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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 PMCID: PMC11383168 DOI: 10.1172/jci.insight.179392] [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] [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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2
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Gore S, Meche B, Shao D, Ginnett B, Zhou K, Azad RK. DiseaseNet: a transfer learning approach to noncommunicable disease classification. BMC Bioinformatics 2024; 25:107. [PMID: 38468193 PMCID: PMC10926612 DOI: 10.1186/s12859-024-05734-5] [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: 11/18/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
As noncommunicable diseases (NCDs) pose a significant global health burden, identifying effective diagnostic and predictive markers for these diseases is of paramount importance. Epigenetic modifications, such as DNA methylation, have emerged as potential indicators for NCDs. These have previously been exploited in other contexts within the framework of neural network models that capture complex relationships within the data. Applications of neural networks have led to significant breakthroughs in various biological or biomedical fields but these have not yet been effectively applied to NCD modeling. This is, in part, due to limited datasets that are not amenable to building of robust neural network models. In this work, we leveraged a neural network trained on one class of NCDs, cancer, as the basis for a transfer learning approach to non-cancer NCD modeling. Our results demonstrate promising performance of the model in predicting three NCDs, namely, arthritis, asthma, and schizophrenia, for the respective blood samples, with an overall accuracy (f-measure) of 94.5%. Furthermore, a concept based explanation method called Testing with Concept Activation Vectors (TCAV) was used to investigate the importance of the sample sources and understand how future training datasets for multiple NCD models may be improved. Our findings highlight the effectiveness of transfer learning in developing accurate diagnostic and predictive models for NCDs.
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Affiliation(s)
- Steven Gore
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Bailey Meche
- Department of Mathematics, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Danyang Shao
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Benjamin Ginnett
- Department of Engineering, Eastern Arizona College, Thatcher, AZ, USA
| | - Kelly Zhou
- Department of Computer Science and Engineering, University of North Texas, Denton, TX, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.
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3
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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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4
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Pelissier A, Laragione T, Harris C, Martínez MR, Gulko PS. Gene Network Analyses Identify Co-regulated Transcription Factors and BACH1 as a Key Driver in Rheumatoid Arthritis Fibroblast-like Synoviocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.28.573506. [PMID: 38234777 PMCID: PMC10793426 DOI: 10.1101/2023.12.28.573506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
RNA-sequencing and differential gene expression studies have significantly advanced our understanding of pathogenic pathways underlying Rheumatoid Arthritis (RA). Yet, little is known about cell-specific regulatory networks and their contributions to disease. In this study, we focused on fibroblast-like synoviocytes (FLS), a cell type central to disease pathogenesis and joint damage in RA. We used a strategy that computed sample-specific gene regulatory networks (GRNs) to compare network properties between RA and osteoarthritis FLS. We identified 28 transcription factors (TFs) as key regulators central to the signatures of RA FLS. Six of these TFs are new and have not been previously implicated in RA, and included BACH1, HLX, and TGIF1. Several of these TFs were found to be co-regulated, and BACH1 emerged as the most significant TF and regulator. The main BACH1 targets included those implicated in fatty acid metabolism and ferroptosis. The discovery of BACH1 was validated in experiments with RA FLS. Knockdown of BACH1 in RA FLS significantly affected the gene expression signatures, reduced cell adhesion and mobility, interfered with the formation of thick actin fibers, and prevented the polarized formation of lamellipodia, all required for the RA destructive behavior of FLS. This is the first time that BACH1 is shown to have a central role in the regulation of FLS phenotypes, and gene expression signatures, as well as in ferroptosis and fatty acid metabolism. These new discoveries have the potential to become new targets for treatments aimed at selectively targeting the RA FLS.
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Affiliation(s)
- Aurelien Pelissier
- IBM Research Europe, 8803 Ruschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Currently at Institute of Computational Life Sciences, ZHAW, 8400 Winterthur, Switzerland
| | - Teresina Laragione
- Division of Rheumatology, Icahn School of Medicine at Mount Sinai, 10029 New York, United States
| | - Carolyn Harris
- Division of Rheumatology, Icahn School of Medicine at Mount Sinai, 10029 New York, United States
| | - María Rodríguez Martínez
- IBM Research Europe, 8803 Ruschlikon, Switzerland
- Currently at Yale School of Medicine, 06510 New Haven, United States
| | - Percio S. Gulko
- Division of Rheumatology, Icahn School of Medicine at Mount Sinai, 10029 New York, United States
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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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6
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Elhai M, Micheroli R, Houtman M, Mirrahimi M, Moser L, Pauli C, Bürki K, Laimbacher A, Kania G, Klein K, Schätzle P, Frank Bertoncelj M, Edalat SG, Keusch L, Khmelevskaya A, Toitou M, Geiss C, Rauer T, Sakkou M, Kollias G, Armaka M, Distler O, Ospelt C. The long non-coding RNA HOTAIR contributes to joint-specific gene expression in rheumatoid arthritis. Nat Commun 2023; 14:8172. [PMID: 38071204 PMCID: PMC10710443 DOI: 10.1038/s41467-023-44053-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Although patients with rheumatoid arthritis (RA) typically exhibit symmetrical joint involvement, some patients develop alternative disease patterns in response to treatment, suggesting that different molecular mechanism may underlie disease progression depending on joint location. Here, we identify joint-specific changes in RA synovium and synovial fibroblasts (SF) between knee and hand joints. We show that the long non-coding RNA HOTAIR, which is only expressed in knee SF, regulates more than 50% of this site-specific gene expression in SF. HOTAIR is downregulated after stimulation with pro-inflammatory cytokines and is expressed at lower levels in knee samples from patients with RA, compared with osteoarthritis. Knockdown of HOTAIR in knee SF increases PI-Akt signalling and IL-6 production, but reduces Wnt signalling. Silencing HOTAIR inhibits the migratory function of SF, decreases SF-mediated osteoclastogenesis, and increases the recruitment of B cells by SF. We propose that HOTAIR is an important epigenetic factor in joint-specific gene expression in RA.
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Affiliation(s)
- Muriel Elhai
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Raphael Micheroli
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Miranda Houtman
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Masoumeh Mirrahimi
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Larissa Moser
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Chantal Pauli
- Institute for Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Kristina Bürki
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Andrea Laimbacher
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Gabriela Kania
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Kerstin Klein
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
- Department of BioMedical Research, University of Bern, Bern, Switzerland
- Department of Rheumatology and Immunology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Mojca Frank Bertoncelj
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Sam G Edalat
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Leandra Keusch
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Alexandra Khmelevskaya
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Melpomeni Toitou
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Celina Geiss
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas Rauer
- Department of Trauma Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Maria Sakkou
- Institute for Bioinnovation, Biomedical Sciences Research Center (BSRC) 'Alexander Fleming', Vari, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George Kollias
- Institute for Bioinnovation, Biomedical Sciences Research Center (BSRC) 'Alexander Fleming', Vari, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Marietta Armaka
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland.
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7
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Ciurea A, Distler O, Kwok K, Jo H, Wang L, Killeen T, Ospelt C, Frank Bertoncelj M. Joint-level responses to tofacitinib and methotrexate: a post hoc analysis of data from ORAL Start. Arthritis Res Ther 2023; 25:185. [PMID: 37773189 PMCID: PMC10540368 DOI: 10.1186/s13075-023-03144-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 08/23/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) has a variable impact on different synovial joints, with inflammation being more commonly observed in some joints than others. Emerging evidence suggests that the anatomical variation in pathophysiology could result in differential responses to treatments across the joints, both within and between modes of action. This analysis aimed to characterize joint-specific responses to tofacitinib and methotrexate monotherapy in patients with RA. METHODS This was a post hoc analysis of data from the phase III trial ORAL Start (NCT01039688), in methotrexate-naïve patients with RA. A paired joint pathology score (PJPS), derived from bilateral tender/swollen joint counts, was calculated. The percentage change from baseline in PJPS (%∆PJPS) and treatment-specific responses (tofacitinib 5 and 10 mg twice daily [BID] vs methotrexate; tofacitinib 5 vs 10 mg BID) for each patient joint pair, except for those with baseline/post-baseline PJPS = 0, were calculated at month 3, month 6, and month 12. Radiographic progression was similarly assessed using the Modified Total Sharp Score at month 6 and month 12. RESULTS In methotrexate-naïve patients, differences in %∆PJPS demonstrated greater responses with tofacitinib vs methotrexate in most joint locations. Lesser responses with tofacitinib vs methotrexate were observed in most joints of the feet, particularly at month 12. Despite this, radiographic progression at month 12 was significantly worse in the foot (and metacarpophalangeal) joints of patients receiving methotrexate vs tofacitinib. CONCLUSION We observed variation in joint-specific responses with tofacitinib and methotrexate monotherapy. Despite a proximal-distal efficacy gradient, with better clinical responses in the feet, patients receiving methotrexate monotherapy demonstrated more radiographic progression in the foot joints compared with those receiving tofacitinib. These findings suggest that body site- and therapy-specific characteristics may interact to produce differential treatment responses. TRIAL REGISTRATION ClinicalTrials.gov, NCT01039688.
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Affiliation(s)
- Adrian Ciurea
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Kenneth Kwok
- Inflammation & Immunology, Pfizer Inc., New York, NY, USA
| | - Hyejin Jo
- Inflammation & Immunology, Pfizer Inc., New York, NY, USA
| | - Lisy Wang
- Inflammation & Immunology, Pfizer Inc., Groton, CT, USA
| | - Tim Killeen
- Inflammation & Immunology, Pfizer AG, Schärenmoosstrasse 99, 8052, Zürich, Switzerland.
| | - Caroline Ospelt
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Mojca Frank Bertoncelj
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
- BioMed X Institute, Heidelberg, Germany
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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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9
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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: 9] [Impact Index Per Article: 9.0] [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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10
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El-Sayed A, Aleya L, Kamel M. Epigenetics and the role of nutraceuticals in health and disease. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:28480-28505. [PMID: 36694069 DOI: 10.1007/s11356-023-25236-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
In the post-genomic era, the data provided by complete genome sequencing could not answer several fundamental questions about the causes of many noninfectious diseases, diagnostic biomarkers, and novel therapeutic approaches. The rapidly expanding understanding of epigenetic mechanisms, as well as widespread acceptance of their hypothesized role in disease induction, facilitated the development of a number of novel diagnostic markers and therapeutic concepts. Epigenetic aberrations are reversible in nature, which enables the treatment of serious incurable diseases. Therefore, the interest in epigenetic modulatory effects has increased over the last decade, so about 60,000 publications discussing the expression of epigenetics could be detected in the PubMed database. Out of these, 58,442 were published alone in the last 10 years, including 17,672 reviews (69 historical articles), 314 clinical trials, 202 case reports, 197 meta-analyses, 156 letters to the editor, 108 randomized controlled trials, 87 observation studies, 40 book chapters, 22 published lectures, and 2 clinical trial protocols. The remaining publications are either miscellaneous or a mixture of the previously mentioned items. According to the species and gender, the publications included 44,589 human studies (17,106 females, 14,509 males, and the gender is not mentioned in the remaining papers) and 30,253 animal studies. In the present work, the role of epigenetic modulations in health and disease and the influencing factors in epigenetics are discussed.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, 25030, Besançon Cedex, France
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
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11
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Affiliation(s)
- Ellen M Gravallese
- From the Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston (E.M.G.); and the Division of Rheumatology, Allergy, and Immunology, University of California at San Diego School of Medicine, La Jolla (G.S.F.)
| | - Gary S Firestein
- From the Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston (E.M.G.); and the Division of Rheumatology, Allergy, and Immunology, University of California at San Diego School of Medicine, La Jolla (G.S.F.)
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12
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Tsaltskan V, Firestein GS. Targeting fibroblast-like synoviocytes in rheumatoid arthritis. Curr Opin Pharmacol 2022; 67:102304. [PMID: 36228471 PMCID: PMC9942784 DOI: 10.1016/j.coph.2022.102304] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 01/30/2023]
Abstract
Fibroblast-like synoviocytes (FLS) are mesenchymal-derived cells that play an important role in the physiology of the synovium by producing certain components of the synovial fluid and articular cartilage. In rheumatoid arthritis (RA), however, fibroblasts become a key driver of synovial inflammation and joint damage. Because of this, there has been recent interest in FLS as a therapeutic target in RA to avoid side effects such as systemic immune suppression associated with many existing RA treatments. In this review, we describe how approved treatments for RA affect FLS signaling and function and discuss the effects of investigational FLS-targeted drugs for RA.
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Affiliation(s)
- Vladislav Tsaltskan
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego School of Medicine, La Jolla, CA, USA.
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13
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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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14
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Romão VC, Fonseca JE. Disease mechanisms in preclinical rheumatoid arthritis: A narrative review. Front Med (Lausanne) 2022; 9:689711. [PMID: 36059838 PMCID: PMC9437632 DOI: 10.3389/fmed.2022.689711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/04/2022] [Indexed: 11/20/2022] Open
Abstract
In the last decades, the concept of preclinical rheumatoid arthritis (RA) has become established. In fact, the discovery that disease mechanisms start years before the onset of clinical RA has been one of the major recent insights in the understanding of RA pathogenesis. In accordance with the complex nature of the disease, preclinical events extend over several sequential phases. In a genetically predisposed host, environmental factors will further increase susceptibility for incident RA. In the initial steps of preclinical disease, immune disturbance mechanisms take place outside the joint compartment, namely in mucosal surfaces, such as the lung, gums or gut. Herein, the persistent immunologic response to altered antigens will lead to breach of tolerance and trigger autoimmunity. In a second phase, the immune response matures and is amplified at a systemic level, with epitope spreading and widening of the autoantibody repertoire. Finally, the synovial and bone compartment are targeted by specific autoantibodies against modified antigens, initiating a local inflammatory response that will eventually culminate in clinically evident synovitis. In this review, we discuss the elaborate disease mechanisms in place during preclinical RA, providing a broad perspective in the light of current evidence.
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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, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - João Eurico Fonseca
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
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15
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Kang I, Hundhausen C, Evanko SP, Malapati P, Workman G, Chan CK, Rims C, Firestein GS, Boyle DL, MacDonald KM, Buckner JH, Wight TN. Crosstalk between CD4 T cells and synovial fibroblasts from human arthritic joints promotes hyaluronan-dependent leukocyte adhesion and inflammatory cytokine expression in vitro. Matrix Biol Plus 2022; 14:100110. [PMID: 35573706 PMCID: PMC9097711 DOI: 10.1016/j.mbplus.2022.100110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022] Open
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16
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Floudas A, Gorman A, Neto N, Monaghan MG, Elliott Z, Fearon U, Marzaioli V. Inside the Joint of Inflammatory Arthritis Patients: Handling and Processing of Synovial Tissue Biopsies for High Throughput Analysis. Front Med (Lausanne) 2022; 9:830998. [PMID: 35372383 PMCID: PMC8967180 DOI: 10.3389/fmed.2022.830998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Inflammatory arthritis is a chronic systemic autoimmune disease of unknown etiology, which affects the joints. If untreated, these diseases can have a detrimental effect on the patient's quality of life, leading to disabilities, and therefore, exhibit a significant socioeconomic impact and burden. While studies of immune cell populations in arthritis patient's peripheral blood have been informative regarding potential immune cell dysfunction and possible patient stratification, there are considerable limitations in identifying the early events that lead to synovial inflammation. The joint, as the site of inflammation and the local microenvironment, exhibit unique characteristics that contribute to disease pathogenesis. Understanding the contribution of immune and stromal cell interactions within the inflamed joint has been met with several technical challenges. Additionally, the limited availability of synovial tissue biopsies is a key incentive for the utilization of high-throughput techniques in order to maximize information gain. This review aims to provide an overview of key methods and novel techniques that are used in the handling, processing and analysis of synovial tissue biopsies and the potential synergy between these techniques. Herein, we describe the utilization of high dimensionality flow cytometric analysis, single cell RNA sequencing, ex vivo functional assays and non-intrusive metabolic characterization of synovial cells on a single cell level based on fluorescent lifetime imaging microscopy. Additionally, we recommend important points of consideration regarding the effect of different storage and handling techniques on downstream analysis of synovial tissue samples. The introduction of new powerful techniques in the study of synovial tissue inflammation, brings new challenges but importantly, significant opportunities. Implementation of novel approaches will accelerate our path toward understanding of the mechanisms involved in the pathogenesis of inflammatory arthritis and lead to the identification of new avenues of therapeutic intervention.
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Affiliation(s)
- Achilleas Floudas
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
- *Correspondence: Achilleas Floudas
| | - Aine Gorman
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
| | - Nuno Neto
- Trinity Centre for Biomedical Engineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Michael G. Monaghan
- Trinity Centre for Biomedical Engineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Zoe Elliott
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
| | - Ursula Fearon
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
| | - Viviana Marzaioli
- Molecular Rheumatology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- European League Against Rheumatism (EULAR) Centre of Excellence, Centre for Arthritis and Rheumatic Diseases, St. Vincent's University Hospital, University College Dublin (UCD), Dublin, Ireland
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17
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Abstract
Significance: Epigenetic dysregulation plays an important role in the pathogenesis and development of autoimmune diseases. Oxidative stress is associated with autoimmunity and is also known to alter epigenetic mechanisms. Understanding the interplay between oxidative stress and epigenetics will provide insights into the role of environmental triggers in the development of autoimmunity in genetically susceptible individuals. Recent Advances: Abnormal DNA and histone methylation patterns in genes and pathways involved in interferon and tumor necrosis factor signaling, cellular survival, proliferation, metabolism, organ development, and autoantibody production have been described in autoimmunity. Inhibitors of DNA and histone methyltransferases showed potential therapeutic effects in animal models of autoimmune diseases. Oxidative stress can regulate epigenetic mechanisms via effects on DNA damage repair mechanisms, cellular metabolism and the local redox environment, and redox-sensitive transcription factors and pathways. Critical Issues: Studies looking into oxidative stress and epigenetics in autoimmunity are relatively limited. The number of available longitudinal studies to explore the role of DNA methylation in the development of autoimmune diseases is small. Future Directions: Exploring the relationship between oxidative stress and epigenetics in autoimmunity will provide clues for potential preventative measures and treatment strategies. Inception cohorts with longitudinal follow-up would help to evaluate epigenetic marks as potential biomarkers for disease development, progression, and treatment response in autoimmunity. Antioxid. Redox Signal. 36, 423-440.
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Affiliation(s)
- Xiaoqing Zheng
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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18
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Unal U, Comertpay B, Demirtas TY, Gov E. Drug repurposing for rheumatoid arthritis: Identification of new drug candidates via bioinformatics and text mining analysis. Autoimmunity 2022; 55:147-156. [PMID: 35048767 DOI: 10.1080/08916934.2022.2027922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease that results in the destruction of tissue by attacks on the patient by his or her own immune system. Current treatment strategies are not sufficient to overcome RA. In the present study, various transcriptomic data from synovial fluids, synovial fluid-derived macrophages, and blood samples from patients with RA were analysed using bioinformatics approaches to identify tissue-specific repurposing drug candidates for RA. Differentially expressed genes (DEGs) were identified by integrating datasets for each tissue and comparing diseased to healthy samples. Tissue-specific protein-protein interaction (PPI) networks were generated and topologically prominent proteins were selected. Transcription-regulating biomolecules for each tissue type were determined from protein-DNA interaction data. Common DEGs and reporter biomolecules were used to identify drug candidates for repurposing using the hypergeometric test. As a result of bioinformatic analyses, 19 drugs were identified as repurposing candidates for RA, and text mining analyses supported our findings. We hypothesize that the FDA-approved drugs momelotinib, ibrutinib, and sodium butyrate may be promising candidates for RA. In addition, CHEMBL306380, Compound 19a (CHEMBL3116050), ME-344, XL-019, TG100801, JNJ-26483327, and NV-128 were identified as novel repurposing candidates for the treatment of RA. Preclinical and further validation of these drugs may provide new treatment options for RA.
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Affiliation(s)
- Ulku Unal
- Department of Bioengineering, Adana Alparslan Türkeş Science and Technology University, Adana, Turkey
| | - Betul Comertpay
- Department of Bioengineering, Adana Alparslan Türkeş Science and Technology University, Adana, Turkey
| | - Talip Yasir Demirtas
- Department of Bioengineering, Adana Alparslan Türkeş Science and Technology University, Adana, Turkey
| | - Esra Gov
- Department of Bioengineering, Adana Alparslan Türkeş Science and Technology University, Adana, Turkey
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19
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O'Byrne AM, de Jong TA, van Baarsen LGM. Bridging Insights From Lymph Node and Synovium Studies in Early Rheumatoid Arthritis. Front Med (Lausanne) 2022; 8:820232. [PMID: 35096912 PMCID: PMC8795611 DOI: 10.3389/fmed.2021.820232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease of unknown etiology characterized by inflammation of the peripheral synovial joints leading to pannus formation and bone destruction. Rheumatoid Factor (RF) and anti-citrullinated protein antibodies (ACPA) are present years before clinical manifestations and are indicative of a break in tolerance that precedes chronic inflammation. The majority of studies investigating disease pathogenesis focus on the synovial joint as target site of inflammation while few studies explore the initial break in peripheral tolerance which occurs within secondary lymphoid organs such as lymph nodes. If explored during the earliest phases of RA, lymph node research may provide innovative drug targets for disease modulation or prevention. RA research largely centers on the role and origin of lymphocytes, such as pro-inflammatory T cells and macrophages that infiltrate the joint, as well as growing efforts to determine the role of stromal cells within the synovium. It is therefore important to explore these cell types also within the lymph node as a number of mouse studies suggest a prominent immunomodulatory role for lymph node stromal cells. Synovium and proximal peripheral lymph nodes should be investigated in conjunction with one another to gain understanding of the immunological processes driving RA progression from systemic autoimmunity toward synovial inflammation. This perspective seeks to provide an overview of current literature concerning the immunological changes present within lymph nodes and synovium during early RA. It will also propose areas that warrant further exploration with the aim to uncover novel targets to prevent disease progression.
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Affiliation(s)
- Aoife M. O'Byrne
- Department of Rheumatology and Clinical Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Rheumatology and Immunology Center (ARC), Amsterdam, Netherlands
| | - Tineke A. de Jong
- Department of Rheumatology and Clinical Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Rheumatology and Immunology Center (ARC), Amsterdam, Netherlands
| | - Lisa G. M. van Baarsen
- Department of Rheumatology and Clinical Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Rheumatology and Immunology Center (ARC), Amsterdam, Netherlands
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20
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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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21
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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: 54] [Impact Index Per Article: 18.0] [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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22
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Ge X, Frank-Bertoncelj M, Klein K, McGovern A, Kuret T, Houtman M, Burja B, Micheroli R, Shi C, Marks M, Filer A, Buckley CD, Orozco G, Distler O, Morris AP, Martin P, Eyre S, Ospelt C. Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability. Genome Biol 2021; 22:247. [PMID: 34433485 PMCID: PMC8385949 DOI: 10.1186/s13059-021-02460-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies have reported more than 100 risk loci for rheumatoid arthritis (RA). These loci are shown to be enriched in immune cell-specific enhancers, but the analysis so far has excluded stromal cells, such as synovial fibroblasts (FLS), despite their crucial involvement in the pathogenesis of RA. Here we integrate DNA architecture, 3D chromatin interactions, DNA accessibility, and gene expression in FLS, B cells, and T cells with genetic fine mapping of RA loci. RESULTS We identify putative causal variants, enhancers, genes, and cell types for 30-60% of RA loci and demonstrate that FLS account for up to 24% of RA heritability. TNF stimulation of FLS alters the organization of topologically associating domains, chromatin state, and the expression of putative causal genes such as TNFAIP3 and IFNAR1. Several putative causal genes constitute RA-relevant functional networks in FLS with roles in cellular proliferation and activation. Finally, we demonstrate that risk variants can have joint-specific effects on target gene expression in RA FLS, which may contribute to the development of the characteristic pattern of joint involvement in RA. CONCLUSION Overall, our research provides the first direct evidence for a causal role of FLS in the genetic susceptibility for RA accounting for up to a quarter of RA heritability.
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Affiliation(s)
- Xiangyu Ge
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Mojca Frank-Bertoncelj
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kerstin Klein
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Amanda McGovern
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Tadeja Kuret
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia
| | - Miranda Houtman
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Blaž Burja
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia
| | - Raphael Micheroli
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Chenfu Shi
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Andrew Filer
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK
| | - Christopher D Buckley
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University Foundation Trust, Manchester, UK
| | - Oliver Distler
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul Martin
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University Foundation Trust, Manchester, UK
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University Foundation Trust, Manchester, UK
| | - Caroline Ospelt
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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23
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Cheng L, Wang Y, Wu R, Ding T, Xue H, Gao C, Li X, Wang C. New Insights From Single-Cell Sequencing Data: Synovial Fibroblasts and Synovial Macrophages in Rheumatoid Arthritis. Front Immunol 2021; 12:709178. [PMID: 34349767 PMCID: PMC8326910 DOI: 10.3389/fimmu.2021.709178] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/01/2021] [Indexed: 12/16/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technology can analyze the transcriptome expression level of cells with high-throughput from the single cell level, fully show the heterogeneity of cells, and provide a new way for the study of multicellular biological heterogeneity. Synovitis is the pathological basis of rheumatoid arthritis (RA). Synovial fibroblasts (SFs) and synovial macrophages are the core target cells of RA, which results in the destruction of articular cartilage, as well as bone. Recent scRNA-seq technology has made breakthroughs in the differentiation and development of two types of synovial cells, identification of subsets, functional analysis, and new therapeutic targets, which will bring remarkable changes in RA treatment.
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Affiliation(s)
- Liyun Cheng
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yanyan Wang
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Ruihe Wu
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Tingting Ding
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongwei Xue
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Chong Gao
- Pathology, Joint Program in Transfusion Medicine, Brigham and Women's Hospital/Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Xiaofeng Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Caihong Wang
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
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24
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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: 25] [Impact Index Per Article: 8.3] [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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25
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Liebold I, Grützkau A, Göckeritz A, Gerl V, Lindquist R, Feist E, Zänker M, Häupl T, Poddubnyy D, Zernicke J, Smiljanovic B, Alexander T, Burmester GR, Gay S, Stuhlmüller B. Peripheral blood mononuclear cells are hypomethylated in active rheumatoid arthritis and methylation correlates with disease activity. Rheumatology (Oxford) 2021; 60:1984-1995. [PMID: 33200208 DOI: 10.1093/rheumatology/keaa649] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/31/2020] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE Epigenetic modifications are dynamic and influence cellular disease activity. The aim of this study was to investigate global DNA methylation in peripheral blood mononuclear cells (PBMCs) of RA patients to clarify whether global DNA methylation pattern testing might be useful in monitoring disease activity as well as the response to therapeutics. METHODS Flow cytometric measurement of 5-methyl-cytosine (5'-mC) was established using the cell line U937. In the subsequent prospective study, 62 blood samples were investigated, including 17 healthy donors and 45 RA patients at baseline and after 3 months of treatment with methotrexate, the IL-6 receptor inhibitor sarilumab, and Janus kinase inhibitors. Methylation status was assessed with an anti-5'-mC antibody and analysed in PBMCs and CD4+, CD8+, CD14+ and CD19+ subsets. Signal intensities of 5'-mC were correlated with 28-joint DASs with ESR and CRP (DAS28-ESR and DAS28-CRP). RESULTS Compared with healthy individuals, PBMCs of RA patients showed a significant global DNA hypomethylation. Signal intensities of 5'-mC correlated with transcription levels of DNMT1, DNMT3B and MTR genes involved in methylation processes. Using flow cytometry, significant good correlations and linear regression values were achieved in RA patients between global methylation levels and DAS28-ESR values for PBMCs (r = -0.55, P = 0.002), lymphocytes (r = -0.57, P = 0.001), CD4+ (r = -0.57, P = 0.001), CD8+ (r = -0.54, P = 0.001), CD14+ (r = -0.49, P = 0.008) and CD19+ (r = -0.52, P = 0.004) cells. CONCLUSIONS The degree of global DNA methylation was found to be associated with disease activity. Based on this novel approach, the degree of global methylation is a promising biomarker for therapy monitoring and the prediction of therapy outcome in inflammatory diseases.
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Affiliation(s)
- Ilka Liebold
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Andreas Grützkau
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz-Institute, Berlin, Germany
| | - Anika Göckeritz
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Velia Gerl
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Randall Lindquist
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz-Institute, Berlin, Germany
| | - Eugen Feist
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany.,Department of Rheumatology, Helios Fachklinik, Vogelsang-Gommern, Germany
| | - Michael Zänker
- Immanuel Klinikum Bernau Herzzentrum Brandenburg, Medizinische Hochschule Brandenburg, Bernau, Germany
| | - Thomas Häupl
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Denis Poddubnyy
- Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité - Universitätsmedizin Berlin, Corporate Member of Berlin Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Jan Zernicke
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Biljana Smiljanovic
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Tobias Alexander
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Gerd R Burmester
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Steffen Gay
- Center of Experimental Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Bruno Stuhlmüller
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
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26
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El-Sayed A, Aleya L, Kamel M. The link among microbiota, epigenetics, and disease development. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:28926-28964. [PMID: 33860421 DOI: 10.1007/s11356-021-13862-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The microbiome is a community of various microorganisms that inhabit or live on the skin of humans/animals, sharing the body space with their hosts. It is a sort of complex ecosystem of trillions of commensals, symbiotic, and pathogenic microorganisms, including trillions of bacteria, archaea, protozoa, fungi, and viruses. The microbiota plays a role in the health and disease status of the host. Their number, species dominance, and viability are dynamic. Their long-term disturbance is usually accompanied by serious diseases such as metabolic disorders, cardiovascular diseases, or even cancer. While epigenetics is a term that refers to different stimuli that induce modifications in gene expression patterns without structural changes in the inherited DNA sequence, these changes can be reversible or even persist for several generations. Epigenetics can be described as cell memory that stores experience against internal and external factors. Results from multiple institutions have contributed to the role and close interaction of both microbiota and epigenetics in disease induction. Understanding the mechanisms of both players enables a better understanding of disease induction and development and also opens the horizon to revolutionary therapeutic approaches. The present review illustrates the roles of diet, microbiome, and epigenetics in the induction of several chronic diseases. In addition, it discusses the application of epigenetic data to develop diagnostic biomarkers and therapeutics and evaluate their safety for patients. Understanding the interaction among all these elements enables the development of innovative preventive/therapeutic approaches for disease control.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, F-25030, Besançon Cedex, France
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
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27
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Sensitization of knee-innervating sensory neurons by tumor necrosis factor-α-activated fibroblast-like synoviocytes: an in vitro, coculture model of inflammatory pain. Pain 2021; 161:2129-2141. [PMID: 32332252 PMCID: PMC7431145 DOI: 10.1097/j.pain.0000000000001890] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/10/2020] [Indexed: 12/13/2022]
Abstract
ABSTRACT Pain is a principal contributor to the global burden of arthritis with peripheral sensitization being a major cause of arthritis-related pain. Within the knee joint, distal endings of dorsal root ganglion neurons (knee neurons) interact with fibroblast-like synoviocytes (FLS) and the inflammatory mediators they secrete, which are thought to promote peripheral sensitization. Correspondingly, RNA sequencing has demonstrated detectable levels of proinflammatory genes in FLS derived from arthritis patients. This study confirms that stimulation with tumor necrosis factor (TNF-α) results in expression of proinflammatory genes in mouse and human FLS (derived from osteoarthritis and rheumatoid arthritis patients), as well as increased secretion of cytokines from mouse TNF-α-stimulated FLS (TNF-FLS). Electrophysiological recordings from retrograde labelled knee neurons cocultured with TNF-FLS, or supernatant derived from TNF-FLS, revealed a depolarized resting membrane potential, increased spontaneous action potential firing, and enhanced TRPV1 function, all consistent with a role for FLS in mediating the sensitization of pain-sensing nerves in arthritis. Therefore, data from this study demonstrate the ability of FLS activated by TNF-α to promote neuronal sensitization, results that highlight the importance of both nonneuronal and neuronal cells to the development of pain in arthritis.
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28
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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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29
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Location, location, location: how the tissue microenvironment affects inflammation in RA. Nat Rev Rheumatol 2021; 17:195-212. [PMID: 33526927 DOI: 10.1038/s41584-020-00570-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Current treatments for rheumatoid arthritis (RA) do not work well for a large proportion of patients, or at all in some individuals, and cannot cure or prevent this disease. One major obstacle to developing better drugs is a lack of complete understanding of how inflammatory joint disease arises and progresses. Emerging evidence indicates an important role for the tissue microenvironment in the pathogenesis of RA. Each tissue is made up of cells surrounded and supported by a unique extracellular matrix (ECM). These complex molecular networks define tissue architecture and provide environmental signals that programme site-specific cell behaviour. In the synovium, a main site of disease activity in RA, positional and disease stage-specific cellular diversity exist. Improved understanding of the architecture of the synovium from gross anatomy to the single-cell level, in parallel with evidence demonstrating how the synovial ECM is vital for synovial homeostasis and how dysregulated signals from the ECM promote chronic inflammation and tissue destruction in the RA joint, has opened up new ways of thinking about the pathogenesis of RA. These new ideas provide novel therapeutic approaches for patients with difficult-to-treat disease and could also be used in disease prevention.
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30
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Epigenomic and transcriptomic analysis of chronic inflammatory diseases. Genes Genomics 2021; 43:227-236. [PMID: 33638813 DOI: 10.1007/s13258-021-01045-8] [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] [Received: 12/30/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022]
Abstract
Chronic inflammatory diseases (CIDs) have complex pathologies that result from aberrant and persistent immune responses. However, the precise triggers and mechanisms remain elusive. An important aspect of CID research focuses on epigenetics modifications, which regulate gene expression and provide a dynamic transcriptional response to inflammation. In recent years, mounting evidence has demonstrated an association between epigenomic and transcriptomic dysregulation and the phenotypes of CIDs. In particular, epigenetic changes at cis-regulatory elements have provided new insights for immune cell-specific alterations that contribute to disease etiology. Furthermore, the advancements in single-cell genomics provide novel solutions to cell type heterogeneity, which has long posed challenges for CID diagnosis and treatment. In this review, we discuss the current state of epigenomics research of CID and the insights derived from single-cell transcriptomic and epigenomic studies.
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31
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Delay L, Gonçalves Dos Santos G, Dias EV, Yaksh TL, Corr M. Sexual Dimorphism in the Expression of Pain Phenotype in Preclinical Models of Rheumatoid Arthritis. Rheum Dis Clin North Am 2021; 47:245-264. [PMID: 33781493 DOI: 10.1016/j.rdc.2020.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rheumatoid arthritis is one of most frequent rheumatic diseases, affecting around 1% of the population worldwide. Pain impacting the quality of life for the patient with rheumatoid arthritis, is often the primary factor leading them to seek medical care. Although sex-related differences in humans and animal models of rheumatoid arthritis are described, the correlation between pain and sex in rheumatoid arthritis has only recently been directly examined. Here we review the literature and explore the mechanisms underlying the expression of the pain phenotype in females and males in preclinical models of rheumatoid arthritis.
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Affiliation(s)
- Lauriane Delay
- Department of Anesthesiology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.
| | | | - Elayne Vieira Dias
- Department of Anesthesiology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Tony L Yaksh
- Department of Anesthesiology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Maripat Corr
- Division of Rheumatology, Allergy and Immunology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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32
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Orr CK, Vieira-Sousa E, Fonseca JE, Veale D. Arthroscopic Guided Synovial Biopsies. Front Med (Lausanne) 2021; 7:604582. [PMID: 33681237 PMCID: PMC7928330 DOI: 10.3389/fmed.2020.604582] [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: 09/09/2020] [Accepted: 11/23/2020] [Indexed: 01/23/2023] Open
Abstract
Synovial tissue can be safely and reliably collected for research and clinical purposes using arthroscopy. This technique offers the obvious advantage of allowing direct visualization, and targeted biopsy of specific areas of interest within the joint, as well as for the collection of tissue which will include a lining layer. Much has been learnt by studying the synovium retrieved using this technique concerning the pathobiology of inflammatory arthritis. Furthermore, recent evidence suggests that the tissue retrieved may enable the identification of unique pathotypes that will allow for a precise approach to treatment selection in individual patients. Although ultrasound guided techniques for sampling synovial tissue have gained in popularity over the last decade, both methodologies are expected to compliment each other, each having unique benefits and drawbacks. We present here a detailed description of the arthroscopy technique reporting on our collective experience at two centers in Europe.
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Affiliation(s)
- Carl Kieran Orr
- Centre for Arthritis and Rheumatic Diseases, Saint Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Elsa Vieira-Sousa
- Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon Academic Medical Center, Lisbon, Portugal.,Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - João Eurico Fonseca
- Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon Academic Medical Center, Lisbon, Portugal.,Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - Douglas Veale
- Centre for Arthritis and Rheumatic Diseases, Saint Vincent's University Hospital, University College Dublin, Dublin, Ireland
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33
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Ai R, Boyle DL, Wang W, Firestein GS. Distinct DNA Methylation Patterns of Rheumatoid Arthritis Peripheral Blood and Synovial Tissue T Cells. ACR Open Rheumatol 2021; 3:127-132. [PMID: 33544432 PMCID: PMC7966880 DOI: 10.1002/acr2.11231] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/28/2020] [Indexed: 01/08/2023] Open
Abstract
Objective To study epigenetic patterns in T lymphocytes that accumulate in the rheumatoid arthritis (RA) synovium, we characterized DNA methylation of CD3+ T cells in peripheral blood and synovial tissue in patients with RA and osteoarthritis (OA). Methods Genomic DNA of CD3+ T cells was isolated from patients with RA (n = 8) and OA (n = 5) from blood or the synovium at the time of an arthroplasty using antibodies and magnetic beads. Methylation was measured by using the Illumina Infinium MethylationEPIC Kit. Differentially methylated loci (DML) and differentially methylated genes (DMGs) were identified by using Welch’s t‐test. Principal component analysis, hierarchical clustering, and pathway analysis were used to determine relationships among groups. Results When we compared DNA methylation of CD3+ T cells between peripheral blood and synovial tissue within each disease, 4615 and 164 DML were identified in RA and OA samples, respectively, resulting in 832 and 36 DMGs. A principal component analysis showed that methylation differences in T cells were greater on the basis of on location (blood vs synovium) rather than disease (RA vs OA). Differentially modified pathways were significantly enriched between RA blood and synovial T cells, especially in genes related to complement, integrin cell surface interactions, and the P53 pathway. The limited number of DMGs identified between OA blood and synovial T cells did not conform to biologic pathways. Conclusion The patterns of DNA methylation in RA show location‐specific differences related to immune pathways, whereas methylation differences in OA are limited. The RA joint‐specific signatures could be due to selective accumulation of T‐cell populations or expansion of differentially marked adaptive immune cells. Understanding epigenetic patterns could provide clues to the types of T cells that accumulate in the RA joint and identify potential therapeutic targets.
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Affiliation(s)
- Rizi Ai
- University of CaliforniaSan Diego
| | | | - Wei Wang
- University of CaliforniaSan Diego
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34
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Bonek K, Roszkowski L, Massalska M, Maslinski W, Ciechomska M. Biologic Drugs for Rheumatoid Arthritis in the Context of Biosimilars, Genetics, Epigenetics and COVID-19 Treatment. Cells 2021; 10:323. [PMID: 33557301 PMCID: PMC7914976 DOI: 10.3390/cells10020323] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/24/2021] [Accepted: 01/30/2021] [Indexed: 01/08/2023] Open
Abstract
Rheumatoid arthritis (RA) affects around 1.2% of the adult population. RA is one of the main reasons for work disability and premature retirement, thus substantially increasing social and economic burden. Biological disease-modifying antirheumatic drugs (bDMARDs) were shown to be an effective therapy especially in those rheumatoid arthritis (RA) patients, who did not adequately respond to conventional synthetic DMARD therapy. However, despite the proven efficacy, the high cost of the therapy resulted in limitation of the widespread use and unequal access to the care. The introduction of biosimilars, which are much cheaper relative to original drugs, may facilitate the achievement of the therapy by a much broader spectrum of patients. In this review we present the properties of original biologic agents based on cytokine-targeted (blockers of TNF, IL-6, IL-1, GM-CSF) and cell-targeted therapies (aimed to inhibit T cells and B cells properties) as well as biosimilars used in rheumatology. We also analyze the latest update of bDMARDs' possible influence on DNA methylation, miRNA expression and histone modification in RA patients, what might be the important factors toward precise and personalized RA treatment. In addition, during the COVID-19 outbreak, we discuss the usage of biologicals in context of effective and safe COVID-19 treatment. Therefore, early diagnosing along with therapeutic intervention based on personalized drugs targeting disease-specific genes is still needed to relieve symptoms and to improve the quality of life of RA patients.
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Affiliation(s)
- Krzysztof Bonek
- Department of Rheumatology, National Institute of Geriatrics Rheumatology and Rehabilitation, 02-635 Warsaw, Poland; (K.B.); (L.R.)
| | - Leszek Roszkowski
- Department of Rheumatology, National Institute of Geriatrics Rheumatology and Rehabilitation, 02-635 Warsaw, Poland; (K.B.); (L.R.)
| | - Magdalena Massalska
- Department of Pathophysiology and Immunology, National Institute of Geriatrics Rheumatology and Rehabilitation, 02-635 Warsaw, Poland; (M.M.); (W.M.)
| | - Wlodzimierz Maslinski
- Department of Pathophysiology and Immunology, National Institute of Geriatrics Rheumatology and Rehabilitation, 02-635 Warsaw, Poland; (M.M.); (W.M.)
| | - Marzena Ciechomska
- Department of Pathophysiology and Immunology, National Institute of Geriatrics Rheumatology and Rehabilitation, 02-635 Warsaw, Poland; (M.M.); (W.M.)
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35
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The progress on the estimation of DNA methylation level and the detection of abnormal methylation. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-022-0289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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36
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Sepsis and Autoimmune Disease: Pathology, Systems Medicine, and Artificial Intelligence. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11643-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Mo XB, Zhang YH, Lei SF. Integrative analysis identifies potential causal methylation-mRNA regulation chains for rheumatoid arthritis. Mol Immunol 2020; 131:89-96. [PMID: 33386149 DOI: 10.1016/j.molimm.2020.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies have identified many genetic loci for rheumatoid arthritis (RA). However, causal factors underlying these loci were largely unknown. The aim of this study was to identify potential causal methylation-mRNA regulation chains for RA. We identified differentially expressed mRNAs and methylations and conducted summary statistic data-based Mendelian randomization (SMR) analysis to detect potential causal mRNAs and methylations for RA. Then causal inference test (CIT) was performed to determine if the methylation-mRNA pairs formed causal chains. We identified 11,170 mRNAs and 24,065 methylations that were nominally associated with RA. Among them, 197 mRNAs and 104 methylations passed the SMR test. According to physical positions, we defined 16 cis methylation-mRNA pairs and inferred 5 chains containing 4 methylations and 4 genes (BACH2, MBP, MX1 and SYNGR1) to be methylation→mRNA→RA causal chains. The effect of SYNGR1 expression in peripheral blood mononuclear cells on RA risk was found to be consistent in both the in-house and public data. The identified methylations located in CpG Islands that overlap promoters in the 5' region of the genes. The promoter regions showed long-range interactions with other enhancers and promoters, suggesting a regulatory potential of these methylations. Therefore, the present study provided a new integrative analysis strategy and highlighted potential causal methylation-mRNA chains for RA. Taking the evidences together, SYNGR1 promoter methylations most probably affect mRNA expressions and then affect RA risk.
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Affiliation(s)
- Xing-Bo Mo
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, 215123, PR China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Yong-Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, 215123, PR China
| | - Shu-Feng Lei
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, 215123, PR China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, Jiangsu, 215123, PR China.
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Effects of Biological Therapies on Molecular Features of Rheumatoid Arthritis. Int J Mol Sci 2020; 21:ijms21239067. [PMID: 33260629 PMCID: PMC7731249 DOI: 10.3390/ijms21239067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/15/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune and chronic inflammatory disease primarily affecting the joints, and closely related to specific autoantibodies that mostly target modified self-epitopes. Relevant findings in the field of RA pathogenesis have been described. In particular, new insights come from studies on synovial fibroblasts and cells belonging to the innate and adaptive immune system, which documented the aberrant production of inflammatory mediators, oxidative stress and NETosis, along with relevant alterations of the genome and on the regulatory epigenetic mechanisms. In recent years, the advances in the understanding of RA pathogenesis by identifying key cells and cytokines allowed the development of new targeted disease-modifying antirheumatic drugs (DMARDs). These drugs considerably improved treatment outcomes for the majority of patients. Moreover, numerous studies demonstrated that the pharmacological therapy with biologic DMARDs (bDMARDs) promotes, in parallel to their clinical efficacy, significant improvement in all these altered molecular mechanisms. Thus, continuous updating of the knowledge of molecular processes associated with the pathogenesis of RA, and on the specific effects of bDMARDs in the correction of their dysregulation, are essential in the early and correct approach to the treatment of this complex autoimmune disorder. The present review details basic mechanisms related to the physiopathology of RA, along with the core mechanisms of response to bDMARDs.
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Yan M, Su J, Li Y. Rheumatoid arthritis-associated bone erosions: evolving insights and promising therapeutic strategies. Biosci Trends 2020; 14:342-348. [PMID: 32908076 DOI: 10.5582/bst.2020.03253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The human immune system has evolved to recognize and eradicate pathogens, a process that is known as "host defense". If, however, the immune system does not work properly, it can mistakenly attack the body's own tissues and induce autoimmune diseases. Rheumatoid arthritis (RA) is such an autoimmune disease in which the synovial joints are predominately attacked by the immune system. Moreover, RA is associated with bone destruction and joint deformity. Although biologic agents have propelled RA treatment forward dramatically over the past 30 years, a considerable number of patients with RA still experience progressive bone damage and joint disability. That is to be expected since current RA therapies are all intended to halt inflammation but not to alleviate bone destruction. A better understanding of bone erosions is crucial to developing a novel strategy to treat RA-associated erosions. This review provides insights into RA-associated bone destruction and perspectives for future clinical interventions.
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Affiliation(s)
- Minglu Yan
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jianling Su
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yang Li
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Judge M, Parker E, Naniche D, Le Souëf P. Gene Expression: the Key to Understanding HIV-1 Infection? Microbiol Mol Biol Rev 2020; 84:e00080-19. [PMID: 32404327 PMCID: PMC7233484 DOI: 10.1128/mmbr.00080-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Gene expression profiling of the host response to HIV infection has promised to fill the gaps in our knowledge and provide new insights toward vaccine and cure. However, despite 20 years of research, the biggest questions remained unanswered. A literature review identified 62 studies examining gene expression dysregulation in samples from individuals living with HIV. Changes in gene expression were dependent on cell/tissue type, stage of infection, viremia, and treatment status. Some cell types, notably CD4+ T cells, exhibit upregulation of cell cycle, interferon-related, and apoptosis genes consistent with depletion. Others, including CD8+ T cells and natural killer cells, exhibit perturbed function in the absence of direct infection with HIV. Dysregulation is greatest during acute infection. Differences in study design and data reporting limit comparability of existing research and do not as yet provide a coherent overview of gene expression in HIV. This review outlines the extraordinarily complex host response to HIV and offers recommendations to realize the full potential of HIV host transcriptomics.
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Affiliation(s)
- Melinda Judge
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Erica Parker
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Denise Naniche
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigação de Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Peter Le Souëf
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
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Tang J, Zou J, Zhang X, Fan M, Tian Q, Fu S, Gao S, Fan S. PretiMeth: precise prediction models for DNA methylation based on single methylation mark. BMC Genomics 2020; 21:364. [PMID: 32414326 PMCID: PMC7227319 DOI: 10.1186/s12864-020-6768-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/04/2020] [Indexed: 11/29/2022] Open
Abstract
Background The computational prediction of methylation levels at single CpG resolution is promising to explore the methylation levels of CpGs uncovered by existing array techniques, especially for the 450 K beadchip array data with huge reserves. General prediction models concentrate on improving the overall prediction accuracy for the bulk of CpG loci while neglecting whether each locus is precisely predicted. This leads to the limited application of the prediction results, especially when performing downstream analysis with high precision requirements. Results Here we reported PretiMeth, a method for constructing precise prediction models for each single CpG locus. PretiMeth used a logistic regression algorithm to build a prediction model for each interested locus. Only one DNA methylation feature that shared the most similar methylation pattern with the CpG locus to be predicted was applied in the model. We found that PretiMeth outperformed other algorithms in the prediction accuracy, and kept robust across platforms and cell types. Furthermore, PretiMeth was applied to The Cancer Genome Atlas data (TCGA), the intensive analysis based on precise prediction results showed that several CpG loci and genes (differentially methylated between the tumor and normal samples) were worthy for further biological validation. Conclusion The precise prediction of single CpG locus is important for both methylation array data expansion and downstream analysis of prediction results. PretiMeth achieved precise modeling for each CpG locus by using only one significant feature, which also suggested that our precise prediction models could be probably used for reference in the probe set design when the DNA methylation beadchip update. PretiMeth is provided as an open source tool via https://github.com/JxTang-bioinformatics/PretiMeth.
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Affiliation(s)
- Jianxiong Tang
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Jianxiao Zou
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Xiaoran Zhang
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China.,Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Mei Fan
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Qi Tian
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Shuyao Fu
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Shihong Gao
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Shicai Fan
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China. .,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, China.
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Nygaard G, Firestein GS. Restoring synovial homeostasis in rheumatoid arthritis by targeting fibroblast-like synoviocytes. Nat Rev Rheumatol 2020; 16:316-333. [PMID: 32393826 DOI: 10.1038/s41584-020-0413-5] [Citation(s) in RCA: 415] [Impact Index Per Article: 103.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 12/31/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic immune-mediated disease that primarily affects the synovium of diarthrodial joints. During the course of RA, the synovium transforms into a hyperplastic invasive tissue that causes destruction of cartilage and bone. Fibroblast-like synoviocytes (FLS), which form the lining of the joint, are epigenetically imprinted with an aggressive phenotype in RA and have an important role in these pathological processes. In addition to producing the extracellular matrix and joint lubricants, FLS in RA produce pathogenic mediators such as cytokines and proteases that contribute to disease pathogenesis and perpetuation. The development of multi-omics integrative analyses have enabled new ways to dissect the mechanisms that imprint FLS, have helped to identify potential FLS subsets with distinct functions and have identified differences in FLS phenotypes between joints in individual patients. This Review provides an overview of advances in understanding of FLS biology and highlights omics approaches and studies that hold promise for identifying future therapeutic targets.
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Affiliation(s)
- Gyrid Nygaard
- Division of Rheumatology, Allergy and Immunology, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California San Diego School of Medicine, San Diego, CA, USA.
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Huang YS, Ogbechi J, Clanchy FI, Williams RO, Stone TW. IDO and Kynurenine Metabolites in Peripheral and CNS Disorders. Front Immunol 2020; 11:388. [PMID: 32194572 PMCID: PMC7066259 DOI: 10.3389/fimmu.2020.00388] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
The importance of the kynurenine pathway in normal immune system function has led to an appreciation of its possible contribution to autoimmune disorders such as rheumatoid arthritis. Indoleamine-2,3-dioxygenase (IDO) activity exerts a protective function, limiting the severity of experimental arthritis, whereas deletion or inhibition exacerbates the symptoms. Other chronic disorder with an inflammatory component, such as atherosclerosis, are also suppressed by IDO activity. It is suggested that this overall anti-inflammatory activity is mediated by a change in the relative production or activity of Th17 and regulatory T cell populations. Kynurenines may play an anti-inflammatory role also in CNS disorders such as Huntington's disease, Alzheimer's disease and multiple sclerosis, in which signs of inflammation and neurodegeneration are involved. The possibility is discussed that in Huntington's disease kynurenines interact with other anti-inflammatory molecules such as Human Lymphocyte Antigen-G which may be relevant in other disorders. Kynurenine involvement may account for the protection afforded to animals with cerebral malaria and trypanosomiasis when they are treated with an inhibitor of kynurenine-3-monoxygenase (KMO). There is some evidence that changes in IL-10 may contribute to this protection and the relationship between kynurenines and IL-10 in arthritis and other inflammatory conditions should be explored. In addition, metabolites of kynurenine downstream of KMO, such as anthranilic acid and 3-hydroxy-anthranilic acid can influence inflammation, and the ratio of these compounds is a valuable biomarker of inflammatory status although the underlying molecular mechanisms of the changes require clarification. Hence it is essential that more effort be expended to identify their sites of action as potential targets for drug development. Finally, we discuss increasing awareness of the epigenetic regulation of IDO, for example by DNA methylation, a phenomenon which may explain differences between individuals in their susceptibility to arthritis and other inflammatory disorders.
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Affiliation(s)
- Yi-Shu Huang
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Joy Ogbechi
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Felix I Clanchy
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Richard O Williams
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Trevor W Stone
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
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Abstract
Cells, the basic units of life, have striking differences at transcriptomic, proteomic and epigenomic levels across tissues, organs, organ systems and organisms. The coordination of individual immune cells is essential for the generation of effective immune responses to pathogens while immune tolerance is maintained to protect the host. In rheumatic diseases, when immune responses are dysregulated, pathologically important cells might represent only a small fraction of the immune system. Interrogation of the contributions of individual immune cells to pathogenesis and disease progression should therefore reveal important insights into the complicated aetiology of rheumatic diseases. Technological advances are enabling the high-dimensional dissection of single cells at multiple omics levels, which could facilitate the identification of dysregulated molecular mechanisms in patients with rheumatic diseases and the discovery of new therapeutic targets and biomarkers. The single-cell technologies that have been developed over the past decade and the experimental platforms that enable multi-omics integrative analyses have already made inroads into immunology-related fields of study and have potential for use in rheumatology. Layers of omics data derived from single cells are likely to fundamentally change our understanding of the molecular pathways that underpin the pathogenesis of rheumatic diseases.
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Barreto G, Soliymani R, Baumann M, Waris E, Eklund KK, Zenobi-Wong M, Lalowski M. Functional analysis of synovial fluid from osteoarthritic knee and carpometacarpal joints unravels different molecular profiles. Rheumatology (Oxford) 2020; 58:897-907. [PMID: 30085131 DOI: 10.1093/rheumatology/key232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/25/2018] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE In this work, we aimed to elucidate the molecular mechanisms driving primary OA. By studying the dynamics of protein expression in two different types of OA joints we searched for similarities and disparities to identify key molecular mechanisms driving OA. METHODS For this purpose, human SF samples were obtained from CMC-I OA and knee joint of OA patients. SF samples were analysed by label-free quantitative liquid chromatography mass spectrometry. Disease-relevant proteins identified in proteomics studies, such as clusterin, paraoxonase/arylesterase 1 (PON1) and transthyretin were validated by enzyme-linked immunosorbent assays, and on the mRNA level by droplet digital PCR. Functional studies were performed in vitro using primary chondrocytes. RESULTS Differential proteomic changes were observed in the concentration of 40 proteins including clusterin, PON1 and transthyretin. Immunoassay analyses of clusterin, PON1, transthyretin and other inflammatory cytokines confirmed significant differences in protein concentration in SF of CMC-I and knee OA patients, with primarily lower protein expression levels in CMC-I. Functional studies on chondrocytes unequivocally demonstrated that stimulation with SF obtained from knee OA, in contrast to CMC-I OA joint, caused a significant upregulation in pro-inflammatory response, cell death and hypertrophy. CONCLUSION This study demonstrates that differential expression of molecular players in SF from different OA joints evokes diverse effects on primary chondrocytes. The pathomolecular mechanisms of OA may significantly differ in various joints, a finding that brings a new dimension into the pathogenesis of primary OA.
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Affiliation(s)
- Goncalo Barreto
- Tissue Engineering + Biofabrication, ETH Zürich, Zürich, Switzerland
| | - Rabah Soliymani
- Helsinki Institute for Life Science (HiLIFE) and Faculty of Medicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Finland
| | - Marc Baumann
- Helsinki Institute for Life Science (HiLIFE) and Faculty of Medicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Finland
| | - Eero Waris
- Department of Hand Surgery, University of Helsinki and Helsinki University Central Hospital, Finland
| | - Kari K Eklund
- Rheumatology, University of Helsinki and Helsinki University Central Hospital, Finland.,Orton Orthopaedic Hospital and Research Institute, Invalid Foundation, Helsinki, Finland
| | - Marcy Zenobi-Wong
- Tissue Engineering + Biofabrication, ETH Zürich, Zürich, Switzerland
| | - Maciej Lalowski
- Helsinki Institute for Life Science (HiLIFE) and Faculty of Medicine, Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Finland
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Scarneo SA, Eibschutz LS, Bendele PJ, Yang KW, Totzke J, Hughes P, Fox DA, Haystead TAJ. Pharmacological inhibition of TAK1, with the selective inhibitor takinib, alleviates clinical manifestation of arthritis in CIA mice. Arthritis Res Ther 2019; 21:292. [PMID: 31847895 PMCID: PMC6918687 DOI: 10.1186/s13075-019-2073-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To examine the ability of takinib, a selective transforming growth factor beta-activated kinase 1 (TAK1) inhibitor, to reduce the severity of murine type II collagen-induced arthritis (CIA), and to affect function of synovial cells. METHODS Following the induction of CIA, mice were treated daily with takinib (50 mg/kg) and clinical scores assessed. Thirty-six days post-CIA induction, histology was performed on various joints of treated and vehicle-treated animals. Inflammation, pannus, cartilage damage, bone resorption, and periosteal bone formation were quantified. Furthermore, pharmacokinetics of takinib were evaluated by LC-MS in various tissues. Rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS) cells were cultured with 10 μM takinib and cytokine secretion analyzed by cytokine/chemokine proteome array. Cytotoxicity of takinib for RA-FLS was measured with 24 to 48 h cultures in the presence or absence of tumor necrosis factor (TNF). RESULTS Here, we show takinib's ability to reduce the clinical score in the CIA mouse model of rheumatoid arthritis (RA) (p < 0.001). TAK1 inhibition reduced inflammation (p < 0.01), cartilage damage (p < 0.01), pannus, bone resorption, and periosteal bone formation and periosteal bone width in all joints of treated mice compared to vehicle treated. Significant reduction of inflammation (p < 0.004) and cartilage damage (p < 0.004) were observed in the knees of diseased treated animals, with moderate reduction seen in the forepaws and hind paws. Furthermore, the pharmacokinetics of takinib show rapid plasma clearance (t½ = 21 min). In stimulated RA-FLS cells, takinib reduced GROα, G-CSF, and ICAM-1 pro-inflammatory cytokine signaling. CONCLUSION Our findings support the hypothesis that TAK1 targeted therapy represents a novel therapeutic axis to treat RA and other inflammatory diseases.
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Affiliation(s)
- Scott A Scarneo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, LSRC C112, 308 Research Drive, Durham, NC, 27710, USA
| | - Liesl S Eibschutz
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, LSRC C112, 308 Research Drive, Durham, NC, 27710, USA
| | - Phillip J Bendele
- Bolder BioPATH, Inc., 5541 Central Ave., Suite 160, Boulder, CO, 80301, USA
| | - Kelly W Yang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, LSRC C112, 308 Research Drive, Durham, NC, 27710, USA
| | - Juliane Totzke
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, LSRC C112, 308 Research Drive, Durham, NC, 27710, USA
| | - Philip Hughes
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, LSRC C112, 308 Research Drive, Durham, NC, 27710, USA
| | - David A Fox
- Division of Rheumatology and Clinical Autoimmunity Center of Excellence, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Timothy A J Haystead
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, LSRC C112, 308 Research Drive, Durham, NC, 27710, USA.
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Increased presence and differential molecular imprinting of transit amplifying cells in psoriasis. J Mol Med (Berl) 2019; 98:111-122. [PMID: 31832701 DOI: 10.1007/s00109-019-01860-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/07/2019] [Accepted: 11/26/2019] [Indexed: 01/01/2023]
Abstract
Psoriasis is a very common chronic inflammatory skin disease characterized by epidermal thickening and scaling resulting from keratinocyte hyperproliferation and impaired differentiation. Pathomechanistic studies in psoriasis are often limited by using whole skin tissue biopsies, neglecting their stratification and cellular diversity. This study aimed at characterizing epidermal alterations in psoriasis at the level of keratinocyte populations. Epidermal cell populations were purified from skin biopsies of psoriasis patients and healthy donors using a novel cell type-specific approach. Molecular characterization of the transit-amplifying cells (TAC), the key players of epidermal renewal, was performed using immunocytofluorescence-technique and integrated multiscale-omics analyses. Already TAC from non-lesional psoriatic skin showed altered methylation and differential expression in 1.7% and 1.0% of all protein-coding genes, respectively. In psoriatic lesions, TAC were strongly expanded showing further increased differentially methylated (10-fold) and expressed (22-fold) genes numbers. Importantly, 17.2% of differentially expressed genes were associated with respective gene methylations. Compared with non-lesional TAC, pathway analyses revealed metabolic alterations as one feature predominantly changed in TAC derived from active psoriatic lesions. Overall, our study showed stage-specific molecular alterations, allows new insights into the pathogenesis, and implies the involvement of epigenetic mechanisms in lesion development in psoriasis. KEY MESSAGES: Transit amplifying cell (TAC) numbers are highly increased in psoriatic lesions Psoriatic TAC show profound molecular alterations & stage-specific identity TAC from unaffected areas already show first signs of molecular alterations Lesional TAC show a preference in metabolic-related alterations.
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Iwamoto N, Kawakami A. Recent findings regarding the effects of microRNAs on fibroblast-like synovial cells in rheumatoid arthritis. Immunol Med 2019; 42:156-161. [PMID: 31770498 DOI: 10.1080/25785826.2019.1695490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease with severe joint inflammation and destruction characterized by marked hyperplasia of the lining layer of the synovium. Fibroblast-like synovial cells (FLS) is a key cellular component within the synovia; it plays pivotal roles in RA pathogenesis by unfavorable behaviors such as producing inflammatory cytokines and chemokines, and hyperproliferation. MicroRNAs are evolutionarily conserved small non-coding RNAs (length is 18-25 nucleotides) that regulate gene expression at the post-transcriptional level. There is increasing interest in the involvement of microRNAs in autoimmune diseases including RA. Recent studies revealed the regulation of the function of FLS by microRNAs. Here, we review the known functional microRNAs in RA and summarize the potential uses of these small molecules in the treatment of RA.
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Affiliation(s)
- Naoki Iwamoto
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Nielsen MA, Lomholt S, Mellemkjaer A, Andersen MN, Buckley CD, Kragstrup TW. Responses to Cytokine Inhibitors Associated with Cellular Composition in Models of Immune-Mediated Inflammatory Arthritis. ACR Open Rheumatol 2019; 2:3-10. [PMID: 31943973 PMCID: PMC6957916 DOI: 10.1002/acr2.11094] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
Objective Immune‐mediated inflammatory arthritis (IMIA) is a heterogeneous group of diseases including rheumatoid arthritis (RA), psoriatic arthritis (PsA), and spondyloarthritis (SpA). Disease‐modifying antirheumatic drugs (DMARDs) target very different cellular components of the disease processes. Characterization of the pathobiological subtypes of IMIA could provide more specific treatment approaches for each disease. For example, RA has been proposed to consist of at least three synovial pathotypes (lymphoid, myeloid, and fibroid), and only a subgroup of RA patients have erosive disease. The objective of this study was to evaluate the effects of various DMARDs on different synovial cell subsets using human ex vivo models of IMIA. Methods Synovial fluid and blood samples were obtained from a study population consisting of patients with RA, PsA, or peripheral SpA with at least one swollen joint (n = 18). The DMARDs used in this study were methotrexate, adalimumab, etanercept, tocilizumab, anakinra, ustekinumab, secukinumab, tofacitinib, and baricitinib. Paired synovial fluid mononuclear cells (SFMCs), peripheral blood mononuclear cells (PBMCs), and fibroblast‐like synovial cells (FLSs) were used in three different previously optimized ex vivo models. Results In SFMCs cultured for 48 hours, all DMARDs except anakinra decreased the production of monocyte chemoattractant protein (MCP)‐1. In SFMCs cultured for 21 days, only the two tumor necrosis factor alpha (TNFα) inhibitors adalimumab and etanercept decreased the secretion of tartrate‐resistant acid phosphatase (P < 0.01, P < 0.001). In the FLS and PBMC 48‐hour co‐cultures, only tocilizumab (P < 0.001) and the two Janus kinase inhibitors tofacitinib and baricitinib (both P < 0.05) decreased the production of MCP‐1 by around 50%. Conclusion TNFα inhibition was effective in preventing inflammatory osteoclastogenesis, whereas tocilizumab, tofacitinib, and baricitinib had superior efficacy in cultures dominated by FLSs. Taken together, this study reveals that responses to cytokine inhibitors associate with cellular composition in models of IMIA. In particular, this study provides new evidence on the differential effect of DMARDs on leukocytes compared with stromal cells.
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Affiliation(s)
| | | | | | | | - Christopher D Buckley
- University of Oxford, Oxford, and University of Birmingham, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Tue W Kragstrup
- Aarhus University and Aarhus University Hospital, Aarhus, Denmark
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Wu M, Li X, Zhang C, Zhang C, Qian D, Ma J, Cai M, Tang L, Cheng H, Shen C, Chen G, Zheng X, Zhang X, Zhou F. DNA methylation profile of psoriatic skins from different body locations. Epigenomics 2019; 11:1613-1625. [PMID: 31701765 DOI: 10.2217/epi-2018-0225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To understand whether the anatomical location of origin plays a role in shaping the DNA methylation (DNAm) landscape of psoriatic skins. Patients & methods: A number of 108 psoriatic and 57 control skin samples were grouped based on their anatomical locations. Two group t-tests were used to identify those differentially methylated sites and regions. Target region methylation loci were validated by bisulfate conversion sequencing. The correlations of DNAm with pathological features, DNAm and gene expression were also interrogated. Results: Our analysis revealed 315 location-specific differentially methylated sites for back, 291 for the extremities and 801 for abdomen. Moreover, we observed that the extremity-specific loci cg21942490 located on HOXA9 is associated with hyperkeratosis. We further observed that HOXA5 and KIAA1949 are differential methylation regions. Conclusion: Our study shown evidence of anatomical location-dependent DNAm pattern in psoriasis skins, and thus provided new insights into the pathogenesis of this disease.
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Affiliation(s)
- Mingshun Wu
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Xueying Li
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Chaowen Zhang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Chuanliang Zhang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Danfeng Qian
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Jie Ma
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Minglong Cai
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Lili Tang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Hui Cheng
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Changbing Shen
- Department of Dermatology, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Gang Chen
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Xiaodong Zheng
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Xuejun Zhang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,Department of Dermatology, Institute of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, PR China
| | - Fusheng Zhou
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
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