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Lee H, Machado CRL, Hammaker D, Choi E, Prideaux EB, Wang W, Boyle DL, Firestein GS. Joint-specific regulation of homeobox D10 expression in rheumatoid arthritis fibroblast-like synoviocytes. PLoS One 2024; 19:e0304530. [PMID: 38829908 PMCID: PMC11146700 DOI: 10.1371/journal.pone.0304530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Rheumatoid arthritis (RA) is a systemic immune-mediated disease characterized by joint inflammation and destruction. The disease typically affects small joints in the hands and feet, later progressing to involve larger joints such as the knees, shoulders, and hips. While the reasons for these joint-specific differences are unclear, distinct epigenetic patterns associated with joint location have been reported. In this study, we evaluated the unique epigenetic landscapes of fibroblast-like synoviocytes (FLS) from hip and knee synovium in RA patients, focusing on the expression and regulation of Homeobox (HOX) transcription factors. These highly conserved genes play a critical role in embryonic development and are known to maintain distinct expression patterns in various adult tissues. We found that several HOX genes, especially HOXD10, were differentially expressed in knee FLS compared with hip FLS. Epigenetic differences in chromatin accessibility and histone marks were observed in HOXD10 promoter between knee and hip FLS. Histone modification, particularly histone acetylation, was identified as an important regulator of HOXD10 expression. To understand the mechanism of differential HOXD10 expression, we inhibited histone deacetylases (HDACs) with small molecules and siRNA. We found that HDAC1 blockade or deficiency normalized the joint-specific HOXD10 expression patterns. These observations suggest that epigenetic differences, specifically histone acetylation related to increased HDAC1 expression, play a crucial role in joint-specific HOXD10 expression. Understanding these mechanisms could provide insights into the regional aspects of RA and potentially lead to therapeutic strategies targeting specific patterns of joint involvement during the course of disease.
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Affiliation(s)
- Hyeonjeong Lee
- Division of Rheumatology, Allergy and Immunology, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Camilla R. L. Machado
- Division of Rheumatology, Allergy and Immunology, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Deepa Hammaker
- Division of Rheumatology, Allergy and Immunology, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Eunice Choi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Edward B. Prideaux
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - David L. Boyle
- Division of Rheumatology, Allergy and Immunology, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Gary S. Firestein
- Division of Rheumatology, Allergy and Immunology, School of Medicine, University of California San Diego, La Jolla, California, United States of America
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2
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Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Al Suqri M, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nat Commun 2024; 15:4650. [PMID: 38821936 PMCID: PMC11143375 DOI: 10.1038/s41467-024-48620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. Here, we examine genome-wide open chromatin at single-cell resolution in 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identify 24 chromatin classes and predict their associated transcription factors, including a CD8 + GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating with an RA tissue transcriptional atlas, we propose that these chromatin classes represent 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrate the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance, as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
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Affiliation(s)
- Kathryn Weinand
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine Division of Rheumatology and Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Majd Al Suqri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
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3
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Choi E, Machado CR, Okano T, Boyle D, Wang W, Firestein GS. Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity. JCI Insight 2024; 9:e179392. [PMID: 38781031 DOI: 10.1172/jci.insight.179392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Abstract
The mechanisms responsible for the distribution and severity of joint involvement in rheumatoid arthritis (RA) are not known. To explore whether site-specific fibroblast-like synoviocyte (FLS) biology might be associated with location-specific synovitis and explain the predilection for hand (wrist/metacarpal phalangeal joints) involvement in RA, we generated transcriptomic and chromatin accessibility data from FLS to identify the transcription factors and pathways. Networks were constructed by integration of chromatin accessibility and gene expression data. Analysis revealed joint-specific patterns of FLS phenotype, with proliferative, migratory, proinflammatory, and matrix-degrading characteristics observed in resting FLS derived from the hand joints compared with hip or knee. TNF stimulation amplified these differences, with greater enrichment of proinflammatory and proliferative genes in hand FLS compared with hip and knee FLS. Hand FLS also had the greatest expression of markers associated with an "activated" state relative to the "resting" state, with the greatest cytokine and MMP expression in TNF-stimulated hand FLS. Predicted differences in proliferation and migration were biologically validated with hand FLS exhibiting greater migration and cell growth than hip or knee FLS. Distinctive joint-specific FLS biology associated with a more aggressive inflammatory response might contribute to the distribution and severity of joint involvement in RA.
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Affiliation(s)
| | | | | | | | - Wei Wang
- Department of Chemistry and Biochemistry
- Department of Cellular and Molecular Medicine, UCSD, La Jolla, California, USA
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4
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Chang MH, Fuhlbrigge RC, Nigrovic PA. Joint-specific memory, resident memory T cells and the rolling window of opportunity in arthritis. Nat Rev Rheumatol 2024; 20:258-271. [PMID: 38600215 PMCID: PMC11295581 DOI: 10.1038/s41584-024-01107-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
In rheumatoid arthritis, juvenile idiopathic arthritis and other forms of inflammatory arthritis, the immune system targets certain joints but not others. The pattern of joints affected varies by disease and by individual, with flares most commonly involving joints that were previously inflamed. This phenomenon, termed joint-specific memory, is difficult to explain by systemic immunity alone. Mechanisms of joint-specific memory include the involvement of synovial resident memory T cells that remain in the joint during remission and initiate localized disease recurrence. In addition, arthritis-induced durable changes in synovial fibroblasts and macrophages can amplify inflammation in a site-specific manner. Together with ongoing systemic processes that promote extension of arthritis to new joints, these local factors set the stage for a stepwise progression in disease severity, a paradigm for arthritis chronicity that we term the joint accumulation model. Although durable drug-free remission through early treatment remains elusive for most forms of arthritis, the joint accumulation paradigm defines new therapeutic targets, emphasizes the importance of sustained treatment to prevent disease extension to new joints, and identifies a rolling window of opportunity for altering the natural history of arthritis that extends well beyond the initiation phase of disease.
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Affiliation(s)
- Margaret H Chang
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Robert C Fuhlbrigge
- Department of Paediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Peter A Nigrovic
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA.
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5
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Gao Y, Zhang Y, Liu X. Rheumatoid arthritis: pathogenesis and therapeutic advances. MedComm (Beijing) 2024; 5:e509. [PMID: 38469546 PMCID: PMC10925489 DOI: 10.1002/mco2.509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by the unresolved synovial inflammation for tissues-destructive consequence, which remains one of significant causes of disability and labor loss, affecting about 0.2-1% global population. Although treatments with disease-modifying antirheumatic drugs (DMARDs) are effective to control inflammation and decrease bone destruction, the overall remission rates of RA still stay at a low level. Therefore, uncovering the pathogenesis of RA and expediting clinical transformation are imminently in need. Here, we summarize the immunological basis, inflammatory pathways, genetic and epigenetic alterations, and metabolic disorders in RA, with highlights on the abnormality of immune cells atlas, epigenetics, and immunometabolism. Besides an overview of first-line medications including conventional DMARDs, biologics, and small molecule agents, we discuss in depth promising targeted therapies under clinical or preclinical trials, especially epigenetic and metabolic regulators. Additionally, prospects on precision medicine based on synovial biopsy or RNA-sequencing and cell therapies of mesenchymal stem cells or chimeric antigen receptor T-cell are also looked forward. The advancements of pathogenesis and innovations of therapies in RA accelerates the progress of RA treatments.
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Affiliation(s)
- Ying Gao
- Department of RheumatologyChanghai HospitalNaval Medical UniversityShanghaiChina
| | - Yunkai Zhang
- Naval Medical CenterNaval Medical UniversityShanghaiChina
| | - Xingguang Liu
- National Key Laboratory of Immunity & InflammationNaval Medical UniversityShanghaiChina
- Department of Pathogen BiologyNaval Medical UniversityShanghaiChina
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6
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Choi E, Machado CRL, Okano T, Boyle D, Wang W, Firestein GS. Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575379. [PMID: 38293079 PMCID: PMC10827126 DOI: 10.1101/2024.01.12.575379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The mechanisms responsible for the distribution and severity of joint involvement in rheumatoid arthritis (RA) are not known. To explore whether site-specific FLS biology might be associated with location-specific synovitis and explain the predilection for hand (wrist/metacarpal phalangeal joints) involvement in RA, we generated transcriptomic and chromatin accessibility data from FLS to identify the transcription factors (TFs) and pathways. Networks were constructed by integration of chromatin accessibility and gene expression data. Analysis revealed joint-specific patterns of FLS phenotype, with proliferative, migratory, proinflammatory, and matrix-degrading characteristics observed in resting FLS derived from the hand joints compared with hip or knee. TNF-stimulation amplified these differences, with greater enrichment of proinflammatory and proliferative genes in hand FLS compared with hip and knee FLS. Hand FLS also had the greatest expression of markers associated with an 'activated' state relative to the 'resting' state, with the greatest cytokine and MMP expression in TNF-stimulated hand FLS. Predicted differences in proliferation and migration were biologically validated with hand FLS exhibiting greater migration and cell growth than hip or knee FLS. Distinctive joint-specific FLS biology associated with a more aggressive inflammatory response might contribute to the distribution and severity of joint involvement in RA.
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7
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Hageman I, Mol F, Atiqi S, Joustra V, Sengul H, Henneman P, Visman I, Hakvoort T, Nurmohamed M, Wolbink G, Levin E, Li Yim AY, D’Haens G, de Jonge WJ. Novel DNA methylome biomarkers associated with adalimumab response in rheumatoid arthritis patients. Front Immunol 2023; 14:1303231. [PMID: 38187379 PMCID: PMC10771853 DOI: 10.3389/fimmu.2023.1303231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Background and aims Rheumatoid arthritis (RA) patients are currently treated with biological agents mostly aimed at cytokine blockade, such as tumor necrosis factor-alpha (TNFα). Currently, there are no biomarkers to predict therapy response to these agents. Here, we aimed to predict response to adalimumab (ADA) treatment in RA patients using DNA methylation in peripheral blood (PBL). Methods DNA methylation profiling on whole peripheral blood from 92 RA patients before the start of ADA treatment was determined using Illumina HumanMethylationEPIC BeadChip array. After 6 months, treatment response was assessed according to the European Alliance of Associations for Rheumatology (EULAR) criteria for disease activity. Patients were classified as responders (Disease Activity Score in 28 Joints (DAS28) < 3.2 or decrease of 1.2 points) or as non-responders (DAS28 > 5.1 or decrease of less than 0.6 points). Machine learning models were built through stability-selected gradient boosting to predict response prior to ADA treatment with predictor DNA methylation markers. Results Of the 94 RA patients, we classified 49 and 43 patients as responders and non-responders, respectively. We were capable of differentiating responders from non-responders with a high performance (area under the curve (AUC) 0.76) using a panel of 27 CpGs. These classifier CpGs are annotated to genes involved in immunological and pathophysiological pathways related to RA such as T-cell signaling, B-cell pathology, and angiogenesis. Conclusion Our findings indicate that the DNA methylome of PBL provides discriminative capabilities in discerning responders and non-responders to ADA treatment and may therefore serve as a tool for therapy prediction.
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Affiliation(s)
- Ishtu Hageman
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Femke Mol
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Sadaf Atiqi
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center, Vrije Universiteit (VU) University Medical Center, Amsterdam, Netherlands
| | - Vincent Joustra
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Hilal Sengul
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Ingrid Visman
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center, Vrije Universiteit (VU) University Medical Center, Amsterdam, Netherlands
| | - Theodorus Hakvoort
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Mike Nurmohamed
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center, Vrije Universiteit (VU) University Medical Center, Amsterdam, Netherlands
| | - Gertjan Wolbink
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center, Vrije Universiteit (VU) University Medical Center, Amsterdam, Netherlands
| | - Evgeni Levin
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Horaizon BV, Delft, Netherlands
| | - Andrew Y.F. Li Yim
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Geert D’Haens
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
- Department of Surgery, University of Bonn, Bonn, Germany
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Ren L, Cheng SG, Kang PC, Li TF, Li X, Xiao JZ, Jiang D. Silenced LASP1 interacts with DNMT1 to promote TJP2 expression and attenuate articular cartilage injury in mice by suppressing TJP2 methylation. Kaohsiung J Med Sci 2023; 39:1096-1105. [PMID: 37578083 DOI: 10.1002/kjm2.12738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/03/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
To investigate the regulatory mechanisms and effects of LIM and SH3 protein 1 (LASP1) on osteoarthritis (OA). IL-1β was used to induce OA in cell models. Viability and apoptosis of chondrocytes were assessed. The expressions of tumor necrsis factor-α (TNF-α) and IL-6 were measured by ELISA kit, and Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blot were performed to test the expression of related proteins. The STRING database was used to predict the relationship between LASP1 and DNA methyltransferase 1 (DNMT1). The tight junction protein 2 (TJP2) and Gene Expression Omnibus data were analyzed for differential OA genes. Methylation-specific PCR detected methylation of the TJP2 promoter region, and chromatin immunoprecipitation detected the enrichment of DNMT1 in the TJP2 promoter region. Safranin O-Fast Green staining and hematoxylin and eosin staining were used to determine the OARSI score and evaluate the pathological conditions of the joint tissues. LASP1 was highly expressed in IL-1β-induced cell models. Silencing of LASP1 promoted chondrocyte proliferation and expression of Collagen II and Aggrecan and inhibited chondrocyte apoptosis, inflammatory factors, and matrix metalloprotein expression. TJP2 is weakly expressed in OA models, and LASP1 promotes methylation of the TJP2 promoter region by interacting with DNMT1. Silencing of LASP1 attenuated IL-1β-induced chondrocyte degeneration by promoting TJP2 expression. Similarly, silencing LASP1 promotes TJP2 expression to alleviate articular cartilage injury in mice with OA. Silencing of LASP1 inhibited the methylation of the TJP2 promoter region by interacting with DNMT1, thereby alleviating articular cartilage damage in OA mice.
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Affiliation(s)
- Lian Ren
- Department of Orthopedic Surgery, Loudi Central Hospital, Loudi, China
| | - Shi-Gao Cheng
- Department of Orthopedic Surgery, Loudi Central Hospital, Loudi, China
| | - Peng-Cheng Kang
- Department of Orthopedic Surgery, Loudi Central Hospital, Loudi, China
| | - Teng-Fei Li
- Department of Orthopedic Surgery, Loudi Central Hospital, Loudi, China
| | - Xun Li
- Department of Orthopedic Surgery, Loudi Central Hospital, Loudi, China
| | - Jiong-Zhe Xiao
- Department of Orthopedic Surgery, Loudi Central Hospital, Loudi, China
| | - Dong Jiang
- Department of Orthopedic Surgery, Loudi Central Hospital, Loudi, China
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9
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Filipowicz G, Wajda A, Stypińska B, Kmiołek T, Felis-Giemza A, Stańczyk S, Czuszyńska Z, Walczyk M, Olesińska M, Paradowska-Gorycka A. Mixed Connective Tissue Disease as Different Entity: Global Methylation Aspect. Int J Mol Sci 2023; 24:15495. [PMID: 37895173 PMCID: PMC10607312 DOI: 10.3390/ijms242015495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Mixed connective tissue disease (MCTD) is a very rare disorder that belongs in the rare and clinically multifactorial groups of diseases. The pathogenesis of MCTD is still unclear. The best understood epigenetic alteration is DNA methylation whose role is to regulate gene expression. In the literature, there are ever-increasing assumptions that DNA methylation can be one of the possible reasons for the development of Autoimmune Connective Tissue Diseases (ACTDs) such as systemic sclerosis (SSc) and systemic lupus erythematosus (SLE). The aim of this study was to define the global DNA methylation changes between MCTD and other ACTDs patients in whole blood samples. The study included 54 MCTD patients, 43 SSc patients, 45 SLE patients, and 43 healthy donors (HC). The global DNA methylation level was measured by ELISA. Although the global DNA methylation was not significantly different between MCTD and control, we observed that hypomethylation distinguishes the MCTD patients from the SSc and SLE patients. The present analysis revealed a statistically significant difference of global methylation between SLE and MCTD (p < 0.001), SLE and HC (p = 0.008), SSc and MCTD (p ≤ 0.001), and SSc and HC (p < 0.001), but neither between MCTD and HC (p = 0.09) nor SSc and SLE (p = 0.08). The highest % of global methylation (median, IQR) has been observed in the group of patients with SLE [0.73 (0.43, 1.22] and SSc [0,91 (0.59, 1.50)], whereas in the MCTD [0.29 (0.20, 0.54)], patients and healthy subjects [0.51 (0.24, 0.70)] were comparable. In addition, our study provided evidence of different levels of global DNA methylation between the SSc subtypes (p = 0.01). Our study showed that patients with limited SSc had a significantly higher global methylation level when compared to diffuse SSc. Our data has shown that the level of global DNA methylation may not be a good diagnostic marker to distinguish MCTD from other ACTDs. Our research provides the groundwork for a more detailed examination of the significance of global DNA methylation as a distinguishing factor in patients with MCTD compared to other ACTDs patients.
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Affiliation(s)
- Gabriela Filipowicz
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Barbara Stypińska
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Tomasz Kmiołek
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Anna Felis-Giemza
- Biologic Therapy Center, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland (S.S.)
| | - Sandra Stańczyk
- Biologic Therapy Center, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland (S.S.)
| | - Zenobia Czuszyńska
- Department of Rheumatology, Clinical Immunology, Geriatrics and Internal Medicine, Medical University of Gdansk, Smulochowskiego 17, 80-214 Gdansk, Poland
| | - Marcela Walczyk
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland
| | - Marzena Olesińska
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
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10
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Vijaykrishnaraj M, Patil P, Ghate SD, Bhandary AK, Haridas VM, Shetty P. Efficacy of HDAC inhibitors and epigenetic modulation in the amelioration of synovial inflammation, cellular invasion, and bone erosion in rheumatoid arthritis pathogenesis. Int Immunopharmacol 2023; 122:110644. [PMID: 37454631 DOI: 10.1016/j.intimp.2023.110644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Rheumatoid arthritis (RA), an auto-immune disorder affected 1 % of the population around the globe. The pathophysiology of RA is highly concerted process including synovial hyperplasia, pannus formation, bone erosion, synovial cell infiltration in joints, and cartilage destruction. However, recent reports suggest that epigenetics play a pivotal role in the formation and organization of immune response in RA. Particularly, altered DNA methylation and impaired microRNA (miRNA) were detected in several immune cells of RA patients, such as T regulatory cells, fibroblast-like synoviocytes, and blood mononuclear cells. All these processes can be reversed by regulating the ubiquitous or tissue-based expression of histone deacetylases (HDACs) to counteract and terminate them. Hence, HDAC inhibitors (HDACi) could serve as highly potent anti-inflammatory regulators in the uniform amelioration of inflammation. Therefore, this review encompasses the information mainly focussing on the epigenetic modulation in RA pathogenesis and the efficacy of HDACi as an alternative therapeutic option for RA treatment. Overall, these studies have reported the targeting of HDAC1, 2 & 6 molecules would attenuate synoviocyte inflammation, cellular invasion, and bone erosion. Further, the inhibitors such as trichostatin A, suberoyl bis-hydroxamic acid, suberoyl anilide hydroxamic acid, and other compounds are found to attenuate synovial inflammatory immune response, clinical arthritis score, paw swelling, bone erosion, and cartilage destruction. Insight to view this, more clinical studies are required to determine the efficacy of HDACi in RA treatment and to unravel the underlying molecular mechanisms.
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Affiliation(s)
- M Vijaykrishnaraj
- Central Research Laboratory, K.S. Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, India
| | - Prakash Patil
- Central Research Laboratory, K.S. Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, India
| | - Sudeep D Ghate
- Center for Bioinformatics, K.S. Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, India
| | - Adithi K Bhandary
- Department of General Medicine, K.S. Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, India
| | - Vikram M Haridas
- Arthritis Super Speciality Centre, Hubli 580020, Karnataka, India
| | - Praveenkumar Shetty
- Central Research Laboratory, K.S. Hegde Medical Academy, NITTE (Deemed to be University), Deralakatte, Mangaluru 575018, India.
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11
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Wang SS, Lewis MJ, Pitzalis C. DNA Methylation Signatures of Response to Conventional Synthetic and Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) in Rheumatoid Arthritis. Biomedicines 2023; 11:1987. [PMID: 37509625 PMCID: PMC10377185 DOI: 10.3390/biomedicines11071987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Rheumatoid arthritis (RA) is a complex condition that displays heterogeneity in disease severity and response to standard treatments between patients. Failure rates for conventional, target synthetic, and biologic disease-modifying rheumatic drugs (DMARDs) are significant. Although there are models for predicting patient response, they have limited accuracy, require replication/validation, or for samples to be obtained through a synovial biopsy. Thus, currently, there are no prediction methods approved for routine clinical use. Previous research has shown that genetics and environmental factors alone cannot explain the differences in response between patients. Recent studies have demonstrated that deoxyribonucleic acid (DNA) methylation plays an important role in the pathogenesis and disease progression of RA. Importantly, specific DNA methylation profiles associated with response to conventional, target synthetic, and biologic DMARDs have been found in the blood of RA patients and could potentially function as predictive biomarkers. This review will summarize and evaluate the evidence for DNA methylation signatures in treatment response mainly in blood but also learn from the progress made in the diseased tissue in cancer in comparison to RA and autoimmune diseases. We will discuss the benefits and challenges of using DNA methylation signatures as predictive markers and the potential for future progress in this area.
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Affiliation(s)
- Susan Siyu Wang
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
| | - Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
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12
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Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536026. [PMID: 37066336 PMCID: PMC10104143 DOI: 10.1101/2023.04.07.536026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Synovial tissue inflammation is the hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. We measured genome-wide open chromatin at single cell resolution from 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identified 24 chromatin classes and predicted their associated transcription factors, including a CD8+ GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating an RA tissue transcriptional atlas, we found that the chromatin classes represented 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrated the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
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Affiliation(s)
- Kathryn Weinand
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gerald F. M. Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer H. Anolik
- Division of Allergy, Immunology and Rheumatology; Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B. Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T. Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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13
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McBride DA, Kerr MD, Johnson WT, Nguyen A, Zoccheddu M, Yao M, Prideaux EB, Dorn NC, Wang W, Svensson MN, Bottini N, Shah NJ. Immunomodulatory Microparticles Epigenetically Modulate T Cells and Systemically Ameliorate Autoimmune Arthritis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2202720. [PMID: 36890657 PMCID: PMC10104670 DOI: 10.1002/advs.202202720] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 01/09/2023] [Indexed: 05/10/2023]
Abstract
Disease modifying antirheumatic drugs (DMARDs) have improved the prognosis of autoimmune inflammatory arthritides but a large fraction of patients display partial or nonresponsiveness to front-line DMARDs. Here, an immunoregulatory approach based on sustained joint-localized release of all-trans retinoic acid (ATRA), which modulates local immune activation and enhances disease-protective T cells and leads to systemic disease control is reported. ATRA imprints a unique chromatin landscape in T cells, which is associated with an enhancement in the differentiation of naïve T cells into anti-inflammatory regulatory T cells (Treg ) and suppression of Treg destabilization. Sustained release poly-(lactic-co-glycolic) acid (PLGA)-based biodegradable microparticles encapsulating ATRA (PLGA-ATRA MP) are retained in arthritic mouse joints after intra-articular (IA) injection. IA PLGA-ATRA MP enhance migratory Treg which in turn reduce inflammation and modify disease in injected and uninjected joints, a phenotype that is also reproduced by IA injection of Treg . PLGA-ATRA MP reduce proteoglycan loss and bone erosions in the SKG and collagen-induced arthritis mouse models of autoimmune arthritis. Strikingly, systemic disease modulation by PLGA-ATRA MP is not associated with generalized immune suppression. PLGA-ATRA MP have the potential to be developed as a disease modifying agent for autoimmune arthritis.
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Affiliation(s)
- David A. McBride
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Chemical Engineering ProgramUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Matthew D. Kerr
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Chemical Engineering ProgramUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Wade T. Johnson
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Anders Nguyen
- Department of Rheumatology and Inflammation ResearchSahlgrenska AcademyInstitute of MedicineUniversity of GothenburgGothenburg41346Sweden
| | - Martina Zoccheddu
- Department of MedicineDivision of RheumatologyAllergy and ImmunologyUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Mina Yao
- Department of Chemistry and BiochemistryUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Edward B. Prideaux
- Department of Chemistry and BiochemistryUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Nicholas C. Dorn
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Chemical Engineering ProgramUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Wei Wang
- Department of Chemistry and BiochemistryUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Department of Cellular and Molecular MedicineUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Mattias N.D. Svensson
- Department of Rheumatology and Inflammation ResearchSahlgrenska AcademyInstitute of MedicineUniversity of GothenburgGothenburg41346Sweden
| | - Nunzio Bottini
- Department of MedicineDivision of RheumatologyAllergy and ImmunologyUniversity of CaliforniaLa JollaSan DiegoCA92093USA
| | - Nisarg J. Shah
- Department of NanoengineeringUniversity of CaliforniaLa JollaSan DiegoCA92093USA
- Chemical Engineering ProgramUniversity of CaliforniaLa JollaSan DiegoCA92093USA
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14
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Wang T, Zeng F, Li X, Wei Y, Wang D, Zhang W, Xie H, Wei L, Xiong S, Liu C, Li S, Wu J. Identification of key genes and pathways associated with sex differences in rheumatoid arthritis based on bioinformatics analysis. Clin Rheumatol 2023; 42:399-406. [PMID: 36173499 DOI: 10.1007/s10067-022-06387-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Women are more likely than men to develop the chronic, progressive autoimmune disease known as rheumatoid arthritis (RA). Although there may be a complex interplay between sex-based differences and autoimmune dysfunction. Their function in RA is largely unknown, though. The purpose of this study was to pinpoint the crucial genes and metabolic pathways that control biological variations in RA between men and women. METHODS First, the Gene Expression Omnibus database's gene expression information for GSE39340 and GSE55457 was downloaded (GEO). R software was used to find each of the individually identified differentially expressed genes (DEGs) between the sexes. DEGs that overlapped were found. The interactions between the overlapping DEGs were then further examined using a protein-protein interaction (PPI) network. The Kyoto Encyclopedia of Genes and Genomes and Gene Ontology tools, respectively, were used to perform enrichment analyses. RESULTS According to our findings, there were 1169 DEGs that overlapped between RA males and females, comprising 845 up-regulated genes and 324 down-regulated genes. Ten hub genes, including PIK3R1, RAC1, HRAS, PTPN11, UQCRB, NDUFV1, EGF, UBA1, UBE2G1, and UBE2E1, were discovered in the PPI network. According to a functional enrichment analysis, these genes were primarily enriched in neurodegenerative illnesses, including various disease pathways, MAPK signaling, insulin signaling, and autophagy. CONCLUSION The current data point to the possibility that the MAPK pathway and autophagy may be significant contributors to sex differences in RA. PTPN11, EGF, and UBA1 may be important genes linked to the gender development of RA and are anticipated to be therapeutic targets for the disease. Key Points • Our research point to the possibility that the MAPK pathway and autophagy may be significant contributors to sex differences in RA. • PTPN11, EGF, and UBA1 may be important genes linked to the gender development of RA and are anticipated to be therapeutic targets for the disease. • These findings may aid in the development of novel diagnostic and treatment techniques for RA in men and women.
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Affiliation(s)
- Tingting Wang
- Department of Rheumatology, Dazhou Central Hospital, Sichuan, Dazhou, 635000, China
| | - Fanxin Zeng
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, Sichuan, China, 635000
| | - Xue Li
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, Sichuan, China, 635000
| | - Yuanli Wei
- Department of Rheumatology, Dazhou Central Hospital, Sichuan, Dazhou, 635000, China
| | - Dongmei Wang
- Department of Rheumatology, Dazhou Central Hospital, Sichuan, Dazhou, 635000, China
| | - Weihua Zhang
- Department of Rheumatology, Dazhou Central Hospital, Sichuan, Dazhou, 635000, China
| | - Huanhuan Xie
- Department of Rheumatology, Dazhou Central Hospital, Sichuan, Dazhou, 635000, China
| | - Lingli Wei
- Department of Rheumatology, Dazhou Central Hospital, Sichuan, Dazhou, 635000, China
| | - Siying Xiong
- Department of Rheumatology, Dazhou Central Hospital, Sichuan, Dazhou, 635000, China
| | - Caizhen Liu
- Department of Rheumatology, Dazhou Central Hospital, Sichuan, Dazhou, 635000, China
| | - Shilin Li
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, Sichuan, China, 635000
| | - Jianhong Wu
- Department of Rheumatology, Dazhou Central Hospital, Sichuan, Dazhou, 635000, China.
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15
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Ospelt C. Site of invasion revisited: epigenetic drivers of joint destruction in RA. Ann Rheum Dis 2022; 82:734-739. [PMID: 36585124 DOI: 10.1136/ard-2022-222554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022]
Abstract
New analytical methods and the increasing availability of synovial biopsies have recently provided unprecedented insights into synovial activation in general and synovial fibroblast (SF) biology in particular. In the course of this development, SFs have become one of the most rapidly evolving and exciting fields of rheumatoid arthritis (RA) research. While their active role in the invasion of RA synovium into cartilage has long been studied, recent studies have brought new aspects of their heterogeneity and propagation in RA. This review integrates old and new evidence to give an overview picture of the processes active at the sites of invasive synovial tissue growth in RA.
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Affiliation(s)
- Caroline Ospelt
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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16
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Seropositivity-Dependent Association between LINE-1 Methylation and Response to Methotrexate Therapy in Early Rheumatoid Arthritis Patients. Genes (Basel) 2022; 13:genes13112012. [DOI: 10.3390/genes13112012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Methotrexate (MTX) is considered the first choice among disease-modifying anti-rheumatic drugs (DMARDs) for rheumatoid arthritis (RA) treatment. However, response to it varies as approximately 40% of the patients do not respond and would lose the most effective period of treatment time. Therefore, having a predictive biomarker before starting MTX treatment is of utmost importance. Methylation of long interspersed nucleotide element-1 (LINE-1) is generally considered a surrogate marker for global genomic methylation, which has been reported to associate with disease activity after MTX therapy. Methods: We performed a prospective study on 273 naïve early RA (ERA) patients who were treated with MTX, followed up to 12 months, and classified according to their therapy response. The baseline LINE-1 methylation levels in peripheral blood mononuclear cells (PBMC) of cases were assessed by bisulfite pyrosequencing. Results: Baseline LINE-1 methylation level per se turned out not to predict the response to the therapy, nor did age, sex, body mass index, or smoking status. However, if cases were stratified according to positivity to rheumatoid factor (RF) and anti-citrullinated protein antibody (ACPA) or seronegativity, we observed an opposite association between baseline LINE-1 methylation levels and optimal response to MTX therapy among responders. The best response to MTX therapy was associated with hypermethylated LINE-1 among double-positive ERA cases (p-value: 0.002) and with hypomethylated LINE-1 in seronegative ERA patients (p-value: 0.01). Conclusion: The LINE-1 methylation level in PBMCs of naïve ERA cases associates with the degree of response to MTX therapy in an opposite way depending on the presence of RF and ACPA antibodies. Our results suggest LINE-1 methylation level as a new epigenetic biomarker for predicting the degree of response to MTX in both double-positive and seronegative ERA patients.
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17
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Chang MH, Bocharnikov AV, Case SM, Todd M, Laird-Gion J, Alvarez-Baumgartner M, Nigrovic PA. Joint-Specific Memory and Sustained Risk for New Joint Accumulation in Autoimmune Arthritis. Arthritis Rheumatol 2022; 74:1851-1858. [PMID: 35606924 PMCID: PMC9617751 DOI: 10.1002/art.42240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/14/2022] [Accepted: 05/17/2022] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Inflammatory arthritides exhibit hallmark patterns of affected and spared joints, but in each individual, arthritis affects only a subset of all possible sites. The purpose of this study was to identify patient-specific patterns of joint flare to distinguish local from systemic drivers of disease chronicity. METHODS Patients with juvenile idiopathic arthritis followed without interruption from disease onset into adulthood were identified across 2 large academic centers. Joints inflamed at each visit were established by medical record review. Flare was defined as physician-confirmed joint inflammation following documented inactive disease. RESULTS Among 222 adults with JIA, 95 had complete serial joint examinations dating from disease onset in childhood. Mean follow-up was 12.5 years (interquartile range 7.9-16.7 years). Ninety (95%) of 95 patients achieved inactive disease, after which 81% (73 patients) experienced at least 1 flare. Among 940 joints affected in 253 flares, 74% had been involved previously. In flares affecting easily observed large joint pairs where only 1 side had been involved before (n = 53), the original joint was affected in 83% and the contralateral joint in 17% (P < 0.0001 versus random laterality). However, disease extended to at least 1 new joint in ~40% of flares, a risk that remained stable even decades after disease onset, and was greatest in flares that occurred while patients were not receiving medication (54% versus 36% of flares occurring with therapy; odds ratio 2.09, P = 0.015). CONCLUSION Arthritis flares preferentially affect previously inflamed joints but carry an ongoing risk of disease extension. These findings confirm joint-specific memory and suggest that prevention of new joint accumulation should be an important target for arthritis therapy.
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Affiliation(s)
- Margaret H. Chang
- Division of Immunology; Boston Children’s Hospital; Boston, MA, 02115; USA
| | - Alexandra V. Bocharnikov
- Division of Rheumatology, Inflammation, and Immunity; Brigham and Women’s Hospital, Boston, MA, 02115; USA
| | - Siobhan M. Case
- Division of Immunology; Boston Children’s Hospital; Boston, MA, 02115; USA
- Division of Rheumatology, Inflammation, and Immunity; Brigham and Women’s Hospital, Boston, MA, 02115; USA
| | - Marc Todd
- Division of Immunology; Boston Children’s Hospital; Boston, MA, 02115; USA
| | - Jessica Laird-Gion
- Division of Immunology; Boston Children’s Hospital; Boston, MA, 02115; USA
| | - Maura Alvarez-Baumgartner
- Division of Rheumatology, Inflammation, and Immunity; Brigham and Women’s Hospital, Boston, MA, 02115; USA
| | - Peter A. Nigrovic
- Division of Immunology; Boston Children’s Hospital; Boston, MA, 02115; USA
- Division of Rheumatology, Inflammation, and Immunity; Brigham and Women’s Hospital, Boston, MA, 02115; USA
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18
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Ainsworth RI, Hammaker D, Nygaard G, Ansalone C, Machado C, Zhang K, Zheng L, Carrillo L, Wildberg A, Kuhs A, Svensson MND, Boyle DL, Firestein GS, Wang W. Systems-biology analysis of rheumatoid arthritis fibroblast-like synoviocytes implicates cell line-specific transcription factor function. Nat Commun 2022; 13:6221. [PMID: 36266270 PMCID: PMC9584907 DOI: 10.1038/s41467-022-33785-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Rheumatoid arthritis (RA) is an immune-mediated disease affecting diarthrodial joints that remains an unmet medical need despite improved therapy. This limitation likely reflects the diversity of pathogenic pathways in RA, with individual patients demonstrating variable responses to targeted therapies. Better understanding of RA pathogenesis would be aided by a more complete characterization of the disease. To tackle this challenge, we develop and apply a systems biology approach to identify important transcription factors (TFs) in individual RA fibroblast-like synoviocyte (FLS) cell lines by integrating transcriptomic and epigenomic information. Based on the relative importance of the identified TFs, we stratify the RA FLS cell lines into two subtypes with distinct phenotypes and predicted active pathways. We biologically validate these predictions for the top subtype-specific TF RARα and demonstrate differential regulation of TGFβ signaling in the two subtypes. This study characterizes clusters of RA cell lines with distinctive TF biology by integrating transcriptomic and epigenomic data, which could pave the way towards a greater understanding of disease heterogeneity.
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Affiliation(s)
- Richard I Ainsworth
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Deepa Hammaker
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gyrid Nygaard
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Cecilia Ansalone
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Camilla Machado
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kai Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Lina Zheng
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Lucy Carrillo
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andre Wildberg
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Kuhs
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mattias N D Svensson
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Rheumatology and Inflammation Research, Sahlgrenska Academy, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - David L Boyle
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gary S Firestein
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.
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Kawabe A, Yamagata K, Kato S, Nakano K, Sakata K, Tsukada YI, Ohmura K, Nakayamada S, Tanaka Y. Role of DNA dioxygenase Ten-Eleven translocation 3 (TET3) in rheumatoid arthritis progression. Arthritis Res Ther 2022; 24:222. [PMID: 36114544 PMCID: PMC9479255 DOI: 10.1186/s13075-022-02908-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/03/2022] [Indexed: 11/14/2022] Open
Abstract
Background Rheumatoid arthritis (RA) patients present with abnormal methylation patterns in their fibroblast-like synoviocytes (FLS). Given that DNA demethylation is critical for producing DNA methylation patterns, we hypothesized that DNA demethylation may facilitate RA progression. Therefore, we designed this study to examine the role of DNA dioxygenase family, Ten-Eleven translocation (TET1/2/3), in the pathological process of RA. Methods Synovial tissues and FLS were obtained from patients with RA and Osteoarthritis. K/BxN serum-induced arthritis was induced in Wild-type (WT) and TET3 heterozygous-deficient (TET3+/−) C57BL/6 mice. Results We found that both TET3 and 5-hydroxymethylcytosine (5hmC) were upregulated in synovitis tissues from RA patients and confirmed this upregulation in the cultured FLS derived from synovitis tissues. Tumor necrosis factor α (TNFα) upregulated TET3 and 5hmC levels in cultured FLS, and the stimulated FLS exhibited high cell mobility with increased transcription of cellular migration-related factors such as C-X-C motif chemokine ligand 8 (CXCL8) and C-C motif chemokine ligand 2 (CCL2) in a TET3-dependent manner. In addition, TET3 haploinsufficiency lowered RA progression in a mouse model of serum-induced arthritis. Conclusions Based on these findings, we can assume that TET3-mediated DNA demethylation acts as an epigenetic regulator of RA progression. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-022-02908-5.
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20
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How does age determine the development of human immune-mediated arthritis? Nat Rev Rheumatol 2022; 18:501-512. [PMID: 35948692 PMCID: PMC9363867 DOI: 10.1038/s41584-022-00814-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2022] [Indexed: 11/08/2022]
Abstract
Does age substantially affect the emergence of human immune-mediated arthritis? Children do not usually develop immune-mediated articular inflammation during their first year of life. In patients with juvenile idiopathic arthritis, this apparent ‘immune privilege’ disintegrates, and chronic inflammation is associated with variable autoantibody signatures and patterns of disease that resemble adult arthritis phenotypes. Numerous mechanisms might be involved in this shift, including genetic and epigenetic predisposing factors, maturation of the immune system with a progressive modulation of putative tolerogenic controls, parallel development of microbial dysbiosis, accumulation of a pro-inflammatory burden driven by environmental exposures (the exposome) and comorbidity-related drivers. By exploring these mechanisms, we expand the discussion of three (not mutually exclusive) hypotheses on how these factors can contribute to the differences and similarities between the loss of immune tolerance in children and the development of established immune-mediated arthritis in adults. These three hypotheses relate to a critical window in genetics and epigenetics, immune maturation, and the accumulation of burden. The varied manifestation of the underlying mechanisms among individuals is only beginning to be clarified, but the establishment of a framework can facilitate the development of an integrated understanding of the pathogenesis of arthritis across all ages. In this Review, the authors discuss age-related arthropathy and the similarities and differences between childhood loss of immune tolerance and adult development of immune-mediated arthritis, and develop three hypotheses describing age-related mechanisms that contribute to the onset of arthritis. The arthritis-free ‘immune privilege’ of early childhood is overridden by multiple mechanisms, progressively and age-dependently, generating recognizable patterns of chronic inflammatory arthritis. The emergence of arthritis involves interconnected mechanisms related to immune priming, to a situational susceptibility and to the accumulation of an inflammatory burden. The accumulation of epigenetic drift may contribute to differences across ages. The exposome is expected to contribute to arthritis emergence in adults as well as in children.
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Németh T, Nagy G, Pap T. Synovial fibroblasts as potential drug targets in rheumatoid arthritis, where do we stand and where shall we go? Ann Rheum Dis 2022; 81:annrheumdis-2021-222021. [PMID: 35715191 PMCID: PMC9279838 DOI: 10.1136/annrheumdis-2021-222021] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/22/2022] [Indexed: 12/14/2022]
Abstract
Fibroblast-like synoviocytes or synovial fibroblasts (FLS) are important cellular components of the inner layer of the joint capsule, referred to as the synovial membrane. They can be found in both layers of this synovial membrane and contribute to normal joint function by producing extracellular matrix components and lubricants. However, under inflammatory conditions like in rheumatoid arthritis (RA), they may start to proliferate, undergo phenotypical changes and become central elements in the perpetuation of inflammation through their direct and indirect destructive functions. Their importance in autoimmune joint disorders makes them attractive cellular targets, and as mesenchymal-derived cells, their inhibition may be carried out without immunosuppressive consequences. Here, we aim to give an overview of our current understanding of the target potential of these cells in RA.
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Affiliation(s)
- Tamás Németh
- Department of Physiology, Semmelweis University, Budapest, Hungary
- Department of Rheumatology and Clinical Immunology, Semmelweis University, Budapest, Hungary
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - György Nagy
- Department of Rheumatology and Clinical Immunology, Semmelweis University, Budapest, Hungary
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
- Department of Genetics, Cell and Immunobiology, Semmelweis University, Budapest, Hungary
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Thomas Pap
- Institute of Musculoskeletal Medicine, Medical Faculty of the Westphalian Wilhelm University, Münster, Germany
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22
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López-Armada MJ, Fernández-Rodríguez JA, Blanco FJ. Mitochondrial Dysfunction and Oxidative Stress in Rheumatoid Arthritis. Antioxidants (Basel) 2022; 11:antiox11061151. [PMID: 35740048 PMCID: PMC9220001 DOI: 10.3390/antiox11061151] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 02/04/2023] Open
Abstract
Control of excessive mitochondrial oxidative stress could provide new targets for both preventive and therapeutic interventions in the treatment of chronic inflammation or any pathology that develops under an inflammatory scenario, such as rheumatoid arthritis (RA). Increasing evidence has demonstrated the role of mitochondrial alterations in autoimmune diseases mainly due to the interplay between metabolism and innate immunity, but also in the modulation of inflammatory response of resident cells, such as synoviocytes. Thus, mitochondrial dysfunction derived from several danger signals could activate tricarboxylic acid (TCA) disruption, thereby favoring a vicious cycle of oxidative/mitochondrial stress. Mitochondrial dysfunction can act through modulating innate immunity via redox-sensitive inflammatory pathways or direct activation of the inflammasome. Besides, mitochondria also have a central role in regulating cell death, which is deeply altered in RA. Additionally, multiple evidence suggests that pathological processes in RA can be shaped by epigenetic mechanisms and that in turn, mitochondria are involved in epigenetic regulation. Finally, we will discuss about the involvement of some dietary components in the onset and progression of RA.
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Affiliation(s)
- María José López-Armada
- Grupo de Investigación en Envejecimiento e Inflamación (ENVEINF), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, 15006 A Coruña, Spain;
- Correspondence: (M.J.L.-A.); (F.J.B.); Tel./Fax: +34-981-178272-73 (M.J.L.-A.)
| | - Jennifer Adriana Fernández-Rodríguez
- Grupo de Investigación en Envejecimiento e Inflamación (ENVEINF), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, 15006 A Coruña, Spain;
| | - Francisco Javier Blanco
- Grupo de Investigación de Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, 15006 A Coruña, Spain
- Grupo de Investigación de Reumatología y Salud (GIR-S), Departamento de Fisioterapia, Medicina y Ciencias Biomédicas, Facultad de Fisioterapia, Campus de Oza, Universidade da Coruña, 15001 A Coruña, Spain
- Correspondence: (M.J.L.-A.); (F.J.B.); Tel./Fax: +34-981-178272-73 (M.J.L.-A.)
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23
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Exploration of the pathogenesis of Sjögren's syndrome via DNA methylation and transcriptome analyses. Clin Rheumatol 2022; 41:2765-2777. [PMID: 35562622 DOI: 10.1007/s10067-022-06200-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/07/2022] [Accepted: 05/03/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Sjögren's syndrome (SS), a systemic autoimmune disorder, is characterized by dry mouth and eyes. However, SS pathogenesis is poorly understood. We performed bioinformatics analysis to investigate the potential targets and molecular pathogenesis of SS. METHODS Gene expression profiles (GSE157159) and methylation data (GSE110007) associated with SS patients were obtained from the Gene Expression Omnibus (GEO) database. Differentially methylated positions (DMPs) and differentially expressed genes (DEGs) were identified by the R package limma. The potential biological functions of DEGs were determined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Key DMPs were selected by overlap and the shrunken centroid algorithm, and corresponding genes were identified as hub genes, with their diagnostic value assessed by receiver operating characteristic (ROC) curves. The potential molecular mechanisms of hub genes were analyzed by protein-protein interaction (PPI) networks and single-gene gene set enrichment analysis (GSEA). Peripheral blood mononuclear cells (PBMCs) were collected from control and SS patients at The Affiliated Hospital of Southwest Medical University and Dazhou Central Hospital. The mRNA levels of hub genes were verified by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS We identified 788 DMPs and 2457 DEGs between the two groups. Functional enrichment analysis suggested that the DEGs were significantly enriched in T cell activation, leukocyte cell-cell adhesion, and cytokine-cytokine receptor interaction. TSS200, TSS1500, and 1stExon were identified as highly enriched areas of differentially methylated promoter CpG islands (DMCIs). In total, 61 differentially methylated genes (DMGs) were identified by the overlap of 2457 DEGs and 507 genes related to DMPs (DMPGs), of which 21 genes located near TSS200, TSS1500, and 1stExon were selected. Then, three key DMPs and the corresponding hub genes (RUNX3, HLA-DPA1, and CD6) were screened by the shrunken centroid algorithm and calculated to have areas under the ROC curve of 1.000, 0.931, and 0.986, respectively, indicating good diagnostic value. The GSEA results suggested that all three hub genes were highly associated with the immune response. Finally, positive mRNA expression of the three hub genes in clinical SS samples was verified by qRT-PCR, consistent with the GSE157159 data. CONCLUSIONS The identification of three hub genes provides novel insight into molecular mechanisms and therapeutic targets for SS. Key Points • Hub genes were screened by DNA methylation and transcriptome analyses. • The relative expression of hub genes in peripheral blood samples was verified by qRT-PCR. • HLA-DPA1 was correlated with the pathogenic mechanism of SS.
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24
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Saeki N, Inoue K, Ideta-Otsuka M, Watamori K, Mizuki S, Takenaka K, Igarashi K, Miura H, Takeda S, Imai Y. Epigenetic regulator UHRF1 suppressively orchestrates pro-inflammatory gene expression in rheumatoid arthritis. J Clin Invest 2022; 132:150533. [PMID: 35472067 PMCID: PMC9151705 DOI: 10.1172/jci150533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is characterized by chronic synovial inflammation with aberrant epigenetic alterations, eventually leading to joint destruction. However, the epigenetic regulatory mechanisms underlying RA pathogenesis remain largely unknown. Here we showed that Ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) is a central epigenetic regulator that suppressively orchestrates multiple pathogeneses in RA. UHRF1 expression was remarkably up-regulated in synovial fibroblasts (SF) from arthritis model mice and RA patients. Mice with SF-specific Uhrf1 conditional knockout showed more severe arthritic phenotypes than littermate control. Uhrf1-deficient SF also exhibited enhanced apoptosis resistance and up-regulated expression of several cytokines including Ccl20. In RA patients, DAS28, CRP, and Th17 accumulation as well as apoptosis resistance were negatively correlated with UHRF1 expression in synovium. Finally, Ryuvidine administration that stabilizes UHRF1 ameliorated arthritis pathogeneses in a mouse model of RA. This study demonstrated that UHRF1 expressed in RA SF can contribute to negative feedback mechanisms that suppress multiple pathogenic events in arthritis, suggesting that targeting UHRF1 could be one of the therapeutic strategies for RA.
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Affiliation(s)
- Noritaka Saeki
- Division of Laboratory Animal Research, Ehime University, Toon, Japan
| | - Kazuki Inoue
- Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Shenzhen, China
| | - Maky Ideta-Otsuka
- Laboratory of Instrumental Analysis, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Kunihiko Watamori
- Department of Bone and Joint Surgery, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Shinichi Mizuki
- The Center for Rheumatic Diseases, Matsuyama Red Cross Hospital, Matsuyama, Japan
| | - Katsuto Takenaka
- Department of Hematology, Clinical Immunology and Infectious Diseases, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Katsuhide Igarashi
- Laboratory of Biofunctional Science, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Hiromasa Miura
- Department of Bone and Joint Surgery, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Shu Takeda
- Division of Endocrinology, Toranomon Hospital Endocrine Center, Tokyo, Japan
| | - Yuuki Imai
- Division of Laboratory Animal Research, Ehime University, Toon, Japan
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25
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Chen Q, Li H, Liu Y, Zhao M. Epigenetic Regulation of Immune and Inflammatory Responses in Rheumatoid Arthritis. Front Immunol 2022; 13:881191. [PMID: 35479077 PMCID: PMC9035598 DOI: 10.3389/fimmu.2022.881191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose Rheumatoid arthritis (RA) is a disease associated with multiple factors. Epigenetics can affect gene expression without altering the DNA sequence. In this study, we aimed to comprehensively analyze epigenetic regulation in RA. Methods Using the Gene Expression Omnibus database, we identified a methylation chip, RNA-sequencing, and miRNA microarray for RA. First, we searched for DNA methylation, genes, and miRNAs associated with RA using differential analysis. Second, we determined the regulatory networks for RA-specific methylation, miRNA, and m6A using cross-analysis. Based on these three regulatory networks, we built a comprehensive epigenetic regulatory network and identified hub genes. Results Using a differential analysis, we identified 16,852 differentially methylated sites, 4877 differentially expressed genes, and 32 differentially expressed miRNAs. The methylation-expression regulatory network was mainly associated with the PI3K-Akt and T-cell receptor signaling pathways. The miRNA expression regulatory network was mainly related to the MAPK and chemokine signaling pathways. M6A regulatory network was mainly associated with the MAPK signaling pathway. Additionally, five hub genes were identified in the epigenetic regulatory network: CHD3, SETD1B, FBXL19, SMARCA4, and SETD1A. Functional analysis revealed that these five genes were associated with immune cells and inflammatory responses. Conclusion We constructed a comprehensive epigenetic network associated with RA and identified core regulatory genes. This study provides a new direction for future research on the epigenetic mechanisms of RA.
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Affiliation(s)
- Qi Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Hao Li
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yusi Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Min Zhao
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
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26
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Zhao Z, Zhang Y, Gao D, Zhang Y, Han W, Xu X, Song Q, Zhao C, Yang J. Inhibition of Histone H3 Lysine-27 Demethylase Activity Relieves Rheumatoid Arthritis Symptoms via Repression of IL6 Transcription in Macrophages. Front Immunol 2022; 13:818070. [PMID: 35371061 PMCID: PMC8965057 DOI: 10.3389/fimmu.2022.818070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
Rheumatoid arthritis (RA) occurs in about 5 per 1,000 people and can lead to severe joint damage and disability. However, the knowledge of pathogenesis and treatment for RA remains limited. Here, we found that histone demethylase inhibitor GSK-J4 relieved collagen induced arthritis (CIA) symptom in experimental mice model, and the underlying mechanism is related to epigenetic transcriptional regulation in macrophages. The role of epigenetic regulation has been introduced in the process of macrophage polarization and the pathogenesis of inflammatory diseases. As a repressive epigenetic marker, tri-methylation of lysine 27 on histone H3 (H3K27me3) was shown to be important for transcriptional gene expression regulation. Here, we comprehensively analyzed H3K27me3 binding promoter and corresponding genes function by RNA sequencing in two differentially polarized macrophage populations. The results revealed that H3K27me3 binds on the promoter regions of multiple critical cytokine genes and suppressed their transcription, such as IL6, specifically in M-CSF derived macrophages but not GM-CSF derived counterparts. Our results may provide a new approach for the treatment of inflammatory and autoimmune disorders.
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Affiliation(s)
- Zhan Zhao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Yazhuo Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Danling Gao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Yidan Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Wenwei Han
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Ximing Xu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qiaoling Song
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chenyang Zhao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jinbo Yang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Innovation Platform of Marine Drug Screening & Evaluation, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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27
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Epigenome editing and epigenetic gene regulation in disease phenotypes. KOREAN J CHEM ENG 2022; 39:1361-1367. [DOI: 10.1007/s11814-022-1076-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Prediction of Drug Targets for Specific Diseases Leveraging Gene Perturbation Data: A Machine Learning Approach. Pharmaceutics 2022; 14:pharmaceutics14020234. [PMID: 35213968 PMCID: PMC8878225 DOI: 10.3390/pharmaceutics14020234] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 12/15/2022] Open
Abstract
Identification of the correct targets is a key element for successful drug development. However, there are limited approaches for predicting drug targets for specific diseases using omics data, and few have leveraged expression profiles from gene perturbations. We present a novel computational approach for drug target discovery based on machine learning (ML) models. ML models are first trained on drug-induced expression profiles with outcomes defined as whether the drug treats the studied disease. The goal is to “learn” the expression patterns associated with treatment. Then, the fitted ML models were applied to expression profiles from gene perturbations (overexpression (OE)/knockdown (KD)). We prioritized targets based on predicted probabilities from the ML model, which reflects treatment potential. The methodology was applied to predict targets for hypertension, diabetes mellitus (DM), rheumatoid arthritis (RA), and schizophrenia (SCZ). We validated our approach by evaluating whether the identified targets may ‘re-discover’ known drug targets from an external database (OpenTargets). Indeed, we found evidence of significant enrichment across all diseases under study. A further literature search revealed that many candidates were supported by previous studies. For example, we predicted PSMB8 inhibition to be associated with the treatment of RA, which was supported by a study showing that PSMB8 inhibitors (PR-957) ameliorated experimental RA in mice. In conclusion, we propose a new ML approach to integrate the expression profiles from drugs and gene perturbations and validated the framework. Our approach is flexible and may provide an independent source of information when prioritizing drug targets.
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29
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OUP accepted manuscript. Rheumatology (Oxford) 2022; 61:4521-4534. [DOI: 10.1093/rheumatology/keac069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/16/2022] [Indexed: 11/12/2022] Open
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30
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Romão VC, Fonseca JE. Etiology and Risk Factors for Rheumatoid Arthritis: A State-of-the-Art Review. Front Med (Lausanne) 2021; 8:689698. [PMID: 34901047 PMCID: PMC8661097 DOI: 10.3389/fmed.2021.689698] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022] Open
Abstract
Rheumatoid arthritis (RA) is the most common systemic inflammatory rheumatic disease. It is associated with significant burden at the patient and societal level. Extensive efforts have been devoted to identifying a potential cause for the development of RA. Epidemiological studies have thoroughly investigated the association of several factors with the risk and course of RA. Although a precise etiology remains elusive, the current understanding is that RA is a multifactorial disease, wherein complex interactions between host and environmental factors determine the overall risk of disease susceptibility, persistence and severity. Risk factors related to the host that have been associated with RA development may be divided into genetic; epigenetic; hormonal, reproductive and neuroendocrine; and comorbid host factors. In turn, environmental risk factors include smoking and other airborne exposures; microbiota and infectious agents; diet; and socioeconomic factors. In the present narrative review, aimed at clinicians and researchers in the field of RA, we provide a state-of-the-art overview of the current knowledge on this topic, focusing on recent progresses that have improved our comprehension of disease risk and development.
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Affiliation(s)
- Vasco C Romão
- Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon Academic Medical Centre and European Reference Network on Rare Connective Tissue and Musculoskeletal Diseases Network (ERN-ReCONNET), Lisbon, Portugal.,Rheumatology Research Unit, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - João Eurico Fonseca
- Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon Academic Medical Centre and European Reference Network on Rare Connective Tissue and Musculoskeletal Diseases Network (ERN-ReCONNET), Lisbon, Portugal.,Rheumatology Research Unit, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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31
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Li P, Wu C, Guo X, Wen Y, Liu L, Liang X, Du Y, Zhang L, Ma M, Cheng S, Cheng B, Wang S, Zhang F. Integrative Analysis of Genome-Wide Association Studies and DNA Methylation Profile Identified Genetic Control Genes of DNA Methylation for Kashin-Beck Disease. Cartilage 2021; 13:780S-788S. [PMID: 31220921 PMCID: PMC8808895 DOI: 10.1177/1947603519858748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Epigenetic modifications of DNA are regarded as a crucial factor for understanding the molecular basis of complex phenotypes. This study aims to uncover insight into the epigenetic modifications for Kashin-Beck disease (KBD) by integrating genome-wide association studies (GWAS), methylation quantitative trait loci (meQTLs), and DNA methylation profiles data. DESIGN The knee articular cartilages of 5 KBD patients and 5 healthy controls were collected for DNA methylation profiling, using Illumina Infinium HumanMethylation450 BeadChip. Mass spectrograph validation of identified differently methylated genes was conducted using independent samples of 4 KBD patients and 3 healthy controls, together with a previous sample of 2743 Han Chinese individuals of GWAS study for KBD and a study of 697 normal subjects for meQTLs annotation datasets. KBD GWAS single nucleotide polymorphisms (SNPs) and normal meQTLs SNPs were integrated with DNA methylation profiles of KBD articular cartilage to identify genetic control (GC) genes of DNA methylation for KBD. Quantitative polymerase chain reaction (qPCR) was performed to validate the mRNA expression of several identified candidate genes. RESULTS A total of 162 CpG sites, 253 SNPs, and 123 GC genes for KBD were identified. Enrichment analysis detected 642 marked GO terms and 19 KEGG pathways (P < 0.05). Six potential key GC genes were conducted for qPCR experiment (ERG, MN1, MITF, WISP1, TRIO, and NOSTRIN). CONCLUSIONS The results suggest that GC genes of DNA methylation may lead to the erosion of cartilage in KBD, which may help us in understanding the epigenetic alteration of KBD.
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Affiliation(s)
- Ping Li
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Cuiyan Wu
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Xiong Guo
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Yan Wen
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Li Liu
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Xiao Liang
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Yanan Du
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Lu Zhang
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Mei Ma
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Sen Wang
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China
| | - Feng Zhang
- Key Laboratory of Trace Elements and
Endemic Disease of National Health Commission of the People’s Republic of China,
School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an,
People’s Republic of China,Feng Zhang, Key Laboratory of Trace Elements
and Endemic Disease of National Health Commission of the People’s Republic of
China, School of Public Health, Health Science Center, Xi’an Jiaotong
University, No.76 Yan Ta West Road, Xi’an, Shaanxi 710061, People’s Republic of
China.
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32
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Li J, Li L, Wang Y, Huang G, Li X, Xie Z, Zhou Z. Insights Into the Role of DNA Methylation in Immune Cell Development and Autoimmune Disease. Front Cell Dev Biol 2021; 9:757318. [PMID: 34790667 PMCID: PMC8591242 DOI: 10.3389/fcell.2021.757318] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
To date, nearly 100 autoimmune diseases have been an area of focus, and these diseases bring health challenges to approximately 5% of the population worldwide. As a type of disease caused by tolerance breakdown, both environmental and genetic risk factors contribute to autoimmune disease development. However, in most cases, there are still gaps in our understanding of disease pathogenesis, diagnosis, and treatment. Therefore, more detailed knowledge of disease pathogenesis and potential therapies is indispensable. DNA methylation, which does not affect the DNA sequence, is one of the key epigenetic silencing mechanisms and has been indicated to play a key role in gene expression regulation and to participate in the development of certain autoimmune diseases. Potential epigenetic regulation via DNA methylation has garnered more attention as a disease biomarker in recent years. In this review, we clarify the basic function and distribution of DNA methylation, evaluate its effects on gene expression and discuss related key enzymes. In addition, we summarize recent aberrant DNA methylation modifications identified in the most important cell types related to several autoimmune diseases and then provide potential directions for better diagnosing and monitoring disease progression driven by epigenetic control, which may broaden our understanding and contribute to further epigenetic research in autoimmune diseases.
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Affiliation(s)
- Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yimeng Wang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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Payet M, Dargai F, Gasque P, Guillot X. Epigenetic Regulation (Including Micro-RNAs, DNA Methylation and Histone Modifications) of Rheumatoid Arthritis: A Systematic Review. Int J Mol Sci 2021; 22:ijms222212170. [PMID: 34830057 PMCID: PMC8625518 DOI: 10.3390/ijms222212170] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/03/2021] [Accepted: 11/06/2021] [Indexed: 11/16/2022] Open
Abstract
The inflammatory reaction in rheumatoid arthritis (RA) is controlled by major epigenetic modifications that modulate the phenotype of synovial and immune cells. The aim of this work was to perform a systematic review focusing on miR expression, DNA methylation and histone modifications in RA. We demonstrated that, in human samples, the expressions of miR-155, miR-146a and miR-150 were significantly decreased while the expression of miR-410-3p was significantly increased in the RA group. Moreover, miR-146a significantly decreased pro-autoimmune IL-17 cytokine expression in RA. In a murine model, miR-34a inhibition can ameliorate the arthritis score. However, this evidence remain critically insufficient to support current therapeutic applications in RA patients.
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Affiliation(s)
- Melissa Payet
- Research Unit ‘Etudes en Pharmaco-Immunologie’ UR EPI, Université de la Réunion, 97400 Réunion, France; (P.G.); (X.G.)
- Correspondence:
| | - Farouk Dargai
- Orthopedic Clinical Department, CHU Bellepierre, Reunion University Hospital, 97400 Réunion, France;
| | - Philippe Gasque
- Research Unit ‘Etudes en Pharmaco-Immunologie’ UR EPI, Université de la Réunion, 97400 Réunion, France; (P.G.); (X.G.)
- Immunology Laboratory (LICE-OI), CHU Bellepierre, Reunion University Hospital, 97400 Réunion, France
| | - Xavier Guillot
- Research Unit ‘Etudes en Pharmaco-Immunologie’ UR EPI, Université de la Réunion, 97400 Réunion, France; (P.G.); (X.G.)
- Rheumatology Clinical Department, CHU Bellepierre, Reunion University Hospital, 97400 Réunion, France
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Corbet M, Pineda MA, Yang K, Tarafdar A, McGrath S, Nakagawa R, Lumb FE, Suckling CJ, Harnett W, Harnett MM. Epigenetic drug development for autoimmune and inflammatory diseases. PLoS Pathog 2021; 17:e1010069. [PMID: 34748611 PMCID: PMC8601611 DOI: 10.1371/journal.ppat.1010069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/18/2021] [Accepted: 10/27/2021] [Indexed: 01/21/2023] Open
Abstract
ES-62 is the major secreted protein of the parasitic filarial nematode, Acanthocheilonema viteae. The molecule exists as a large tetramer (MW, ~240kD), which possesses immunomodulatory properties by virtue of multiple phosphorylcholine (PC) moieties attached to N-type glycans. By suppressing inflammatory immune responses, ES-62 can prevent disease development in certain mouse models of allergic and autoimmune conditions, including joint pathology in collagen-induced arthritis (CIA), a model of rheumatoid arthritis (RA). Such protection is associated with functional suppression of "pathogenic" hyper-responsive synovial fibroblasts (SFs), which exhibit an aggressive inflammatory and bone-damaging phenotype induced by their epigenetic rewiring in response to the inflammatory microenvironment of the arthritic joint. Critically, exposure to ES-62 in vivo induces a stably-imprinted CIA-SF phenotype that exhibits functional responses more typical of healthy, Naïve-SFs. Consistent with this, ES-62 "rewiring" of SFs away from the hyper-responsive phenotype is associated with suppression of ERK activation, STAT3 activation and miR-155 upregulation, signals widely associated with SF pathogenesis. Surprisingly however, DNA methylome analysis of Naïve-, CIA- and ES-62-CIA-SF cohorts reveals that rather than simply preventing pathogenic rewiring of SFs, ES-62 induces further changes in DNA methylation under the inflammatory conditions pertaining in the inflamed joint, including targeting genes associated with ciliogenesis, to programme a novel "resolving" CIA-SF phenotype. In addition to introducing a previously unsuspected aspect of ES-62's mechanism of action, such unique behaviour signposts the potential for developing DNA methylation signatures predictive of pathogenesis and its resolution and hence, candidate mechanisms by which novel therapeutic interventions could prevent SFs from perpetuating joint inflammation and destruction in RA. Pertinent to these translational aspects of ES-62-behavior, small molecule analogues (SMAs) based on ES-62's active PC-moieties mimic the rewiring of SFs as well as the protection against joint disease in CIA afforded by the parasitic worm product.
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Affiliation(s)
- Marlene Corbet
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Miguel A. Pineda
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Kun Yang
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Anuradha Tarafdar
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Sarah McGrath
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Rinako Nakagawa
- Immunity and Cancer, Francis Crick Institute, London, United Kingdom
| | - Felicity E. Lumb
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Colin J. Suckling
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - William Harnett
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- * E-mail: (MMH); (WH)
| | - Margaret M. Harnett
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (MMH); (WH)
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Mueller AL, Payandeh Z, Mohammadkhani N, Mubarak SMH, Zakeri A, Alagheband Bahrami A, Brockmueller A, Shakibaei M. Recent Advances in Understanding the Pathogenesis of Rheumatoid Arthritis: New Treatment Strategies. Cells 2021; 10:cells10113017. [PMID: 34831240 PMCID: PMC8616543 DOI: 10.3390/cells10113017] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 02/07/2023] Open
Abstract
Rheumatoid arthritis (RA) is considered a chronic systemic, multi-factorial, inflammatory, and progressive autoimmune disease affecting many people worldwide. While patients show very individual courses of disease, with RA focusing on the musculoskeletal system, joints are often severely affected, leading to local inflammation, cartilage destruction, and bone erosion. To prevent joint damage and physical disability as one of many symptoms of RA, early diagnosis is critical. Auto-antibodies play a pivotal clinical role in patients with systemic RA. As biomarkers, they could help to make a more efficient diagnosis, prognosis, and treatment decision. Besides auto-antibodies, several other factors are involved in the progression of RA, such as epigenetic alterations, post-translational modifications, glycosylation, autophagy, and T-cells. Understanding the interplay between these factors would contribute to a deeper insight into the causes, mechanisms, progression, and treatment of the disease. In this review, the latest RA research findings are discussed to better understand the pathogenesis, and finally, treatment strategies for RA therapy are presented, including both conventional approaches and new methods that have been developed in recent years or are currently under investigation.
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Affiliation(s)
- Anna-Lena Mueller
- Musculoskeletal Research Group and Tumor Biology, Chair of Vegetative Anatomy, Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilian-University Munich, 80336 Munich, Germany; (A.-L.M.); (A.B.)
| | - Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran;
| | - Niloufar Mohammadkhani
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
- Children’s Medical Center, Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran 1419733151, Iran
| | - Shaden M. H. Mubarak
- Department of Clinical Laboratory Science, Faculty of Pharmacy, University of Kufa, Najaf 1967365271, Iraq;
| | - Alireza Zakeri
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran 1678815811, Iran;
| | - Armina Alagheband Bahrami
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | - Aranka Brockmueller
- Musculoskeletal Research Group and Tumor Biology, Chair of Vegetative Anatomy, Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilian-University Munich, 80336 Munich, Germany; (A.-L.M.); (A.B.)
| | - Mehdi Shakibaei
- Musculoskeletal Research Group and Tumor Biology, Chair of Vegetative Anatomy, Institute of Anatomy, Faculty of Medicine, Ludwig-Maximilian-University Munich, 80336 Munich, Germany; (A.-L.M.); (A.B.)
- Correspondence: ; Tel.: +49-89-2180-72624
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Contribution of Dysregulated DNA Methylation to Autoimmunity. Int J Mol Sci 2021; 22:ijms222111892. [PMID: 34769338 PMCID: PMC8584328 DOI: 10.3390/ijms222111892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/22/2021] [Accepted: 10/29/2021] [Indexed: 12/24/2022] Open
Abstract
Epigenetic mechanisms, such as DNA methylation, histone modifications, and non-coding RNAs are known regulators of gene expression and genomic stability in cell growth, development, and differentiation. Because epigenetic mechanisms can regulate several immune system elements, epigenetic alterations have been found in several autoimmune diseases. The purpose of this review is to discuss the epigenetic modifications, mainly DNA methylation, involved in autoimmune diseases in which T cells play a significant role. For example, Rheumatoid Arthritis and Systemic Lupus Erythematosus display differential gene methylation, mostly hypomethylated 5′-C-phosphate-G-3′ (CpG) sites that may associate with disease activity. However, a clear association between DNA methylation, gene expression, and disease pathogenesis must be demonstrated. A better understanding of the impact of epigenetic modifications on the onset of autoimmunity will contribute to the design of novel therapeutic approaches for these diseases.
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Kondo N, Kuroda T, Kobayashi D. Cytokine Networks in the Pathogenesis of Rheumatoid Arthritis. Int J Mol Sci 2021; 22:ijms222010922. [PMID: 34681582 PMCID: PMC8539723 DOI: 10.3390/ijms222010922] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic systemic inflammation causing progressive joint damage that can lead to lifelong disability. The pathogenesis of RA involves a complex network of various cytokines and cells that trigger synovial cell proliferation and cause damage to both cartilage and bone. Involvement of the cytokines tumor necrosis factor (TNF)-α and interleukin (IL)-6 is central to the pathogenesis of RA, but recent research has revealed that other cytokines such as IL-7, IL-17, IL-21, IL-23, granulocyte macrophage colony-stimulating factor (GM-CSF), IL-1β, IL-18, IL-33, and IL-2 also play a role. Clarification of RA pathology has led to the development of therapeutic agents such as biological disease-modifying anti-rheumatic drugs (DMARDs) and Janus kinase (JAK) inhibitors, and further details of the immunological background to RA are emerging. This review covers existing knowledge regarding the roles of cytokines, related immune cells and the immune system in RA, manipulation of which may offer the potential for even safer and more effective treatments in the future.
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Affiliation(s)
- Naoki Kondo
- Division of Orthopedic Surgery, Department of Regenerative and Transplant Medicine, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-Dori, Chuo-ku, Niigata City 951-8510, Japan;
| | - Takeshi Kuroda
- Health Administration Center, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata City 950-2181, Japan
- Correspondence: ; Tel.: +81-25-262-6244; Fax: +81-25-262-7517
| | - Daisuke Kobayashi
- Division of Clinical Nephrology and Rheumatology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-Dori, Chuo-ku, Niigata City 951-8510, Japan;
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Kemble S, Croft AP. Critical Role of Synovial Tissue-Resident Macrophage and Fibroblast Subsets in the Persistence of Joint Inflammation. Front Immunol 2021; 12:715894. [PMID: 34539648 PMCID: PMC8446662 DOI: 10.3389/fimmu.2021.715894] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/17/2021] [Indexed: 12/11/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic prototypic immune-mediated inflammatory disease which is characterized by persistent synovial inflammation, leading to progressive joint destruction. Whilst the introduction of targeted biological drugs has led to a step change in the management of RA, 30-40% of patients do not respond adequately to these treatments, regardless of the mechanism of action of the drug used (ceiling of therapeutic response). In addition, many patients who acheive clinical remission, quickly relapse following the withdrawal of treatment. These observations suggest the existence of additional pathways of disease persistence that remain to be identified and targeted therapeutically. A major barrier for the identification of therapeutic targets and successful clinical translation is the limited understanding of the cellular mechanisms that operate within the synovial microenvironment to sustain joint inflammation. Recent insights into the heterogeneity of tissue resident synovial cells, including macropahges and fibroblasts has revealed distinct subsets of these cells that differentially regulate specific aspects of inflammatory joint pathology, paving the way for targeted interventions to specifically modulate the behaviour of these cells. In this review, we will discuss the phenotypic and functional heterogeneity of tissue resident synovial cells and how this cellular diversity contributes to joint inflammation. We discuss how critical interactions between tissue resident cell types regulate the disease state by establishing critical cellular checkpoints within the synovium designed to suppress inflammation and restore joint homeostasis. We propose that failure of these cellular checkpoints leads to the emergence of imprinted pathogenic fibroblast cell states that drive the persistence of joint inflammation. Finally, we discuss therapeutic strategies that could be employed to specifically target pathogenic subsets of fibroblasts in RA.
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Affiliation(s)
| | - Adam P. Croft
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom
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Zeng Y, Zhao K, Oros Klein K, Shao X, Fritzler MJ, Hudson M, Colmegna I, Pastinen T, Bernatsky S, Greenwood CMT. Thousands of CpGs Show DNA Methylation Differences in ACPA-Positive Individuals. Genes (Basel) 2021; 12:1349. [PMID: 34573331 PMCID: PMC8472734 DOI: 10.3390/genes12091349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/27/2022] Open
Abstract
High levels of anti-citrullinated protein antibodies (ACPA) are often observed prior to a diagnosis of rheumatoid arthritis (RA). We undertook a replication study to confirm CpG sites showing evidence of differential methylation in subjects positive vs. negative for ACPA, in a new subset of 112 individuals sampled from the population cohort and biobank CARTaGENE in Quebec, Canada. Targeted custom capture bisulfite sequencing was conducted at approximately 5.3 million CpGs located in regulatory or hypomethylated regions from whole blood; library and protocol improvements had been instituted between the original and this replication study, enabling better coverage and additional identification of differentially methylated regions (DMRs). Using binomial regression models, we identified 19,472 ACPA-associated differentially methylated cytosines (DMCs), of which 430 overlapped with the 1909 DMCs reported by the original study; 814 DMRs of relevance were clustered by grouping adjacent DMCs into regions. Furthermore, we performed an additional integrative analysis by looking at the DMRs that overlap with RA related loci published in the GWAS Catalog, and protein-coding genes associated with these DMRs were enriched in the biological process of cell adhesion and involved in immune-related pathways.
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Affiliation(s)
- Yixiao Zeng
- PhD Program in Quantitative Life Sciences, Interfaculty Studies, McGill University, Montréal, QC H3A 1E3, Canada;
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; (K.Z.); (K.O.K.); (M.H.)
| | - Kaiqiong Zhao
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; (K.Z.); (K.O.K.); (M.H.)
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 1A2, Canada
| | - Kathleen Oros Klein
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; (K.Z.); (K.O.K.); (M.H.)
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON K1A 0R6, Canada;
| | - Marvin J. Fritzler
- Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Marie Hudson
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; (K.Z.); (K.O.K.); (M.H.)
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada; (I.C.); (S.B.)
- Division of Rheumatology, Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Inés Colmegna
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada; (I.C.); (S.B.)
- Division of Rheumatology, McGill University, Montréal, QC H3G 1A4, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada;
- Center for Pediatric Genomic Medicine, Children’s Mercy, Kansas City, MO 64108, USA
| | - Sasha Bernatsky
- Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada; (I.C.); (S.B.)
- Division of Rheumatology, McGill University, Montréal, QC H3G 1A4, Canada
| | - Celia M. T. Greenwood
- PhD Program in Quantitative Life Sciences, Interfaculty Studies, McGill University, Montréal, QC H3A 1E3, Canada;
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; (K.Z.); (K.O.K.); (M.H.)
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 1A2, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada;
- Gerald Bronfman Department of Oncology, McGill University, Montréal, QC H4A 3T2, Canada
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Hashimoto T, Yoshida K, Hashiramoto A, Matsui K. Cell-Free DNA in Rheumatoid Arthritis. Int J Mol Sci 2021; 22:ijms22168941. [PMID: 34445645 PMCID: PMC8396202 DOI: 10.3390/ijms22168941] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023] Open
Abstract
Endogenous DNA derived from the nuclei or mitochondria is released into the bloodstream following cell damage or death. Extracellular DNA, called cell-free DNA (cfDNA), is associated with various pathological conditions. Recently, multiple aspects of cfDNA have been assessed, including cfDNA levels, integrity, methylation, and mutations. Rheumatoid arthritis (RA) is the most common form of autoimmune arthritis, and treatment of RA has highly varied outcomes. cfDNA in patients with RA is elevated in peripheral blood and synovial fluid and is associated with disease activity. Profiling of cfDNA in patients with RA may then be utilized in various aspects of clinical practice, such as the prediction of prognosis and treatment responses; monitoring disease state; and as a diagnostic marker. In this review, we discuss cfDNA in patients with RA, particularly the sources of cfDNA and the correlation of cfDNA with RA pathogenesis. We also highlight the potential of analyzing cfDNA profiles to guide individualized treatment approaches for RA.
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Affiliation(s)
- Teppei Hashimoto
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya 6638501, Japan;
- Correspondence: ; Tel.: +81-798-48-6591
| | - Kohsuke Yoshida
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe 6540142, Japan; (K.Y.); (A.H.)
| | - Akira Hashiramoto
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe 6540142, Japan; (K.Y.); (A.H.)
| | - Kiyoshi Matsui
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya 6638501, Japan;
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41
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Qiu S, Munir A, Malik SI, Khan S, Hassan A. Identification of differentially expressed genes and pathways crosstalk analysis in Rheumatoid and Osteoarthritis using next-generation sequencing and protein-protein networks. Saudi J Biol Sci 2021; 28:4656-4663. [PMID: 34354452 PMCID: PMC8325051 DOI: 10.1016/j.sjbs.2021.04.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/29/2022] Open
Abstract
Osteoarthritis occurs when protective cartilage of bones worn out. Similarlty, cartilage damage occurs mainly in the pannus cartilage in rheumatoid arthritis. It is a potentially debilitating condition, affecting women two to three times more often than men. The cause and prognosis of rheumatoid and osteoarthritis are still poorly known. However, advances in the study of disease pathogenesis have encouraged the creation of new therapeutics with improved outcomes. The purpose of this study is to investigate the differentially expressed genes potentially involved in dysregulated rheumatoid arthritis (RA) and their association to other types of arthritis, including osteoarthritis (OA). Complete RNAs were isolated for RNA expression profiling using next-generation sequencing from human primary cultured normal and RA chondrocytes. From RNA sequencing results 250 differentially expressed genes were identified using bioinformatics analysis, of which 32 were found to be significantly playing role in RA pathogenesis and its associated diseases. Molecular ontologies of the identified genes showed they are connected to Innate immune response, Protein phosphorylation, Transcription initiation from RNA polymerase II promoter, Immune response, Neoplasms of bones, as well as osteorthritis, and Rheumatoid arthritis. Among the identified genes, TRAF1, TRAF2, BAMP, STX11, MEOX2, AES, REL, FHL3, PNMA1, SGTA, LZTS2, SIAH2, PNMA1, and TFCP2 were found to be highly enriched in the protein-protein interaction network. The significant cross talks were found in Hypertrophic cardiomyopathy, Small cell lung cancer, Proteasome, p53 signaling pathway, Arrhythmogenic right ventricular cardiomyopathy, Small cell lung cancer, SNARE interactions in vesicular transport, RIG-I-like receptor signaling pathway, and Hypertrophic cardiomyopathy pathways. The results offer new opportunities for target gene control in RA and OA cartilage destruction.
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Affiliation(s)
- Shenqiang Qiu
- Department of Hand and Foot Surgery, Shandong Provincial Hospital affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, Shandong Province 250021, PR China
| | - Anum Munir
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, 22010 Abbottabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology, Islamabad 44000, Pakistan
| | - Sajid Khan
- Department of Bioinformatics, Govt. Postgraduate College Mandian, Abbottabad 22010, Pakistan
| | - Amjad Hassan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, 22010 Abbottabad, Pakistan
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Yamamoto K, Suzuki A, Guerrini MM. Functional genetics for studying the human immune system. Int Immunol 2021; 33:647-651. [PMID: 34313763 DOI: 10.1093/intimm/dxab046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/27/2021] [Indexed: 12/21/2022] Open
Abstract
Although small numbers of immune-mediated diseases are inherited due to rare genetic mutations, most are multifactorial diseases caused by multiple elements including genetic and environmental factors. In the case of autoimmune diseases, many disease-susceptibility genes, including several in the major histocompatibility gene complex, have been reported, and over the past 10 years, genome-wide association studies (GWAS) have been used to analyze disease-susceptibility loci in representative diseases. Furthermore, many disease susceptibility variants have been found to be related to gene expression levels. The expression of genes involved in disease pathogenesis is often cell type-specific, and this is closely related to epigenome alterations. Genomic information is present even before the onset of a disease and has a clear causal relationship to the disease (i.e., the outcome). Therefore, it is important to establish functional genetics in human immunology to understand the pathogenesis of diseases using these pieces of information. We can then apply these results to drug discovery. Here, we will review these issues, especially focusing on autoimmune diseases, and discuss current and future directions of human immune system research.
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Affiliation(s)
- Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Matteo Maurizio Guerrini
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Huang J, Fu X, Chen X, Li Z, Huang Y, Liang C. Promising Therapeutic Targets for Treatment of Rheumatoid Arthritis. Front Immunol 2021; 12:686155. [PMID: 34305919 PMCID: PMC8299711 DOI: 10.3389/fimmu.2021.686155] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
Rheumatoid arthritis (RA) is a systemic poly-articular chronic autoimmune joint disease that mainly damages the hands and feet, which affects 0.5% to 1.0% of the population worldwide. With the sustained development of disease-modifying antirheumatic drugs (DMARDs), significant success has been achieved for preventing and relieving disease activity in RA patients. Unfortunately, some patients still show limited response to DMARDs, which puts forward new requirements for special targets and novel therapies. Understanding the pathogenetic roles of the various molecules in RA could facilitate discovery of potential therapeutic targets and approaches. In this review, both existing and emerging targets, including the proteins, small molecular metabolites, and epigenetic regulators related to RA, are discussed, with a focus on the mechanisms that result in inflammation and the development of new drugs for blocking the various modulators in RA.
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Affiliation(s)
- Jie Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xuekun Fu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xinxin Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zheng Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Yuhong Huang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Chao Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
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Marsh LJ, Kemble S, Reis Nisa P, Singh R, Croft AP. Fibroblast pathology in inflammatory joint disease. Immunol Rev 2021; 302:163-183. [PMID: 34096076 DOI: 10.1111/imr.12986] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022]
Abstract
Rheumatoid arthritis is an immune-mediated inflammatory disease in which fibroblasts contribute to both joint damage and inflammation. Fibroblasts are a major cell constituent of the lining of the joint cavity called the synovial membrane. Under resting conditions, fibroblasts have an important role in maintaining joint homeostasis, producing extracellular matrix and joint lubricants. In contrast, during joint inflammation, fibroblasts contribute to disease pathology by producing pathogenic levels of inflammatory mediators that drive the recruitment and retention of inflammatory cells within the joint. Recent advances in single-cell profiling techniques have transformed our ability to examine fibroblast biology, leading to the identification of specific fibroblast subsets, defining a previously underappreciated heterogeneity of disease-associated fibroblast populations. These studies are challenging the previously held dogma that fibroblasts are homogeneous and are providing unique insights into their role in inflammatory joint pathology. In this review, we discuss the recent advances in our understanding of how fibroblast heterogeneity contributes to joint pathology in rheumatoid arthritis. Finally, we address how these insights could lead to the development of novel therapies that directly target selective populations of fibroblasts in the future.
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Affiliation(s)
- Lucy-Jayne Marsh
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
| | - Samuel Kemble
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
| | - Patricia Reis Nisa
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
| | - Ruchir Singh
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
| | - Adam P Croft
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
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Association of methylation level and transcript level in TRAF5 gene with ankylosing spondylitis: a case-control study. Genes Immun 2021; 22:101-107. [PMID: 34021268 DOI: 10.1038/s41435-021-00135-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/27/2021] [Accepted: 05/10/2021] [Indexed: 02/04/2023]
Abstract
To explore the association between methylation level and transcript level of TNF receptor-associated factor 5 (TRAF5) gene with ankylosing spondylitis (AS) in Chinese Han population. Methylation and mRNA expression level of the TRAF5 gene were tested in 98 patients and 98 healthy controls. Among the 21 CpG sites, methylation levels at eight sites were significantly different between AS patients and healthy controls. However, only three sites remained significantly different after the correction by the Benjamini-Hochberg method. Compared with controls, the CpG island of TRAF5 gene promoter was highly methylated in AS patients, and the relative mRNA expression level of TRAF5 was significantly reduced in AS patients. And the mRNA level was negatively correlated with the methylation level of TRAF5 gene in AS patients (rs = -0.453, P < 0.001). Subgroup analyses indicated that there was no significant difference in the level of methylation between groups of different status of HLA-B27 and medications in AS patients. Multiple linear regression showed that disease-modifying antirheumatic drugs could reduce methylation levels of AS patients after adjusting for the effects of other drugs. In conclusion, the hypermethylation of the TRAF5 might contribute to the pathogenesis of AS, but many open questions remain.
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Nair N, Barton A, Wilson AG. Cell-specific epigenetic drivers of pathogenesis in rheumatoid arthritis. Epigenomics 2021; 13:549-560. [PMID: 33820439 DOI: 10.2217/epi-2020-0380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rheumatoid arthritis is a complex, inflammatory autoimmune disease, which is characterized by pain, swelling and joint damage driven by the altered behavior of a number of different cell types such as synovial fibroblasts macrophages and lymphocytes. The mechanism underlying pathogenesis is unclear but increasing evidence points to altered epigenetic regulation within these cell types which promotes the activated destructive behavior that underlies disease pathogenesis. This review summarizes the key epigenetic modifications in the most important cells types in rheumatoid arthritis, which are associated with disease activity. We also discuss emerging avenues of research focusing on readers of epigenetic markers which may serve to be potential therapeutic targets.
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Affiliation(s)
- Nisha Nair
- Centre for Genetics & Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Anne Barton
- Centre for Genetics & Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PT, UK.,NIHR Manchester Musculoskeletal BRU, Central Manchester Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
| | - Anthony G Wilson
- University College Dublin School of Medicine & Medical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
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Pagiatakis C, Musolino E, Gornati R, Bernardini G, Papait R. Epigenetics of aging and disease: a brief overview. Aging Clin Exp Res 2021; 33:737-745. [PMID: 31811572 PMCID: PMC8084772 DOI: 10.1007/s40520-019-01430-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022]
Abstract
Aging is an important risk factor for several human diseases such as cancer, cardiovascular disease and neurodegenerative disorders, resulting from a combination of genetic and environmental factors (e.g., diet, smoking, obesity and stress), which, at molecular level, cause changes in gene expression underlying the decline of physiological function. Epigenetics, which include mechanisms regulating gene expression independently of changes to DNA sequence, regulate gene expression by modulating the structure of chromatin or by regulating the binding of transcriptional machinery to DNA. Several studies showed that an impairment of epigenetic mechanisms promotes alteration of gene expression underlying several aging-related diseases. Alteration of these mechanisms is also linked with changes of gene expression that occurs during aging processes of different tissues. In this review, we will outline the potential role of epigenetics in the onset of two age-related pathologies, cancer and cardiovascular diseases.
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Abstract
Type 1 diabetes (T1D) is an autoimmune disease that resulted from the severe destruction of the insulin-producing β cells in the pancreases of individuals with a genetic predisposition. Genome-wide studies have identified HLA and other risk genes associated with T1D susceptibility in humans. However, evidence obtained from the incomplete concordance of diabetes incidence among monozygotic twins suggests that environmental factors also play critical roles in T1D pathogenesis. Epigenetics is a rapidly growing field that serves as a bridge to link T1D risk genes and environmental exposures, thereby modulating the expression of critical genes relevant to T1D development beyond the changes of DNA sequences. Indeed, there is compelling evidence that epigenetic changes induced by environmental insults are implicated in T1D pathogenesis. Herein, we sought to summarize the recent progress in terms of epigenetic mechanisms in T1D initiation and progression, and discuss their potential as biomarkers and therapeutic targets in the T1D setting.
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Bangarusamy DK, Lakshmanan AP, Al-Zaidan S, Alabduljabbar S, Terranegra A. Nutri-epigenetics: the effect of maternal diet and early nutrition on the pathogenesis of autoimmune diseases. Minerva Pediatr (Torino) 2021; 73:98-110. [PMID: 33880901 DOI: 10.23736/s2724-5276.20.06166-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Autoimmune diseases comprise a wide group of diseases involving a self-response of the immune system against the host. The etiopathogenesis is very complex involving disease-specific factors but also environmental factors, among which the diet. Maternal diet during pregnancy as well as early nutrition recently attracted the interest of the scientists as contributing to the immune programming. In this paper, we reviewed the most recent literature on the effect of maternal diet and early nutrition in modulating the immune system in a selected subset of autoimmune diseases: type 1 diabetes, celiac disease, inflammatory bowel disease, juvenile idiopathic arthritis and rheumatoid arthritis. Particularly, we focused our narrative on the role of maternal and perinatal nutrition in the epigenetic mechanisms underlying the auto-immune response. Maternal diet during pregnancy as well as breastfeeding and early nutrition play a big role in many epigenetic mechanisms. Most of the nutrients consumed by the mother and the infant are known exerting epigenetic functions, such as folate, methionine, zinc, vitamins B12 and D, fibers, casein and gliadin, and they were linked to gene expression changes in the immune pathways. Despite the common role of maternal diet, breastfeeding and early nutrition in almost all the autoimmune diseases, each disease seems to have specific diet-driver epigenetic mechanisms that require further investigations. The research in this field is opening new routes to establishing a precision nutrition approach to the auto-immune diseases.
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Affiliation(s)
- Dhinoth K Bangarusamy
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar
| | - Arun P Lakshmanan
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar
| | - Sara Al-Zaidan
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar
| | - Shaikha Alabduljabbar
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar
| | - Annalisa Terranegra
- Unit of Maternal and Child Health, Department of Research, Sidra Medicine, Doha, Qatar -
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Tsuchiya H, Ota M, Fujio K. Multiomics landscape of synovial fibroblasts in rheumatoid arthritis. Inflamm Regen 2021; 41:7. [PMID: 33641680 PMCID: PMC7919303 DOI: 10.1186/s41232-021-00157-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 01/27/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is an autoimmune disease characterized by tumor-like hyperplasia and inflammation of the synovium, which causes synovial cell invasion into the bone and cartilage. In RA pathogenesis, various molecules in effector cells (i.e., immune cells and mesenchymal cells) are dysregulated by genetic and environmental factors. Synovial fibroblasts (SFs), the most abundant resident mesenchymal cells in the synovium, are the major local effectors of the destructive joint inflammation and exert their effects through the pathogenic production of molecules such as interleukin-6. MAIN BODY To date, more than 100 RA susceptibility loci have been identified in genome-wide association studies (GWASs), and finding novel therapeutic targets utilizing genome analysis is considered a promising approach because some candidate causal genes identified by GWASs have previously been established as therapeutic targets. For further exploration of RA-responsible cells and cell type-specific therapeutic targets, integrated analysis (or functional genome analysis) of the genome and intermediate traits (e.g., transcriptome and epigenome) is crucial. CONCLUSION This review builds on the existing knowledge regarding the epigenomic abnormalities in RASFs and discusses the recent advances in single-cell analysis, highlighting the prospects of SFs as targets for safer and more effective therapies against RA.
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Affiliation(s)
- Haruka Tsuchiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
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