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Hammaker D, Nygaard G, Kuhs A, Ai R, Boyle DL, Wang W, Firestein GS. Joint Location-Specific JAK-STAT Signaling in Rheumatoid Arthritis Fibroblast-like Synoviocytes. ACR Open Rheumatol 2019; 1:640-648. [PMID: 31872186 PMCID: PMC6917316 DOI: 10.1002/acr2.11093] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/24/2019] [Indexed: 12/30/2022] Open
Abstract
Objective Rheumatoid arthritis (RA) fibroblast‐like synoviocytes (FLS) derived from hip and knee have distinctive DNA methylation and transcriptome patterns in interleukin (IL)‐6 signaling and Janus kinase (JAK)–signal transducers and activators of transcription (STAT) pathways. To determine the functional effects of these joint‐specific signatures, we evaluated how RA hip and knee FLS differ in their response to IL‐6. Methods Hip or knee RA FLS were obtained after arthroplasty. Previously published datasets on epigenetic landscape of FLS were mined to identify joint‐specific IL‐6–related epigenomic differences. RNA sequencing was performed on five RA hip and five knee FLS treated with or without IL‐6. Differential gene expression was determined using edgeR software. STAT3 phosphorylation was measured using bead assays. Sensitivity to tofacitinib was evaluated by measuring CCL2 inhibition using quantitative polymerase chain reaction. Results Assay for Transposase‐Accessible Chromatin sequencing and histone chromatin immunoprecipitation sequencing datasets from RA FLS were analyzed to identify epigenomic differences between hip and knee. Differential chromatin accessibility was associated with IL‐6,IL‐6R, and JAK1 genes. H3K27ac was also differentially marked at other JAK‐STAT–related genes, including STAT3‐STAT5A region. Principal component analysis of RNA sequencing data confirmed segregation between RA hip and knee FLS under basal conditions, that persisted following IL‐6 treatment. STAT3 phosphorylation after IL‐6 was significantly higher in knee than hip FLS and was highly correlated with JAK1 protein levels. Knee FLS were less sensitive to the JAK inhibitor tofacitinib than hip FLS. Conclusion RA hip and knee FLS have distinct transcriptomes, epigenetic marks, and STAT3 activation patterns in the IL‐6 pathway. These joint‐specific differences might contribute to a differential clinical response in individual joints to targeted therapies such as JAK inhibitors.
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Affiliation(s)
- Deepa Hammaker
- School of Medicine, Department of Rheumatology, Allergy and Immunology, University of California San Diego, La Jolla, California
| | - Gyrid Nygaard
- School of Medicine, Department of Rheumatology, Allergy and Immunology, University of California San Diego, La Jolla, California
| | - Amanda Kuhs
- School of Medicine, Department of Rheumatology, Allergy and Immunology, University of California San Diego, La Jolla, California
| | - Rizi Ai
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - David L Boyle
- School of Medicine, Department of Rheumatology, Allergy and Immunology, University of California San Diego, La Jolla, California
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Gary S Firestein
- School of Medicine, Department of Rheumatology, Allergy and Immunology, University of California San Diego, La Jolla, California
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Abstract
PURPOSE OF REVIEW This review provides a summary of recent molecular findings that have refined our understanding of the cell types that constitute human synovial tissue, particularly in patients with rheumatoid arthritis (RA). RECENT FINDINGS Recent advances in high-dimensional and single-cell assays have elucidated upwards of 20 cell subsets in the RA synovium. This includes novel fibroblast populations and lymphocyte phenotypes, which in many cases exhibit features that have not been found in other tissues thus far. Molecular profiling studies over the past several years have rapidly generated a comprehensive and detailed outline of the cellular phenotypes in synovial tissue affected by RA. Molecular features of these newly identified cell subsets immediately represent reasonable therapeutic targets and provide the opportunity to design the most clinically relevant mechanistic experiments. Broadly speaking, the ~ 20 cell types thus far identified in RA synovium seem to be fairly well conserved across patients, despite extensive heterogeneity in patient clinical features, stage of disease, and treatment responses. Thus, a next phase in molecular profiling may benefit from quantifying patient samples in terms of the ratios of cell types, with the rationale that certain cellular interactions will predominate in an individual and medications targeting these interactions may be more efficacious for that individual. Such cellular profiling in tissues combined with studies examining how the compendium of these cells interact in their three-dimensional tissue ultrastructures will be important in understanding how collectively these cells drive the disease process and ultimately how best to treat patients.
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Ciechomska M, Roszkowski L, Maslinski W. DNA Methylation as a Future Therapeutic and Diagnostic Target in Rheumatoid Arthritis. Cells 2019; 8:E953. [PMID: 31443448 PMCID: PMC6770174 DOI: 10.3390/cells8090953] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 12/28/2022] Open
Abstract
Rheumatoid arthritis (RA) is a long-term autoimmune disease of unknown etiology that leads to progressive joint destruction and ultimately to disability. RA affects as much as 1% of the population worldwide. To date, RA is not a curable disease, and the mechanisms responsible for RA development have not yet been well understood. The development of more effective treatments and improvements in the early diagnosis of RA is direly needed to increase patients' functional capacity and their quality of life. As opposed to genetic mutation, epigenetic changes, such as DNA methylation, are reversible, making them good therapeutic candidates, modulating the immune response or aggressive synovial fibroblasts (FLS-fibroblast-like synoviocytes) activity when it is necessary. It has been suggested that DNA methylation might contribute to RA development, however, with insufficient and conflicting results. Besides, recent studies have shown that circulating cell-free methylated DNA (ccfDNA) in blood offers a very convenient, non-invasive, and repeatable "liquid biopsy", thus providing a reliable template for assessing molecular markers of various diseases, including RA. Thus, epigenetic therapies controlling autoimmunity and systemic inflammation may find wider implications for the diagnosis and management of RA. In this review, we highlight current challenges associated with the treatment of RA and other autoimmune diseases and discuss how targeting DNA methylation may improve diagnostic, prognostic, and therapeutic approaches.
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Affiliation(s)
- Marzena Ciechomska
- Department of Pathophysiology and Immunology, National Institute of Geriatrics Rheumatology and Rehabilitation, 02-635 Warsaw, Poland.
| | - Leszek Roszkowski
- Department of Rheumatology, National Institute of Geriatrics Rheumatology and Rehabilitation, 02-635 Warsaw, Poland
| | - Wlodzimierz Maslinski
- Department of Pathophysiology and Immunology, National Institute of Geriatrics Rheumatology and Rehabilitation, 02-635 Warsaw, Poland
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54
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Abstract
Autoimmune rheumatic diseases pose many problems that have, in general, already been solved in the field of cancer. The heterogeneity of each disease, the clinical similarities and differences between different autoimmune rheumatic diseases and the large number of patients that remain without a diagnosis underline the need to reclassify these diseases via new approaches. Knowledge about the molecular basis of systemic autoimmune diseases, along with the availability of bioinformatics tools capable of handling and integrating large volumes of various types of molecular data at once, offer the possibility of reclassifying these diseases. A new taxonomy could lead to the discovery of new biomarkers for patient stratification and prognosis. Most importantly, this taxonomy might enable important changes in clinical trial design to reach the expected outcomes or the design of molecularly targeted therapies. In this Review, we discuss the basis for a new molecular taxonomy for autoimmune rheumatic diseases. We highlight the evidence surrounding the idea that these diseases share molecular features related to their pathogenesis and development and discuss previous attempts to classify these diseases. We evaluate the tools available to analyse and combine different types of molecular data. Finally, we introduce PRECISESADS, a project aimed at reclassifying the systemic autoimmune diseases.
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55
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Guo S, Liu J, Jiang T, Lee D, Wang R, Zhou X, Jin Y, Shen Y, Wang Y, Bai F, Ding Q, Wang G, Zhang J, Zhou X, Schrodi SJ, He D. (5R)-5-Hydroxytriptolide (LLDT-8) induces substantial epigenetic mediated immune response network changes in fibroblast-like synoviocytes from rheumatoid arthritis patients. Sci Rep 2019; 9:11155. [PMID: 31371761 PMCID: PMC6671973 DOI: 10.1038/s41598-019-47411-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 07/16/2019] [Indexed: 12/23/2022] Open
Abstract
Tripterygium is a traditional Chinese medicine that has widely been used in the treatment of rheumatic disease. (5R)-5-hydroxytriptolide (LLDT-8) is an extracted compound from Tripterygium, which has been shown to have lower cytotoxicity and relatively higher immunosuppressive activity when compared to Tripterygium. However, our understanding of LLDT-8-induced epigenomic impact and overall regulatory changes in key cell types remains limited. Doing so will provide critically important mechanistic information about how LLDT-8 wields its immunosuppressive activity. The purpose of this study was to assess the effects of LLDT-8 on transcriptome including mRNAs and long non-coding RNA (lncRNAs) in rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS) by a custom genome-wide microarray assay. Significant differential expressed genes were validated by QPCR. Our work shows that 394 genes (281 down- and 113 up-regulated) were significantly differentially expressed in FLS responding to the treatment of LLDT-8. KEGG pathway analysis showed 20 pathways were significantly enriched and the most significantly enriched pathways were relevant to Immune reaction, including cytokine-cytokine receptor interaction (P = 4.61 × 10−13), chemokine signaling pathway (P = 1.01 × 10−5) and TNF signaling pathway (P = 2.79 × 10−4). Furthermore, we identified 618 highly negatively correlated lncRNA-mRNA pairs from the selected significantly differential lncRNA and mRNA including 27 cis-regulated and 591 trans-regulated lncRNA-mRNAs modules. KEGG and GO based function analysis to differential lncRNA also shown the enrichment of immune response. Finally, lncRNA-transcription factor (TF) and lncRNA-TF-mRNA co-expression network were constructed with high specific network characteristics, indicating LLDT-8 would influence the expression network within the whole FLS cells. The results indicated that the LLDT-8 would mainly influence the FLS cells systemically and specially in the process of immune related pathways.
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Affiliation(s)
- Shicheng Guo
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States, 54449
| | - Jia Liu
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, 200052, China.,Arthritis Institute of integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, 200052, China
| | - Ting Jiang
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, 200052, China.,Arthritis Institute of integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, 200052, China
| | - Dungyang Lee
- Division of Biostatistics, University of Texas School of Public Health, Houston, TX, USA
| | - Rongsheng Wang
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, 200052, China.,Arthritis Institute of integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, 200052, China
| | - Xinpeng Zhou
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, 200052, China
| | - Yehua Jin
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, 200052, China
| | - Yi Shen
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, 200052, China.,Arthritis Institute of integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, 200052, China
| | - Yan Wang
- Arthritis Institute of integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, 200052, China
| | - Fengmin Bai
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, 200052, China.,Arthritis Institute of integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, 200052, China
| | - Qin Ding
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, 200052, China.,Arthritis Institute of integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, 200052, China
| | - Grace Wang
- Washington University, St. Louis, Missouri, 63130, USA
| | - Jianyong Zhang
- Shenzhen Traditional Chinese Medicine Hospital and The fourth Clinical Medical College of Guangzhou University of Chinese Medicine. Fuhua Road, Shenzhen, Guangzhou, 518033, China
| | - Xiaodong Zhou
- University of Texas Medical School at Houston, 6431 Fannin, MSB5.270, Houston, TX, 77030, USA
| | - Steven J Schrodi
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States, 54449.,Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dongyi He
- Department of Rheumatology, Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine, Shanghai, 200052, China. .,Arthritis Institute of integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, 200052, China.
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Peeters JGC, Vastert SJ, van Wijk F, van Loosdregt J. Review: Enhancers in Autoimmune Arthritis: Implications and Therapeutic Potential. Arthritis Rheumatol 2019; 69:1925-1936. [PMID: 28666076 PMCID: PMC5659109 DOI: 10.1002/art.40194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/27/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Janneke G C Peeters
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sebastiaan J Vastert
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Femke van Wijk
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jorg van Loosdregt
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital and University Medical Center Utrecht, Utrecht, The Netherlands
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57
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Manzo A, Bugatti S, Rossi S. Clinical Applications of Synovial Biopsy. Front Med (Lausanne) 2019; 6:102. [PMID: 31134204 PMCID: PMC6524205 DOI: 10.3389/fmed.2019.00102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/25/2019] [Indexed: 11/13/2022] Open
Abstract
The synovial tissue is a primary target of multiple diseases characterized by different pathogenic mechanisms, including infective, deposition, neoplastic, and chronic immune-inflammatory pathologies. Synovial biopsy can have a relevant role in differential diagnosis of specific conditions in clinical practice, although its exploitation remains relatively limited. In particular, no validated synovial-tissue-derived biomarkers are currently available in the clinic to aid in the diagnosis and management in most frequent forms of chronic inflammatory arthropathies, namely rheumatoid arthritis (RA) and the spondyloarthritides (SpA). In this brief review, we will discuss the current spectrum of clinical applications of synovial biopsy in routine rheumatologic care and will provide an analysis of the perspectives for its potential exploitation in patients with chronic inflammatory arthritides.
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Affiliation(s)
- Antonio Manzo
- Rheumatology and Translational Immunology Research Laboratories, Division of Rheumatology, IRCCS Policlinico San Matteo Foundation, University of Pavia, Pavia, Italy
| | - Serena Bugatti
- Rheumatology and Translational Immunology Research Laboratories, Division of Rheumatology, IRCCS Policlinico San Matteo Foundation, University of Pavia, Pavia, Italy
| | - Silvia Rossi
- Rheumatology and Translational Immunology Research Laboratories, Division of Rheumatology, IRCCS Policlinico San Matteo Foundation, University of Pavia, Pavia, Italy
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58
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Loh C, Park SH, Lee A, Yuan R, Ivashkiv LB, Kalliolias GD. TNF-induced inflammatory genes escape repression in fibroblast-like synoviocytes: transcriptomic and epigenomic analysis. Ann Rheum Dis 2019; 78:1205-1214. [PMID: 31097419 DOI: 10.1136/annrheumdis-2018-214783] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE We investigated genome-wide changes in gene expression and chromatin remodelling induced by tumour necrosis factor (TNF) in fibroblast-like synoviocytes (FLS) and macrophages to better understand the contribution of FLS to the pathogenesis of rheumatoid arthritis (RA). METHODS FLS were purified from patients with RA and CD14+ human monocyte-derived macrophages were obtained from healthy donors. RNA-sequencing, histone 3 lysine 27 acetylation (H3K27ac), chromatin immunoprecipitation-sequencing (ChIP-seq) and assay for transposable accessible chromatin by high throughput sequencing (ATAC-seq) were performed in control and TNF-stimulated cells. RESULTS We discovered 280 TNF-inducible arthritogenic genes which are transiently expressed and subsequently repressed in macrophages, but in RA, FLS are expressed with prolonged kinetics that parallel the unremitting kinetics of RA synovitis. 80 out of these 280 fibroblast-sustained genes (FSGs) that escape repression in FLS relative to macrophages were desensitised (tolerised) in macrophages. Epigenomic analysis revealed persistent H3K27 acetylation and increased chromatin accessibility in regulatory elements associated with FSGs in TNF-stimulated FLS. The accessible regulatory elements of FSGs were enriched in binding motifs for nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), interferon-regulatory factors (IRFs) and activating protein-1 (AP-1). Inhibition of bromodomain and extra-terminal motif (BET) proteins, which interact with histone acetylation, suppressed sustained induction of FSGs by TNF. CONCLUSION Our genome-wide analysis has identified the escape of genes from transcriptional repression in FLS as a novel mechanism potentially contributing to the chronic unremitting synovitis observed in RA. Our finding that TNF induces sustained chromatin activation in regulatory elements of the genes that escape repression in RA FLS suggests that altering or targeting chromatin states in FLS (eg, with inhibitors of BET proteins) is an attractive therapeutic strategy.
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Affiliation(s)
- Christopher Loh
- David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.,Arthritis & Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
| | - Sung-Ho Park
- David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.,Arthritis & Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
| | - Angela Lee
- David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.,Arthritis & Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
| | - Ruoxi Yuan
- David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.,Arthritis & Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
| | - Lionel B Ivashkiv
- David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.,Arthritis & Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
| | - George D Kalliolias
- David Z Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA .,Arthritis & Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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59
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Ramos PS, Zimmerman KD, Haddad S, Langefeld CD, Medsger TA, Feghali-Bostwick CA. Integrative analysis of DNA methylation in discordant twins unveils distinct architectures of systemic sclerosis subsets. Clin Epigenetics 2019; 11:58. [PMID: 30947741 PMCID: PMC6449959 DOI: 10.1186/s13148-019-0652-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/11/2019] [Indexed: 02/08/2023] Open
Abstract
Background Systemic sclerosis (SSc) is a rare autoimmune fibrosing disease with an incompletely understood genetic and non-genetic etiology. Defining its etiology is important to allow the development of effective predictive, preventative, and therapeutic strategies. We conducted this epigenomic study to investigate the contributions of DNA methylation to the etiology of SSc while minimizing confounding due to genetic heterogeneity. Methods Genomic methylation in whole blood from 27 twin pairs discordant for SSc was assayed over 450 K CpG sites. In silico integration with reported differentially methylated cytosines, differentially expressed genes, and regulatory annotation was conducted to validate and interpret the results. Results A total of 153 unique cytosines in limited cutaneous SSc (lcSSc) and 266 distinct sites in diffuse cutaneous SSc (dcSSc) showed suggestive differential methylation levels in affected twins. Integration with available data revealed 76 CpGs that were also differentially methylated in blood cells from lupus patients, suggesting their role as potential epigenetic blood biomarkers of autoimmunity. It also revealed 27 genes with concomitant differential expression in blood from SSc patients, including IFI44L and RSAD2. Regulatory annotation revealed that dcSSc-associated CpGs (but not lcSSc) are enriched at Encyclopedia of DNA Elements-, Roadmap-, and BLUEPRINT-derived regulatory regions, supporting their potential role in disease presentation. Notably, the predominant enrichment of regulatory regions in monocytes and macrophages is consistent with the role of these cells in fibrosis, suggesting that the observed cellular dysregulation might be, at least partly, due to altered epigenetic mechanisms of these cells in dcSSc. Conclusions These data implicate epigenetic changes in the pathogenesis of SSc and suggest functional mechanisms in SSc etiology. Electronic supplementary material The online version of this article (10.1186/s13148-019-0652-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.,Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Kip D Zimmerman
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Thomas A Medsger
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carol A Feghali-Bostwick
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
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60
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DNA methylation and transcriptome signature of the IL12B gene in ankylosing spondylitis. Int Immunopharmacol 2019; 71:109-114. [PMID: 30889422 DOI: 10.1016/j.intimp.2019.03.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Ankylosing spondylitis (AS) is an autoimmune disease without a reliable biomarker. This study investigated the IL12B gene methylation as a robust marker by integrating DNA methylation and mRNA data. METHODS A two-stage design was used for methylome and transcriptome investigation. The first phase detected methylation level from 99 AS patients and 99 healthy controls (HCs) whilst the second phase measured mRNA level from 20 patients and 20 HCs. We conducted analysis of differential methylation sites and receiver operating characteristic (ROC) as well as mRNA level to verify methylation. RESULTS We investigated 37 methylation sites that were mapped to 2 CpG islands (IL12B-1 and IL12B-2). Compared with HCs, the two islands were hypermethylated (IL12B-1: P = 4.6 ∗ 10 ^ -4; IL12B-2: P = 1.3 ∗ 10 ^ -5) and the mRNA level was overexpressed (P = 0.004) in AS patients. The subgroup analysis results showed a significant hypermethylation of the two islands in B27 positive group (IL12B-1: P = 3.7 ∗ 10 ^ -4; IL12B-2: P = 3.7 ∗ 10 ^ -6) and in male patients (IL12B-1: P = 4.9 ∗ 10 ^ -4; IL12B-2: P = 7.2 ∗ 10 ^ -6). ROC results found that the IL12B-1 island had a sensitivity of 62.6% and a specificity of 66.7%, and the IL12B-2 had a sensitivity of 50.0% and a specificity of 77.7%. CONCLUSION DNA methylation and transcriptome signature of the IL12B gene can discriminate AS patients from HCs, and hypermethylation of the IL12B may contribute to the pathogenesis of AS.
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61
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Humby FC. Synovial Tissue Sampling in Rheumatological Practice-Past Developments and Future Perspectives. Front Med (Lausanne) 2019; 6:4. [PMID: 30761301 PMCID: PMC6361834 DOI: 10.3389/fmed.2019.00004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/09/2019] [Indexed: 11/21/2022] Open
Abstract
Synovial biopsies are performed in routine clinical care in order to refine diagnosis as well as within a research setting. Progress in the development of minimally invasive synovial sampling methods in the last century has accelerated and facilitated novel insights into disease pathogenesis. This review discusses the development of synovial biopsy techniques as well as examining the three currently most commonly used approaches: arthroscopic, blind needle biopsy and ultrasound guided approaches. It also highlights major research advances driven through synovial research and considers future developments.
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Affiliation(s)
- Frances C Humby
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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62
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Abstract
PURPOSE OF REVIEW Aberrant epigenetic changes in DNA methylation, histone marks, and noncoding RNA expression regulate the pathogenesis of many rheumatic diseases. The present article will review the recent advances in the epigenetic profile of inflammatory arthritis and discuss diagnostic biomarkers and potential therapeutic targets. RECENT FINDINGS Methylation signatures of fibroblast-like synoviocytes not only distinguish rheumatoid arthritis (RA) and osteoarthritis (OA), but also early RA from late RA or juvenile idiopathic arthritis. Methylation patterns are also specific to individual joint locations, which might explain the distribution of joint involvement in some rheumatic diseases. Hypomethylation in systemic lupus erythematosus (SLE) T cells is, in part, because of active demethylation and 5-hydroxymethylation. The methylation status of some genes in SLE is associated with disease severity and has potential as a diagnostic marker. An integrative analysis of OA methylome, transcriptome, and proteome in chondrocytes has identified multiple-evidence genes that might be evaluated for therapeutic potential. Class-specific histone deacetylase inhibitors are being evaluated for therapy in inflammatory arthritis. SUMMARY Disease pathogenesis is regulated by the interplay of genetics, environment, and epigenetics. Understanding how these mechanisms regulate cell function in health and disease has implications for individualized therapy.
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Zhu H, Wu LF, Mo XB, Lu X, Tang H, Zhu XW, Xia W, Guo YF, Wang MJ, Zeng KQ, Wu J, Qiu YH, Lin X, Zhang YH, Liu YZ, Yi NJ, Deng FY, Lei SF. Rheumatoid arthritis–associated DNA methylation sites in peripheral blood mononuclear cells. Ann Rheum Dis 2018; 78:36-42. [DOI: 10.1136/annrheumdis-2018-213970] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/28/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022]
Abstract
ObjectivesTo identify novel DNA methylation sites significant for rheumatoid arthritis (RA) and comprehensively understand their underlying pathological mechanism.MethodsWe performed (1) genome-wide DNA methylation and mRNA expression profiling in peripheral blood mononuclear cells from RA patients and health controls; (2) correlation analysis and causal inference tests for DNA methylation and mRNA expression data; (3) differential methylation genes regulatory network construction; (4) validation tests of 10 differential methylation positions (DMPs) of interest and corresponding gene expressions; (5) correlation between PARP9 methylation and its mRNA expression level in Jurkat cells and T cells from patients with RA; (6) testing the pathological functions of PARP9 in Jurkat cells.ResultsA total of 1046 DNA methylation positions were associated with RA. The identified DMPs have regulatory effects on mRNA expressions. Causal inference tests identified six DNA methylation–mRNA–RA regulatory chains (eg, cg00959259-PARP9-RA). The identified DMPs and genes formed an interferon-inducible gene interaction network (eg, MX1, IFI44L, DTX3L and PARP9). Key DMPs and corresponding genes were validated their differences in additional samples. Methylation of PARP9 was correlated with mRNA level in Jurkat cells and T lymphocytes isolated from patients with RA. The PARP9 gene exerted significant effects on Jurkat cells (eg, cell cycle, cell proliferation, cell activation and expression of inflammatory factor IL-2).ConclusionsThis multistage study identified an interferon-inducible gene interaction network associated with RA and highlighted the importance of PARP9 gene in RA pathogenesis. The results enhanced our understanding of the important role of DNA methylation in pathology of RA.
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Wade SM, Trenkmann M, McGarry T, Canavan M, Marzaioli V, Wade SC, Veale DJ, Fearon U. Altered expression of microRNA-23a in psoriatic arthritis modulates synovial fibroblast pro-inflammatory mechanisms via phosphodiesterase 4B. J Autoimmun 2018; 96:86-93. [PMID: 30181004 DOI: 10.1016/j.jaut.2018.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/17/2018] [Accepted: 08/26/2018] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To investigate the functional role of miR-23a in synovial fibroblasts (SFC) activation in psoriatic arthritis (PsA). METHODS Differential expression of the miR-23a-27a-24-2 cluster was identified by real-time quantitative PCR in PsA synovial tissue and peripheral blood mononuclear cells (PBMC) compared to osteoarthritis (OA) and correlated with disease activity. For regulation experiments, PsA synovial fibroblasts (SFC) were cultured with Toll-like receptor (TLR) ligands and pro-inflammatory cytokines. PsA SFC were transfected with a miR-23a inhibitor to assess the functional effect on migration, invasion and expression of pro-inflammatory meditators. The direct interaction between miR-23a and predicted target mRNA, phosphodiesterase 4B (PDE4B), was examined by luciferase reporter gene assay, with the expression and regulation confirmed by RT-PCR and western blot. A PDE4 inhibitor was used to analyse the function of PDE4B signalling in both miR-23a and Poly(I:C)-induced PsA SFC activation. RESULTS Synovial tissue expression of miR-23a was lower in PsA compared to OA and correlated inversely with disease activity and synovitis. TLR activation via Poly(I:C) and LPS, but not Pam3CSK4, significantly decreased miR-23a expression, with no significant effect observed in reponse to stimulation with pro-inflammatory cytokines. Decreased miR-23a expression enhanced PsA SFC migration, invasion and secretion of IL-6, IL-8, MCP-1, RANTES and VEGF. We identified PDE4B as a direct target of miR-23a and demonstrated enhanced mRNA and protein expression of PDE4B in anti-miR-23a transfected PsA SFC. Poly(I:C) and/or miR-23a-induced migration and enhanced cytokine expression was suppressed by the blockade of PDE4 signalling. CONCLUSIONS In PsA, dysregulated miR-23a expression contributes to synovial inflammation through enhanced SFC activation, via PDE4B signalling, and identifies a novel anti-inflammatory mechanism of PDE4 blockade.
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Affiliation(s)
- Sarah M Wade
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland; Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Michelle Trenkmann
- Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Trudy McGarry
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland; Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Mary Canavan
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Viviana Marzaioli
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Siobhan C Wade
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Douglas J Veale
- Centre for Arthritis and Rheumatic Diseases, St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Ursula Fearon
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland.
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Sun ZH, Liu YH, Liu JD, Xu DD, Li XF, Meng XM, Ma TT, Huang C, Li J. MeCP2 Regulates PTCH1 Expression Through DNA Methylation in Rheumatoid Arthritis. Inflammation 2018; 40:1497-1508. [PMID: 28573530 DOI: 10.1007/s10753-017-0591-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease, in which pathogenesis is not clear. Many research demonstrated that fibroblast-like synoviocytes (FLSs) play a key role in RA pathogenesis, join in the cartilage injury and hyperplasia of the synovium, and contribute to the release of inflammatory cytokines. We used adjuvant arthritis (AA) rats as RA animal models. The methyl-CpG-binding protein 2 (MeCP2) enables the suppressed chromatin structure to be selectively detected in AA FLSs. Overexpression of this protein leads to an increase of integral methylation levels. Some research has confirmed the hedgehog (Hh) signaling pathway plays an important role in RA pathogenesis; furthermore, patched 1 (PTCH1) is a negative fraction of Hh signaling pathway. We used 5-aza-2'-deoxycytidine (5-azadc) as DNA methylation inhibitor. In our research, we found MeCP2 reduced PTCH1 expression in AA FLSs; 5-azadc obstructed the loss of PTCH1 expression. 5-Azadc, treatment of AA FLSs, also blocks the release of inflammatory cytokines. In order to probe the potential molecular mechanism, we assumed the epigenetic participation in the regulation of PTCH1. Results demonstrated that PTCH1 hypermethylation is related to the persistent FLS activation and inflammation in AA rats. Knockdown of MeCP2 using small-interfering RNA technique added PTCH1 expression in AA FLSs. Our results indicate that DNA methylation may offer molecule mechanisms, and the reduced PTCH1 methylation level could regulate inflammation through knockdown of MeCP2. Graphical Abstract PTCH1 is an inhibitory protein of the Hedgehog signaling pathway. Increased expression of PTCH1 can inhibit the expression of Gli1 and Shh, thereby inhibiting the activation of Hedgehog signaling pathway. Inactivated Hedgehog signaling pathway inhibits the secretion of IL-6 and TNF-α. MeCP2 mediates hypermethylation of PTCH1 gene and decreases the expression of PTCH1 protein, thus activating Hedgehog signaling pathway and increasing secretion of IL-6 and TNF-α.
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Affiliation(s)
- Zheng-Hao Sun
- School of Pharmacy, The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Meishan Road No. 81, Hefei, Anhui Province, 230032, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Meishan Road No. 81, Hefei, 230032, China.,Institute for Liver Diseases, Anhui Medical University, Meishan Road No. 81, Hefei, 230032, China
| | - Yan-Hui Liu
- School of Pharmacy, The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Meishan Road No. 81, Hefei, Anhui Province, 230032, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Meishan Road No. 81, Hefei, 230032, China.,Institute for Liver Diseases, Anhui Medical University, Meishan Road No. 81, Hefei, 230032, China
| | - Jun-da Liu
- School of Pharmacy, The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Meishan Road No. 81, Hefei, Anhui Province, 230032, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Meishan Road No. 81, Hefei, 230032, China.,Institute for Liver Diseases, Anhui Medical University, Meishan Road No. 81, Hefei, 230032, China
| | - Dan-Dan Xu
- School of Pharmacy, The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Meishan Road No. 81, Hefei, Anhui Province, 230032, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Meishan Road No. 81, Hefei, 230032, China.,Institute for Liver Diseases, Anhui Medical University, Meishan Road No. 81, Hefei, 230032, China
| | - Xiao-Feng Li
- School of Pharmacy, The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Meishan Road No. 81, Hefei, Anhui Province, 230032, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Meishan Road No. 81, Hefei, 230032, China.,Institute for Liver Diseases, Anhui Medical University, Meishan Road No. 81, Hefei, 230032, China
| | - Xiao-Ming Meng
- School of Pharmacy, The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Meishan Road No. 81, Hefei, Anhui Province, 230032, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Meishan Road No. 81, Hefei, 230032, China.,Institute for Liver Diseases, Anhui Medical University, Meishan Road No. 81, Hefei, 230032, China
| | - Tao-Tao Ma
- School of Pharmacy, The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Meishan Road No. 81, Hefei, Anhui Province, 230032, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Meishan Road No. 81, Hefei, 230032, China.,Institute for Liver Diseases, Anhui Medical University, Meishan Road No. 81, Hefei, 230032, China
| | - Cheng Huang
- School of Pharmacy, The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Meishan Road No. 81, Hefei, Anhui Province, 230032, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Meishan Road No. 81, Hefei, 230032, China.,Institute for Liver Diseases, Anhui Medical University, Meishan Road No. 81, Hefei, 230032, China
| | - Jun Li
- School of Pharmacy, The Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, Anhui Medical University, Meishan Road No. 81, Hefei, Anhui Province, 230032, China. .,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Meishan Road No. 81, Hefei, 230032, China. .,Institute for Liver Diseases, Anhui Medical University, Meishan Road No. 81, Hefei, 230032, China.
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Donlin LT, Rao DA, Wei K, Slowikowski K, McGeachy MJ, Turner JD, Meednu N, Mizoguchi F, Gutierrez-Arcelus M, Lieb DJ, Keegan J, Muskat K, Hillman J, Rozo C, Ricker E, Eisenhaure TM, Li S, Browne EP, Chicoine A, Sutherby D, Noma A, Nusbaum C, Kelly S, Pernis AB, Ivashkiv LB, Goodman SM, Robinson WH, Utz PJ, Lederer JA, Gravallese EM, Boyce BF, Hacohen N, Pitzalis C, Gregersen PK, Firestein GS, Raychaudhuri S, Moreland LW, Holers VM, Bykerk VP, Filer A, Boyle DL, Brenner MB, Anolik JH. Methods for high-dimensional analysis of cells dissociated from cryopreserved synovial tissue. Arthritis Res Ther 2018; 20:139. [PMID: 29996944 PMCID: PMC6042350 DOI: 10.1186/s13075-018-1631-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 05/24/2018] [Indexed: 12/29/2022] Open
Abstract
Background Detailed molecular analyses of cells from rheumatoid arthritis (RA) synovium hold promise in identifying cellular phenotypes that drive tissue pathology and joint damage. The Accelerating Medicines Partnership RA/SLE Network aims to deconstruct autoimmune pathology by examining cells within target tissues through multiple high-dimensional assays. Robust standardized protocols need to be developed before cellular phenotypes at a single cell level can be effectively compared across patient samples. Methods Multiple clinical sites collected cryopreserved synovial tissue fragments from arthroplasty and synovial biopsy in a 10% DMSO solution. Mechanical and enzymatic dissociation parameters were optimized for viable cell extraction and surface protein preservation for cell sorting and mass cytometry, as well as for reproducibility in RNA sequencing (RNA-seq). Cryopreserved synovial samples were collectively analyzed at a central processing site by a custom-designed and validated 35-marker mass cytometry panel. In parallel, each sample was flow sorted into fibroblast, T-cell, B-cell, and macrophage suspensions for bulk population RNA-seq and plate-based single-cell CEL-Seq2 RNA-seq. Results Upon dissociation, cryopreserved synovial tissue fragments yielded a high frequency of viable cells, comparable to samples undergoing immediate processing. Optimization of synovial tissue dissociation across six clinical collection sites with ~ 30 arthroplasty and ~ 20 biopsy samples yielded a consensus digestion protocol using 100 μg/ml of Liberase™ TL enzyme preparation. This protocol yielded immune and stromal cell lineages with preserved surface markers and minimized variability across replicate RNA-seq transcriptomes. Mass cytometry analysis of cells from cryopreserved synovium distinguished diverse fibroblast phenotypes, distinct populations of memory B cells and antibody-secreting cells, and multiple CD4+ and CD8+ T-cell activation states. Bulk RNA-seq of sorted cell populations demonstrated robust separation of synovial lymphocytes, fibroblasts, and macrophages. Single-cell RNA-seq produced transcriptomes of over 1000 genes/cell, including transcripts encoding characteristic lineage markers identified. Conclusions We have established a robust protocol to acquire viable cells from cryopreserved synovial tissue with intact transcriptomes and cell surface phenotypes. A centralized pipeline to generate multiple high-dimensional analyses of synovial tissue samples collected across a collaborative network was developed. Integrated analysis of such datasets from large patient cohorts may help define molecular heterogeneity within RA pathology and identify new therapeutic targets and biomarkers. Electronic supplementary material The online version of this article (10.1186/s13075-018-1631-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura T Donlin
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | - Deepak A Rao
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin Wei
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kamil Slowikowski
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Mandy J McGeachy
- University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Jason D Turner
- University of Birmingham, Queen Elizabeth Hospital, B15 2WB, Birmingham, UK
| | - Nida Meednu
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Fumitaka Mizoguchi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria Gutierrez-Arcelus
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - David J Lieb
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Joshua Keegan
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kaylin Muskat
- University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Joshua Hillman
- University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Cristina Rozo
- Hospital for Special Surgery, New York, NY, 10021, USA
| | - Edd Ricker
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | | | - Shuqiang Li
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Edward P Browne
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Adam Chicoine
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Danielle Sutherby
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Akiko Noma
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | | | - Chad Nusbaum
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Stephen Kelly
- Mile End Hospital, Barts Health NHS Trust, E1 1BB, London, UK
| | - Alessandra B Pernis
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | - Lionel B Ivashkiv
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | - Susan M Goodman
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | | | - Paul J Utz
- Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James A Lederer
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Brendan F Boyce
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.,Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | | | - Peter K Gregersen
- The Feinstein Institute for Medical Research, Manhasset, NY, 11030, USA
| | - Gary S Firestein
- University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Soumya Raychaudhuri
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Larry W Moreland
- University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - V Michael Holers
- University of Colorado of Denver School of Medicine, Aurora, CO, 80045, USA
| | - Vivian P Bykerk
- Hospital for Special Surgery, New York, NY, 10021, USA.,Weill Cornell Medical College, New York, NY, 10065, USA
| | - Andrew Filer
- University of Birmingham, Queen Elizabeth Hospital, B15 2WB, Birmingham, UK
| | - David L Boyle
- University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Michael B Brenner
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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Abstract
PURPOSE OF REVIEW Stroma is a broad term referring to the connective tissue matrix in which other cells reside. It is composed of diverse cell types with functions such as extracellular matrix maintenance, blood and lymph vessel development, and effector cell recruitment. The tissue microenvironment is determined by the molecular characteristics and relative abundances of different stromal cells such as fibroblasts, endothelial cells, pericytes, and mesenchymal precursor cells. Stromal cell heterogeneity is explained by embryonic developmental lineage, stages of differentiation to other cell types, and activation states. Interaction between immune and stromal cell types is critical to wound healing, cancer, and a wide range of inflammatory diseases. Here, we review recent studies of inflammatory diseases that use functional genomics and single-cell technologies to identify and characterize stromal cell types associated with pathogenesis. RECENT FINDINGS High dimensional strategies using mRNA sequencing, mass cytometry, and fluorescence activated cell-sorting with fresh primary tissue samples are producing detailed views of what is happening in diseased tissue in rheumatoid arthritis, inflammatory bowel disease, and cancer. Fibroblasts positive for CD90 (Thy-1) are enriched in the synovium of rheumatoid arthritis patients. Single-cell RNA-seq studies will lead to more discoveries about the stroma in the near future. SUMMARY Stromal cells form the microenvironment of inflamed and diseased tissues. Functional genomics is producing an increasingly detailed view of subsets of stromal cells with pathogenic functions in rheumatic diseases and cancer. Future genomics studies will discover disease mechanisms by perturbing molecular pathways with chemokines and therapies known to affect patient outcomes. Functional genomics studies with large sample sizes of patient tissues will identify patient subsets with different disease phenotypes or treatment responses.
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68
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Ai R, Laragione T, Hammaker D, Boyle DL, Wildberg A, Maeshima K, Palescandolo E, Krishna V, Pocalyko D, Whitaker JW, Bai Y, Nagpal S, Bachman KE, Ainsworth RI, Wang M, Ding B, Gulko PS, Wang W, Firestein GS. Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes. Nat Commun 2018; 9:1921. [PMID: 29765031 PMCID: PMC5953939 DOI: 10.1038/s41467-018-04310-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/23/2018] [Indexed: 01/09/2023] Open
Abstract
Epigenetics contributes to the pathogenesis of immune-mediated diseases like rheumatoid arthritis (RA). Here we show the first comprehensive epigenomic characterization of RA fibroblast-like synoviocytes (FLS), including histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, and H3K9me3), open chromatin, RNA expression and whole-genome DNA methylation. To address complex multidimensional relationship and reveal epigenetic regulation of RA, we perform integrative analyses using a novel unbiased method to identify genomic regions with similar profiles. Epigenomically similar regions exist in RA cells and are associated with active enhancers and promoters and specific transcription factor binding motifs. Differentially marked genes are enriched for immunological and unexpected pathways, with “Huntington’s Disease Signaling” identified as particularly prominent. We validate the relevance of this pathway to RA by showing that Huntingtin-interacting protein-1 regulates FLS invasion into matrix. This work establishes a high-resolution epigenomic landscape of RA and demonstrates the potential for integrative analyses to identify unanticipated therapeutic targets. Fibroblast-like synoviocytes (FLS) in the intimal layer of the synovium can become invasive and destroy cartilage in patients with rheumatoid arthritis (RA). Here the authors integrate a variety of epigenomic data to map the epigenome of FLS in RA and identify potential therapeutic targets.
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Affiliation(s)
- Rizi Ai
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Teresina Laragione
- Division of Rheumatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Deepa Hammaker
- Division of Rheumatology, Allergy and Immunology, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA
| | - David L Boyle
- Division of Rheumatology, Allergy and Immunology, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA
| | - Andre Wildberg
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Keisuke Maeshima
- Division of Rheumatology, Allergy and Immunology, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA
| | | | - Vinod Krishna
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - David Pocalyko
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - John W Whitaker
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Yuchen Bai
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Sunil Nagpal
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Kurtis E Bachman
- Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA, 19477, USA
| | - Richard I Ainsworth
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Mengchi Wang
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Bo Ding
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA
| | - Percio S Gulko
- Division of Rheumatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Wei Wang
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, UC San Diego, La Jolla, CA, 92093, USA. .,Department of Cellular and Molecular Medicine, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA.
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, 9500 Gilman Drive, UCSD School of Medicine, La Jolla, CA, 92093, USA.
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Shukla NM, Arimoto KI, Yao S, Fan JB, Zhang Y, Sato-Kaneko F, Lao FS, Hosoya T, Messer K, Pu M, Cottam HB, Carson DA, Hayashi T, Zhang DE, Corr M. Identification of Compounds That Prolong Type I Interferon Signaling as Potential Vaccine Adjuvants. SLAS DISCOVERY 2018; 23:960-973. [PMID: 29751735 DOI: 10.1177/2472555218774308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Vaccines are reliant on adjuvants to enhance the immune stimulus, and type I interferons (IFNs) have been shown to be beneficial in augmenting this response. We were interested in identifying compounds that would sustain activation of an endogenous type I IFN response as a co-adjuvant. We began with generation of a human monocytic THP-1 cell line with an IFN-stimulated response element (ISRE)-β-lactamase reporter construct for high-throughput screening. Pilot studies were performed to optimize the parameters and conditions for this cell-based Förster resonance energy transfer (FRET) reporter assay for sustaining an IFN-α-induced ISRE activation signal. These conditions were confirmed in an initial pilot screen, followed by the main screen for evaluating prolongation of an IFN-α-induced ISRE activation signal at 16 h. Hit compounds were identified using a structure enrichment strategy based on chemoinformatic clustering and a naïve "Top X" approach. A select list of confirmed hits was then evaluated for toxicity and the ability to sustain IFN activity by gene and protein expression. Finally, for proof of concept, a panel of compounds was used to immunize mice as co-adjuvant with a model antigen and an IFN-inducing Toll-like receptor 4 agonist, lipopolysaccharide, as an adjuvant. Selected compounds significantly augmented antigen-specific immunoglobulin responses.
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Affiliation(s)
- Nikunj M Shukla
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Kei-Ichiro Arimoto
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Shiyin Yao
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jun-Bao Fan
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Yue Zhang
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Fumi Sato-Kaneko
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Fitzgerald S Lao
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Tadashi Hosoya
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Karen Messer
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA.,2 Department of Family Medicine and Public Health, Division of Biostatistics and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Minya Pu
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA.,2 Department of Family Medicine and Public Health, Division of Biostatistics and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Howard B Cottam
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Dennis A Carson
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | | | - Dong-Er Zhang
- 1 Moores UCSD Cancer Center, University of California, San Diego, La Jolla, CA, USA.,3 Department of Pathology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Maripat Corr
- 4 Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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Karouzakis E, Raza K, Kolling C, Buckley CD, Gay S, Filer A, Ospelt C. Analysis of early changes in DNA methylation in synovial fibroblasts of RA patients before diagnosis. Sci Rep 2018; 8:7370. [PMID: 29743579 PMCID: PMC5943364 DOI: 10.1038/s41598-018-24240-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/26/2018] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an important epigenetic modification that is known to be altered in rheumatoid arthritis synovial fibroblasts (RASF). Here, we compared the status of promoter DNA methylation of SF from patients with very early RA with SF from patients with resolving arthritis, fully established RA and from non-arthritic patients. DNA was hybridized to Infinium Human methylation 450k and 850k arrays and differential methylated genes and pathways were identified. We could identify a significant number of CpG sites that differed between the SF of different disease stages, showing that epigenetic changes in SF occur early in RA development. Principal component analysis confirmed that the different groups of SF were separated according to their DNA methylation state. Furthermore, pathway analysis showed that important functional pathways were altered in both very early and late RASF. By focusing our analysis on CpG sites in CpG islands within promoters, we identified genes that have significant hypermethylated promoters in very early RASF. Our data show that changes in DNA methylation differ in RASF compared to other forms of arthritis and occur at a very early, clinically yet unspecific stage of disease. The identified differential methylated genes might become valuable prognostic biomarkers for RA development.
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Affiliation(s)
- Emmanuel Karouzakis
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Zurich, CH-8952, Switzerland.
| | - Karim Raza
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, UK.,Sandwell and West Birmingham Hospitals NHS Trust, West Bromwich, B71 4HJ, UK
| | | | - Christopher D Buckley
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Steffen Gay
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Zurich, CH-8952, Switzerland
| | - Andrew Filer
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, UK.,University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2 GW, UK
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Zurich, CH-8952, Switzerland
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71
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You S, Koh JH, Leng L, Kim WU, Bucala R. The Tumor-Like Phenotype of Rheumatoid Synovium: Molecular Profiling and Prospects for Precision Medicine. Arthritis Rheumatol 2018; 70:637-652. [PMID: 29287304 PMCID: PMC5920713 DOI: 10.1002/art.40406] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022]
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by destructive hyperplasia of the synovium. Fibroblast-like synoviocytes (FLS) are a major component of synovial pannus and actively participate in the pathologic progression of RA. How rheumatoid FLS acquire and sustain such a uniquely aggressive phenotype remains poorly understood. We describe the current state of knowledge of the molecular alterations in rheumatoid FLS at the genomic, epigenomic, transcriptomic, proteomic, and metabolomic levels, which offers a means to reconstruct the pathways leading to rheumatoid pannus. Such data provide new pathologic insight and suggest means to more sensitively assess disease activity and response to therapy, as well as support new avenues for therapeutic development.
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Affiliation(s)
- Sungyong You
- Department of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jung Hee Koh
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea; Seoul, Korea
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary’s hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Lin Leng
- Department of Medicine, Section of Rheumatology, Yale University School of Medicine, New Haven, CT
| | - Wan-Uk Kim
- Center for Integrative Rheumatoid Transcriptomics and Dynamics, The Catholic University of Korea; Seoul, Korea
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary’s hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Richard Bucala
- Department of Medicine, Section of Rheumatology, Yale University School of Medicine, New Haven, CT
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72
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Stoll ML, Kau CH, Waite PD, Cron RQ. Temporomandibular joint arthritis in juvenile idiopathic arthritis, now what? Pediatr Rheumatol Online J 2018; 16:32. [PMID: 29695255 PMCID: PMC5918758 DOI: 10.1186/s12969-018-0244-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/04/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Arthritis involving the temporomandibular joint (TMJ) complicates 40 - 96% of cases of juvenile idiopathic arthritis (JIA), potentially leading to devastating changes to form and function. Optimal evaluation and management of this joint remains a matter of ongoing discussion. METHODS We performed a PubMed search for all articles with keywords "temporomandibular" and "arthritis", covering the dates 2002 through February 28, 2018. A separate PubMed search was performed for all articles with keywords "temporomandibular joint", "arthritis", and "treatment" covering the same dates. FINDINGS The TMJ is a particularly challenging joint to assess, both clinically and with imaging studies. Clinical assessment of the TMJ is hampered by the low sensitivity of joint pain as well as the absence of physical exam findings early in the disease process. As with all joints, plain radiography and computed tomography only detect arthritic sequelae. Additionally, there is mixed data on the sensitivity of ultrasound, leaving magnetic resonance imaging (MRI) as the optimal diagnostic modality. However, several recent studies have shown that non-arthritic children can have subtle findings on MRI consistent with TMJ arthritis, such as joint effusion and contrast enhancement. Consequently, there has been an intense effort to identify features that can be used to differentiate mild TMJ arthritis from normal TMJs, such as the ratio of the enhancement within the TMJ itself compared to the enhancement in surrounding musculature. With respect to treatment of TMJ arthritis, there is minimal prospective data on medical therapy of this complicated joint. Retrospective studies have suggested that the response to medical therapy of the TMJ may lag behind that of other joints, prompting use of intraarticular (IA) therapy. Although most studies have shown short-term effectiveness of corticosteroids, the long-term safety of this therapy on local growth as well as on the development of IA heterotopic bone have prompted recommendations to limit use of IA corticosteroids. Severe TMJ disease from JIA can also be managed non-operatively with splints in a growing child, as well as with surgery. CONCLUSION In this review, we summarize literature on the diagnosis and management of TMJ arthritis in JIA and suggest a diagnostic and therapeutic algorithm for children with refractory TMJ arthritis.
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Affiliation(s)
- Matthew L. Stoll
- 0000000106344187grid.265892.2Department of Pediatrics, University of Alabama at Birmingham (UAB), 1600 7th Avenue South, Children’s Park Place North Suite G10, Birmingham, 35233 AL USA
| | - Chung H. Kau
- 0000000106344187grid.265892.2Department of Orthodontics, UAB, 1720 2nd Avenue South, School of Dentistry Building 305, Birmingham, 35294 AL USA
| | - Peter D. Waite
- 0000000106344187grid.265892.2Department of Oral and Maxillofacial Surgery, UAB, 1720 2nd Avenue South, School of Dentistry Building 419, Birmingham, 35294 AL USA
| | - Randy Q. Cron
- 0000000106344187grid.265892.2Department of Pediatrics, University of Alabama at Birmingham (UAB), 1600 7th Avenue South, Children’s Park Place North Suite G10, Birmingham, 35233 AL USA
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73
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Carnero-Montoro E, Alarcón-Riquelme ME. Epigenome-wide association studies for systemic autoimmune diseases: The road behind and the road ahead. Clin Immunol 2018; 196:21-33. [PMID: 29605707 DOI: 10.1016/j.clim.2018.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 03/26/2018] [Indexed: 12/20/2022]
Abstract
Epigenetics is known to be an important mechanism in the pathogenesis of autoimmune diseases. Epigenetic variations can act as integrators of environmental and genetic exposures and propagate activated states in immune cells. Studying epigenetic alterations by means of genome-wide approaches promises to unravel novel molecular mechanisms related to disease etiology, disease progression, clinical manifestations and treatment responses. This paper reviews what we have learned in the last five years from epigenome-wide studies for three systemic autoimmune diseases, namely systemic lupus erythematosus, primary Sjögren's syndrome, and rheumatoid arthritis. We examine the degree of epigenetic sharing between different diseases and the possible mediating role of epigenetic associations in genetic and environmental risks. Finally, we also shed light into the use of epigenetic markers towards a better precision medicine regarding disease prediction, prevention and personalized treatment in systemic autoimmunity.
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Affiliation(s)
- Elena Carnero-Montoro
- Pfizer - University of Granada - Andalusian Government Center for Genomics and Oncological Research (GENYO), Granada, Spain.
| | - Marta E Alarcón-Riquelme
- Pfizer - University of Granada - Andalusian Government Center for Genomics and Oncological Research (GENYO), Granada, Spain; Unit of Inflammatory Chronic Diseases, Institute of Environmental Medicine, Karolinska Institutet, Solna, Sweden.
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74
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Peffers MJ, Balaskas P, Smagul A. Osteoarthritis year in review 2017: genetics and epigenetics. Osteoarthritis Cartilage 2018; 26:304-311. [PMID: 28989115 PMCID: PMC6292677 DOI: 10.1016/j.joca.2017.09.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The purpose of this review is to describe highlights from original research publications related to osteoarthritis (OA), epigenetics and genomics with the intention of recognising significant advances. DESIGN To identify relevant papers a Pubmed literature search was conducted for articles published between April 2016 and April 2017 using the search terms 'osteoarthritis' together with 'genetics', 'genomics', 'epigenetics', 'microRNA', 'lncRNA', 'DNA methylation' and 'histone modification'. RESULTS The search term OA generated almost 4000 references. Publications using the combination of descriptors OA and genetics provided the most references (82 references). However this was reduced compared to the same period in the previous year; 8.1-2.1% (expressed as a percentage of the total publications combining the terms OA and genetics). Publications combining the terms OA with genomics (29 references), epigenetics (16 references), long non-coding RNA (lncRNA) (11 references; including the identification of novel lncRNAs in OA), DNA methylation (21 references), histone modification (3 references) and microRNA (miR) (79 references) were reviewed. Potential OA therapeutics such as histone deacetylase (HDAC) inhibitors have been identified. A number of non-coding RNAs may also provide targets for future treatments. CONCLUSION There continues to be a year on year increase in publications researching miRs in OA (expressed as a percentage of the total publications), with a doubling over the last 4 years. An overview on the last year's progress within the fields of epigenetics and genomics with respect to OA will be given.
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Affiliation(s)
- M J Peffers
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - P Balaskas
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
| | - A Smagul
- Institute of Ageing and Chronic Disease, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
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75
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Goodman SM. Do Recent Trends in RA Surgery Reflect Success in Disease Management? J Rheumatol 2018; 45:147-149. [PMID: 29419445 DOI: 10.3899/jrheum.171056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Susan M Goodman
- Attending Rheumatologist, Division of Rheumatology, Hospital for Special Surgery, Professor of Clinical Medicine, Department of Medicine, Weill Cornell Medical School, New York, New York, USA.
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76
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Smolen JS, Aletaha D, Barton A, Burmester GR, Emery P, Firestein GS, Kavanaugh A, McInnes IB, Solomon DH, Strand V, Yamamoto K. Rheumatoid arthritis. Nat Rev Dis Primers 2018; 4:18001. [PMID: 29417936 DOI: 10.1038/nrdp.2018.1] [Citation(s) in RCA: 1337] [Impact Index Per Article: 222.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic, inflammatory, autoimmune disease that primarily affects the joints and is associated with autoantibodies that target various molecules including modified self-epitopes. The identification of novel autoantibodies has improved diagnostic accuracy, and newly developed classification criteria facilitate the recognition and study of the disease early in its course. New clinical assessment tools are able to better characterize disease activity states, which are correlated with progression of damage and disability, and permit improved follow-up. In addition, better understanding of the pathogenesis of RA through recognition of key cells and cytokines has led to the development of targeted disease-modifying antirheumatic drugs. Altogether, the improved understanding of the pathogenetic processes involved, rational use of established drugs and development of new drugs and reliable assessment tools have drastically altered the lives of individuals with RA over the past 2 decades. Current strategies strive for early referral, early diagnosis and early start of effective therapy aimed at remission or, at the least, low disease activity, with rapid adaptation of treatment if this target is not reached. This treat-to-target approach prevents progression of joint damage and optimizes physical functioning, work and social participation. In this Primer, we discuss the epidemiology, pathophysiology, diagnosis and management of RA.
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Affiliation(s)
- Josef S Smolen
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Daniel Aletaha
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics and NIHR Manchester Biomedical Research Centre, Manchester Academic Health Sciences Centre, The University of Manchester and Central Manchester Foundation Trust, Manchester, UK
| | - Gerd R Burmester
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Chapel Allerton Hospital, Leeds, UK.,NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California-San Diego School of Medicine, La Jolla, CA, USA
| | - Arthur Kavanaugh
- Division of Rheumatology, Allergy and Immunology, University of California-San Diego School of Medicine, La Jolla, CA, USA
| | - Iain B McInnes
- Institute of Infection Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Daniel H Solomon
- Division of Rheumatology, Brigham and Women's Hospital, Boston, MA, USA
| | - Vibeke Strand
- Division of Immunology and Rheumatology, Stanford University, Palo Alto, CA, USA
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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77
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Julià A, Absher D, López-Lasanta M, Palau N, Pluma A, Waite Jones L, Glossop JR, Farrell WE, Myers RM, Marsal S. Epigenome-wide association study of rheumatoid arthritis identifies differentially methylated loci in B cells. Hum Mol Genet 2018; 26:2803-2811. [PMID: 28475762 DOI: 10.1093/hmg/ddx177] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/02/2017] [Indexed: 12/20/2022] Open
Abstract
Epigenetic regulation of immune cell types could be critical for the development and maintenance of autoimmune diseases like rheumatoid arthritis (RA). B cells are highly relevant in RA, since patients express autoantibodies and depleting this cell type is a successful therapeutic approach. Epigenetic variation, such as DNA methylation, may mediate the pathogenic activity of B cells. In this study, we performed an epigenome-wide association study (EWAS) for RA with three different replication cohorts, to identify disease-specific alterations in DNA methylation in B cells. CpG methylation in isolated B lymphocytes was assayed on the Illumina HumanMethylation450 BeadChip in a discovery cohort of RA patients (N = 50) and controls (N = 75). Differential methylation was observed in 64 CpG sites (q < 0.05). Six biological pathways were also differentially methylated in RA B cells. Analysis in an independent cohort of patients (N = 15) and controls (N = 15) validated the association of 10 CpG sites located on 8 genes CD1C, TNFSF10, PARVG, NID1, DHRS12, ITPK1, ACSF3 and TNFRSF13C, and 2 intergenic regions. Differential methylation at the CBL signaling pathway was replicated. Using an additional case-control cohort (N = 24), the association between RA risk and CpGs cg18972751 at CD1C (P = 2.26 × 10-9) and cg03055671 at TNFSF10 (P = 1.67 × 10-8) genes was further validated. Differential methylation at genes CD1C, TNFSF10, PARVG, NID1, DHRS12, ITPK1, ACSF3, TNFRSF13C and intergenic region chr10p12.31 was replicated in a cohort of systemic lupus erythematosus (SLE) patients (N = 47) and controls (N = 56). Our results highlight genes that may drive the pathogenic activity of B cells in RA and suggest shared methylation patterns with SLE.
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Affiliation(s)
- Antonio Julià
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona 08035, Spain
| | - Devin Absher
- Absher Lab, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - María López-Lasanta
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona 08035, Spain
| | - Nuria Palau
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona 08035, Spain
| | - Andrea Pluma
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona 08035, Spain
| | - Lindsay Waite Jones
- Absher Lab, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - John R Glossop
- Institute for Science and Technology in Medicine, Keele University, Keele ST4?7QB, UK
| | - William E Farrell
- Institute for Science and Technology in Medicine, Keele University, Keele ST4?7QB, UK
| | - Richard M Myers
- Myers Lab, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona 08035, Spain
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FIRESTEIN GARYS. PATHOGENESIS OF RHEUMATOID ARTHRITIS: THE INTERSECTION OF GENETICS AND EPIGENETICS. TRANSACTIONS OF THE AMERICAN CLINICAL AND CLIMATOLOGICAL ASSOCIATION 2018; 129:171-182. [PMID: 30166712 PMCID: PMC6116585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rheumatoid arthritis is a synovial inflammatory disease marked by joint infiltration by immune cells and damage to the extracellular matrix. Although genetics plays a critical role in heritability and its pathogenesis, the relative lack of disease concordance in identical twins suggests that noncoding influences can affect risk and severity. Environmental stress, which can be reflected in the genome as altered epigenetic marks, also contributes to gene regulation and contributes to disease mechanisms. Studies on DNA methylation suggest that synovial cells, most notably fibroblast-like synoviocytes, are imprinted in rheumatoid arthritis with epigenetic marks and subsequently assume an aggressive phenotype. Even more interesting, the synoviocyte marks are not only disease specific but can vary depending on the joint of origin. Understanding the epigenetic landscape using unbiased methods can potentially identify nonobvious pathways and genes that that are responsible for synovial inflammation as well as the diversity of responses to targeted agents. The information can also be leveraged to identify novel therapeutic approaches.
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Affiliation(s)
- GARY S. FIRESTEIN
- Correspondence and reprint requests: Gary S. Firestein, MD, UCSD School of Medicine,
9500 Gilman Drive, La Jolla, California 92093858-822-0591
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79
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Bergstra SA, Chopra A, Saluja M, Vega-Morales D, Govind N, Huizinga TWJ, van der Helm-van Mil A. Evaluation of the joint distribution at disease presentation of patients with rheumatoid arthritis: a large study across continents. RMD Open 2017; 3:e000568. [PMID: 29299341 PMCID: PMC5729295 DOI: 10.1136/rmdopen-2017-000568] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/20/2017] [Accepted: 11/26/2017] [Indexed: 11/12/2022] Open
Abstract
Background Genetic and environmental risk factors for rheumatoid arthritis (RA) are population dependent and may affect disease expression. Therefore, we studied tender and swollen joint involvement in patients newly diagnosed with RA in four countries and performed a subanalysis within countries to assess whether the influence of autoantibody positivity affected disease expression. Methods Patients with symptom duration <2 years fulfilling the American College of Rheumatology/European League Against Rheumatism 2010 RA classification criteria were selected from METEOR (Measurement of Efficacy of Treatment in the Era of Outcome in Rheumatology), an international observational database, and the Dutch Leiden Early Arthritis Clinic. Indian (n=947), Mexican (n=141), South African (n=164) and Dutch (n=947) autoantibody-positive and negative patients with RA, matched by symptom duration, were studied for swollen and tender joint distribution. Results Between countries, the reported distribution of swollen joint distribution differed, with more knee synovitis in Mexico, South Africa and India compared with the Netherlands (37%, 36%, 30% and 13%) and more elbow (29%, 23%, 7%, 7%) and shoulder synovitis (21%, 11%, 0%, 1%) in Mexico and South Africa compared with India and the Netherlands. Since the number of autoantibody-negative patients in Mexico and South Africa was limited, Indian and Dutch autoantibody-positive and negative patients with RA were compared. The number of swollen and tender joints was higher in autoantibody-negative patients, but the overall distribution of involved joints was similar. Conclusion Joint involvement at diagnosis does not differ between autoantibody-positive and negative patients with RA in India and the Netherlands. However, joint involvement is reported differently across countries. More research is needed whether these differences are cultural and/or pathogenetic.
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Affiliation(s)
- Sytske Anne Bergstra
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arvind Chopra
- Department of Rheumatology, Center for Rheumatic Diseases, Pune, India
| | - Manjit Saluja
- Department of Rheumatology, Center for Rheumatic Diseases, Pune, India
| | - David Vega-Morales
- Department of Rheumatology, Universidad Autonoma de Nuevo Leon, San Nicolas de los Garza, Nuevo Leon, Mexico
| | - Nimmisha Govind
- Department of Rheumatology, University of the Witwatersrand, Johannesburg, South Africa
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
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80
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Abstract
Stromal cells like synovial fibroblasts gained great interest over the years, since it has become clear that they strongly influence their environment and neighbouring cells. The current review describes the role of synovial fibroblasts as cells of the innate immune system and expands on their involvement in inflammation and cartilage destruction in rheumatoid arthritis (RA). Furthermore, epigenetic changes in RA synovial fibroblasts and studies that focused on the identification of different subsets of synovial fibroblasts are discussed.
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Affiliation(s)
- Caroline Ospelt
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital and University of Zurich, Zurich, Switzerland
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81
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Li B, Chen X, Jiang Y, Yang Y, Zhong J, Zhou C, Hu H, Duan S. CCL2 promoter hypomethylation is associated with gout risk in Chinese Han male population. Immunol Lett 2017; 190:15-19. [DOI: 10.1016/j.imlet.2017.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 06/25/2017] [Accepted: 06/30/2017] [Indexed: 12/27/2022]
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82
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Ballestar E, Li T. New insights into the epigenetics of inflammatory rheumatic diseases. Nat Rev Rheumatol 2017; 13:593-605. [DOI: 10.1038/nrrheum.2017.147] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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83
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Abstract
Rheumatoid arthritis (RA) is the most common inflammatory arthropathy. The majority of evidence, derived from genetics, tissue analyses, models, and clinical studies, points to an immune-mediated etiology associated with stromal tissue dysregulation that together propogate chronic inflammation and articular destruction. A pre-RA phase lasting months to years may be characterized by the presence of circulating autoantibodies, increasing concentration and range of inflammatory cytokines and chemokines, and altered metabolism. Clinical disease onset comprises synovitis and systemic comorbidities affecting the vasculature, metabolism, and bone. Targeted immune therapeutics and aggressive treatment strategies have substantially improved clinical outcomes and informed pathogenetic understanding, but no cure as yet exists. Herein we review recent data that support intriguing models of disease pathogenesis. They allude to the possibility of restoration of immunologic homeostasis and thus a state of tolerance associated with drug-free remission. This target represents a bold vision for the future of RA therapeutics.
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Affiliation(s)
| | - Iain B McInnes
- Institute of Infection Immunity and Inflammation, University of Glasgow, Glasgow G128QQ, UK.
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84
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Le Rossignol S, Ketheesan N, Haleagrahara N. Redox-sensitive transcription factors play a significant role in the development of rheumatoid arthritis. Int Rev Immunol 2017; 37:129-143. [PMID: 28898138 DOI: 10.1080/08830185.2017.1363198] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease which is associated with significant morbidity. Redox sensitive transcription factors including NF-κB, HIF, AP-1, and Nrf2 are intimately involved in the pathogenesis of RA. The treatment of this disease is limited by the elusive nature of the pathogenesis of RA. NF-κB is crucial for the maturation of immune cells as well as production of TNFα and MMPs, which escalate RA. HIF is essential for activation of inflammatory cells, angiogenesis and pannus formation in RA. AP-1 regulates cytokine and MMP production as well as synovial hyperplasia which are key processes in RA. Nrf2 is involved with chondrogenesis, osteoblastogenesis, prostaglandin secretion and ROS production in RA. Targeting two or more of these transcription factors may result in increased efficacy than either therapy in isolation. This review will highlight the control specific mediators on these transcription factors, the subsequent effect of these transcription factors once activated, and then mesh this with the pathogenesis of RA. The elucidation of key transcription factor regulation in the pathogenesis of RA may highlight the novel therapy interventions which may prove to have a greater efficacy than those therapies currently available.
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Affiliation(s)
- Scott Le Rossignol
- a College of Medicine and Dentistry , James Cook University Townsville , Queensland , Australia
| | - Natkunam Ketheesan
- b Biomedicine, College of Public Health, Medical and Veterinary Sciences , James Cook University , Townsville , Queensland , Australia.,c Australian Institute of Tropical Health and Medicine , James Cook University , Townsville , Queensland , Australia
| | - Nagaraja Haleagrahara
- b Biomedicine, College of Public Health, Medical and Veterinary Sciences , James Cook University , Townsville , Queensland , Australia.,c Australian Institute of Tropical Health and Medicine , James Cook University , Townsville , Queensland , Australia
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85
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Nair N, Wilson AG, Barton A. DNA methylation as a marker of response in rheumatoid arthritis. Pharmacogenomics 2017; 18:1323-1332. [PMID: 28836487 DOI: 10.2217/pgs-2016-0195] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Rheumatoid arthritis (RA) is a complex disease affecting approximately 0.5-1% of the population. While there are effective biologic therapies, in up to 40% of patients, disease activity remains inadequately controlled. Therefore, identifying factors that predict, prior to the initiation of therapy, which patients are likely to respond best to which treatment is a research priority and DNA methylation is increasingly being explored as a potential theranostic biomarker. DNA methylation is thought to play a role in RA disease pathogenesis and in mediating the relationship between genetic variants and patient outcomes. The role of DNA methylation has been most extensively explored in cancer medicine, where it has been shown to be predictive of treatment response. Studies in RA, however, are in their infancy and, while showing promise, further investigation in well-powered studies is warranted.
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Affiliation(s)
- Nisha Nair
- Arthritis Research UK Centre for Genetics & Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK
| | - Anthony G Wilson
- University College Dublin School of Medicine & Medical Science & Conway Institute, Dublin, Ireland
| | - Anne Barton
- Arthritis Research UK Centre for Genetics & Genomics, Centre for Musculoskeletal Research, University of Manchester, Manchester, UK.,NIHR Manchester Musculoskeletal BRU, Central Manchester Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
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87
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Abstract
Rheumatic diseases follow a characteristic anatomical pattern of joint and organ involvement. This Review explores three interconnected mechanisms that might be involved in the predilection of specific joints for developing specific forms of arthritis: site-specific local cell types that drive disease; systemic triggers that affect local cell types; and site-specific exogenous factors, such as focal mechanical stress, that activate cells locally. The embryonic development of limbs and joints is also relevant to the propensity of certain joints to develop arthritis. Additionally, location-specific homeostasis and disease occurs in skin and blood vessels, thereby extending the concept of site-specificity in human diseases beyond rheumatology. Acknowledging the importance of site-specific parameters increases the complexity of current disease paradigms and brings us closer to understanding why particular disease processes manifest at a particular location.
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88
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Wang B, Shao X, Song R, Xu D, Zhang JA. The Emerging Role of Epigenetics in Autoimmune Thyroid Diseases. Front Immunol 2017; 8:396. [PMID: 28439272 PMCID: PMC5383710 DOI: 10.3389/fimmu.2017.00396] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/21/2017] [Indexed: 12/15/2022] Open
Abstract
Autoimmune thyroid diseases (AITD) are a group of both B cell- and T cell-mediated organ-specific autoimmune diseases. Graves’ disease and Hashimoto thyroiditis are the two main clinical presentations of AITD. Both genetic and environmental factors have important roles in the development of AITD. Epigenetics have been considered to exert key roles in integrating those genetic and environmental factors, and epigenetic modifications caused by environmental factors may drive genetically susceptibility individuals to develop AITD. Recent studies on the epigenetics of AITD have provided some novel insights into the pathogenesis of AITD. The aim of this review is to provide an overview of recent advances in the epigenetic mechanisms of AITD, such as DNA methylation, histone modifications, and non-coding RNAs. This review highlights the key roles of epigenetics in the pathogenesis of AITD and potential clinical utility. However, the epigenetic roles in AITD are still not fully elucidated, and more researches are needed to provide further deeper insights into the roles of epigenetics in AITD and to uncover new therapeutic targets. Although there are many studies assessing the epigenetic modifications in AITD patients, the clinical utility of epigenetics in AITD remains poorly defined. More studies are needed to identify the underlying epigenetic modifications that can contribute to accurate diagnosis of AITD, adequate choice of treatment approach, and precise prediction of treatment outcomes.
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Affiliation(s)
- Bin Wang
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai, China.,Department of Rheumatology and Immunology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Xiaoqing Shao
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai, China.,Department of Rheumatology and Immunology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Ronghua Song
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai, China.,Department of Rheumatology and Immunology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Donghua Xu
- Department of Rheumatology and Immunology, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jin-An Zhang
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai, China.,Department of Rheumatology and Immunology, Jinshan Hospital of Fudan University, Shanghai, China
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89
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Frank-Bertoncelj M, Trenkmann M, Klein K, Karouzakis E, Rehrauer H, Bratus A, Kolling C, Armaka M, Filer A, Michel BA, Gay RE, Buckley CD, Kollias G, Gay S, Ospelt C. Epigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions. Nat Commun 2017; 8:14852. [PMID: 28332497 PMCID: PMC5376654 DOI: 10.1038/ncomms14852] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/02/2017] [Indexed: 01/15/2023] Open
Abstract
A number of human diseases, such as arthritis and atherosclerosis, include characteristic pathology in specific anatomical locations. Here we show transcriptomic differences in synovial fibroblasts from different joint locations and that HOX gene signatures reflect the joint-specific origins of mouse and human synovial fibroblasts and synovial tissues. Alongside DNA methylation and histone modifications, bromodomain and extra-terminal reader proteins regulate joint-specific HOX gene expression. Anatomical transcriptional diversity translates into joint-specific synovial fibroblast phenotypes with distinct adhesive, proliferative, chemotactic and matrix-degrading characteristics and differential responsiveness to TNF, creating a unique microenvironment in each joint. These findings indicate that local stroma might control positional disease patterns not only in arthritis but in any disease with a prominent stromal component. Arthritis affects different joints variably despite systemic inflammatory cues. Here the authors show anatomical differences in the transcriptome, epigenome and function of synovial fibroblasts that might affect susceptibility to site-specific joint diseases.
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Affiliation(s)
- Mojca Frank-Bertoncelj
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Michelle Trenkmann
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Kerstin Klein
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Emmanuel Karouzakis
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anna Bratus
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | - Maria Armaka
- Division of Immunology, Biomedical Sciences Research Center 'Alexander Fleming', 34, Fleming Street, 16672 Vari, Attica, Greece
| | - Andrew Filer
- Institute of Inflammation and Ageing (IIA), University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WB, UK
| | - Beat A Michel
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Renate E Gay
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland
| | - Christopher D Buckley
- Institute of Inflammation and Ageing (IIA), University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WB, UK
| | - George Kollias
- Division of Immunology, Biomedical Sciences Research Center 'Alexander Fleming', 34, Fleming Street, 16672 Vari, Attica, Greece.,Department of Experimental Physiology, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Goudi, Athens, Greece
| | - Steffen Gay
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland.,Center of Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Caroline Ospelt
- Center of Experimental Rheumatology, University Hospital Zurich and University of Zurich, Wagistrasse 14, 8952 Schlieren, Zurich, Switzerland.,Center of Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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90
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Doody KM, Bottini N, Firestein GS. Epigenetic alterations in rheumatoid arthritis fibroblast-like synoviocytes. Epigenomics 2017; 9:479-492. [PMID: 28322585 DOI: 10.2217/epi-2016-0151] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rheumatoid arthritis is an immune-mediated disease that primarily affects diarthrodial joints. Susceptibility and severity of this disease are influenced by nongenetic factors, such as environmental stress, suggesting an important role of epigenetic changes. In this review, we summarize the epigenetic changes (DNA methylation, histone modification and miRNA expression) in fibroblast-like synoviocytes, which are the joint-lining mesenchymal cells that play an important role in joint inflammation and damage. We also review the effects of these epigenetic changes on rheumatoid arthritis pathogenesis and discuss their therapeutic potential.
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Affiliation(s)
- Karen M Doody
- Grenfell Campus, Memorial University of Newfoundland, Corner Brook, Newfoundland, Canada
| | - Nunzio Bottini
- Division of Rheumatology, Allergy & Immunology, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy & Immunology, University of California, San Diego School of Medicine, La Jolla, CA, USA
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91
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Frank-Bertoncelj M, Klein K, Gay S. Interplay between genetic and epigenetic mechanisms in rheumatoid arthritis. Epigenomics 2017; 9:493-504. [PMID: 28322583 DOI: 10.2217/epi-2016-0142] [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: 02/07/2023] Open
Abstract
Genetic and environmental factors contribute to the risk for rheumatoid arthritis (RA), with epigenetics serving as a possible interface through which risk factors contribute to RA. High-throughput technologies for interrogating genome and epigenome, and the availability of genetic and epigenetic datasets across a diversity of cell types, enable the identification of candidate causal genetic variants for RA to study their function in core RA processes. To date, RA risk variants were studied in the immune cells but not joint resident cells, for example, synovial fibroblasts. Synovial fibroblasts from different joints are distinct, anatomically specialized cells, defined by joint-specific transcriptomes, epigenomes and phenotypes. Cell type-specific analysis of epigenetic changes, together with genetic fine mapping and interrogation of chromatin 3D interactions may identify new disease relevant pathways, potential therapeutic targets and biomarkers for RA progression or therapy response.
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Affiliation(s)
| | - Kerstin Klein
- Center of Experimental Rheumatology, University Hospital Zurich, Switzerland
| | - Steffen Gay
- Center of Experimental Rheumatology, University Hospital Zurich, Switzerland
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92
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Malmström V, Catrina AI, Klareskog L. The immunopathogenesis of seropositive rheumatoid arthritis: from triggering to targeting. Nat Rev Immunol 2016; 17:60-75. [PMID: 27916980 DOI: 10.1038/nri.2016.124] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Patients with rheumatoid arthritis can be divided into two major subsets characterized by the presence versus absence of antibodies to citrullinated protein antigens (ACPAs) and of rheumatoid factor (RF). The antibody-positive subset of disease, also known as seropositive rheumatoid arthritis, constitutes approximately two-thirds of all cases of rheumatoid arthritis and generally has a more severe disease course. ACPAs and RF are often present in the blood long before any signs of joint inflammation, which suggests that the triggering of autoimmunity may occur at sites other than the joints (for example, in the lung). This Review summarizes recent progress in our understanding of this gradual disease development in seropositive patients. We also emphasize the implications of this new understanding for the development of preventive and therapeutic strategies. Similar temporal and spatial separation of immune triggering and clinical manifestations, with novel opportunities for early intervention, may also occur in other immune-mediated diseases.
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Affiliation(s)
- Vivianne Malmström
- Rheumatology Unit, Department of Medicine at Solna, Karolinska University Hospital, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Anca I Catrina
- Rheumatology Unit, Department of Medicine at Solna, Karolinska University Hospital, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine at Solna, Karolinska University Hospital, Karolinska Institute, 171 76 Stockholm, Sweden
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93
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New insights into site-specific variations in RA and OA. Nat Rev Rheumatol 2016; 12:506-7. [DOI: 10.1038/nrrheum.2016.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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