lymphoma; systemic involvement clearly marks the disease prognosis, and strongly suggests the need for closer follow-up and more robust therapeutic management. Therapy is established according to the organ involved and severity. As a rule, the management of systemic SjS should be organ-specific, with glucocorticoids and immunosuppressive agents limited to potentially-severe involvements; unfortunately, the limited evidence available for these drugs, together with the potential development of serious adverse events, makes solid therapeutic recommendations difficult. The emergence of biological therapies has increased the therapeutic armamentarium available to treat primary SjS. Biologics currently used in SjS patients are used off-label and are overwhelmingly agents targeting B cells, but the most recent studies are moving on into the evaluation of targeting specific cytokines involved in the SjS pathogenesis. The most recent etiopathogenic advances in SjS are shedding some light in the search for new highly-selective biological therapies without the adverse effects of the standard drugs currently used (corticosteroids and immunosuppressant drugs). This review summarizes the potential pharmacotherapeutic options targeting the main cytokine families involved in the etiopathogenesis of primary SjS and analyzes potential insights for developing new therapies.
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Affiliation(s)
- Soledad Retamozo
- Sjögren Syndrome Research Group (AGAUR), Laboratory of Autoimmune Diseases Josep Font, CELLEX-IDIBAPS, Spain; Hospital Privado Universitario de Córdoba, Instituto Universitario de Ciencias Biomédicas de Córdoba (IUCBC), Córdoba, Argentina; Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Córdoba, Consejo Nacional de Investigaciones Científicas y Técnicas (INICSA-UNC-CONICET), Córdoba, Argentina; Department of Autoimmune Diseases, ICMiD, Hospital Clínic Barcelona, Spain
| | - Alejandra Flores-Chavez
- Sjögren Syndrome Research Group (AGAUR), Laboratory of Autoimmune Diseases Josep Font, CELLEX-IDIBAPS, Spain; Biomedical Research Unit 02, Clinical Epidemiology Research Unit, UMAE, Specialties Hospital, Western Medical Center, Mexican Institute for Social Security (IMSS), Guadalajara, Mexico; Postgraduate Program of Medical Science, University Center for Biomedical Research (CUIB), University of Colima, Colima, Mexico; Department of Autoimmune Diseases, ICMiD, Hospital Clínic Barcelona, Spain
| | - Marta Consuegra-Fernández
- Immunoreceptors del Sistema Innat I Adaptatiu, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Francisco Lozano
- Immunoreceptors del Sistema Innat I Adaptatiu, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain; Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clínic de Barcelona, Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.
| | - Manuel Ramos-Casals
- Sjögren Syndrome Research Group (AGAUR), Laboratory of Autoimmune Diseases Josep Font, CELLEX-IDIBAPS, Spain; Department of Medicine, University of Barcelona, Barcelona, Spain; Department of Autoimmune Diseases, ICMiD, Hospital Clínic Barcelona, Spain.
| | - Pilar Brito-Zerón
- Sjögren Syndrome Research Group (AGAUR), Laboratory of Autoimmune Diseases Josep Font, CELLEX-IDIBAPS, Spain; Autoimmune Diseases Unit, Department of Medicine, Hospital CIMA-Sanitas, Barcelona, Spain; Department of Autoimmune Diseases, ICMiD, Hospital Clínic Barcelona, Spain
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50
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[Influence of epigenetic in Sjögren's syndrome]. Rev Med Interne 2017; 39:346-351. [PMID: 29054585 DOI: 10.1016/j.revmed.2017.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/01/2017] [Accepted: 09/18/2017] [Indexed: 01/15/2023]
Abstract
Sjögren's syndrome (SS) is a systemic autoimmune epithelitis with a major female incidence, and characterized by a dry syndrome, impaired quality of life, visceral involvement, and lymphoma for the most aggressive cases. During this process, epithelial cells acquire the capacity to produce cytokines, chemokines, and autoantigens which can in turn be presented to the immune system. Consequently, this epithelitis is accompanied by lymphocytic infiltrations leading to the formation of pseudo-follicles in which self-reactive B lymphocytes are present. The recent integration of genomic and especially of epigenomic data, which make it possible to analyze the different cellular partners, opens new perspectives and allows to a better understanding of this complex and still incurable disease.
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