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Cecchi I, Radin M, Barinotti A, Foddai SG, Menegatti E, Roccatello D, Suárez A, Sciascia S, Rodríguez-Carrio J. Type I interferon pathway activation across the antiphospholipid syndrome spectrum: associations with disease subsets and systemic antiphospholipid syndrome presentation. Front Immunol 2024; 15:1351446. [PMID: 38550580 PMCID: PMC10972891 DOI: 10.3389/fimmu.2024.1351446] [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: 12/06/2023] [Accepted: 02/29/2024] [Indexed: 04/02/2024] Open
Abstract
Introduction While the type I interferon (IFN-I) pathway is crucial in autoimmunity, its role in antiphospholipid antibody (aPL)-positive subjects, including aPL carriers and antiphospholipid syndrome (APS) patients, is poorly understood. This study aims at characterizing IFN-I pathway activation within the spectrum of aPL-positive subsets. Methods A total of 112 patients [29 aPL carriers, 31 primary APS (PAPS), 25 secondary APS (SAPS), 27 systemic lupus erythematosus (SLE) patients without aPL, and 44 healthy controls (HCs)] were recruited. IFI6, IFI44, IFI44L, MX1, IFI27, OAS1, and RSAD2 gene expression was evaluated in whole blood, and a composite index (IFN score) was calculated. Results An overall activation of the IFN-I pathway was observed across the entire APS spectrum, with differences among genes based on the specific disease subset. The composite score revealed quantitative differences across subsets, being elevated in aPL carriers and PAPS patients compared to HCs (both p < 0.050) and increasing in SAPS (p < 0.010) and SLE patients (p < 0.001). An unsupervised cluster analysis identified three clusters, and correspondence analyses revealed differences in clusters usage across APS subsets (p < 0.001). A network analysis revealed different patterns characterizing different subsets. The associations between IFN-I pathway activation and clinical outcomes differed across APS subsets. Although no differences in gene expression were observed in systemic APS, the network analyses revealed specific gene-gene patterns, and a distinct distribution of the clusters previously identified was noted (p = 0.002). Conclusion IFN-I pathway activation is a common hallmark among aPL-positive individuals. Qualitative and quantitative differences across the APS spectrum can be identified, leading to the identification of distinct IFN-I signatures with different clinical values beyond traditional categorization.
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Affiliation(s)
- Irene Cecchi
- University Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) with Nephrology and Dialysis Unit and Center of Immuno-Rheumatology and Rare Diseases (CMID), Coordinating Center of the Interregional Network for Rare Diseases of Piedmont and Aosta Valley, San Giovanni Bosco Hub Hospital, Turin, Italy
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Massimo Radin
- University Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) with Nephrology and Dialysis Unit and Center of Immuno-Rheumatology and Rare Diseases (CMID), Coordinating Center of the Interregional Network for Rare Diseases of Piedmont and Aosta Valley, San Giovanni Bosco Hub Hospital, Turin, Italy
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Alice Barinotti
- University Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) with Nephrology and Dialysis Unit and Center of Immuno-Rheumatology and Rare Diseases (CMID), Coordinating Center of the Interregional Network for Rare Diseases of Piedmont and Aosta Valley, San Giovanni Bosco Hub Hospital, Turin, Italy
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Silvia Grazietta Foddai
- University Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) with Nephrology and Dialysis Unit and Center of Immuno-Rheumatology and Rare Diseases (CMID), Coordinating Center of the Interregional Network for Rare Diseases of Piedmont and Aosta Valley, San Giovanni Bosco Hub Hospital, Turin, Italy
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Elisa Menegatti
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Dario Roccatello
- University Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) with Nephrology and Dialysis Unit and Center of Immuno-Rheumatology and Rare Diseases (CMID), Coordinating Center of the Interregional Network for Rare Diseases of Piedmont and Aosta Valley, San Giovanni Bosco Hub Hospital, Turin, Italy
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Ana Suárez
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain
- Area of Metabolism, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Savino Sciascia
- University Center of Excellence on Nephrologic, Rheumatologic and Rare Diseases (ERK-Net, ERN-Reconnect and RITA-ERN Member) with Nephrology and Dialysis Unit and Center of Immuno-Rheumatology and Rare Diseases (CMID), Coordinating Center of the Interregional Network for Rare Diseases of Piedmont and Aosta Valley, San Giovanni Bosco Hub Hospital, Turin, Italy
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Javier Rodríguez-Carrio
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain
- Area of Metabolism, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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2
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Lin CMA, Isaacs JD, Cooles FAH. Role of IFN-α in Rheumatoid Arthritis. Curr Rheumatol Rep 2024; 26:37-52. [PMID: 38051494 PMCID: PMC10787895 DOI: 10.1007/s11926-023-01125-6] [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] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
PURPOSE OF REVIEW Type 1 interferons (IFN-I) are of increasing interest across a wide range of autoimmune rheumatic diseases. Historically, research into their role in rheumatoid arthritis (RA) has been relatively neglected, but recent work continues to highlight a potential contribution to RA pathophysiology. RECENT FINDINGS We emphasise the importance of disease stage when examining IFN-I in RA and provide an overview on how IFN-I may have a direct role on a variety of relevant cellular functions. We explore how clinical trajectory may be influenced by increased IFN-I signalling, and also, the limitations of scores composed of interferon response genes. Relevant environmental triggers and inheritable RA genetic risk relating to IFN-I signalling are explored with emphasis on intriguing data potentially linking IFN-I exposure, epigenetic changes, and disease relevant processes. Whilst these data cumulatively illustrate a likely role for IFN-I in RA, they also highlight the knowledge gaps, particularly in populations at risk for RA, and suggest directions for future research to both better understand IFN-I biology and inform targeted therapeutic strategies.
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Affiliation(s)
- Chung M A Lin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - John D Isaacs
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Faye A H Cooles
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
- Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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Wang R, Singaraju A, Marks KE, Shakib L, Dunlap G, Adejoorin I, Greisen SR, Chen L, Tirpack AK, Aude C, Fein MR, Todd DJ, MacFarlane L, Goodman SM, DiCarlo EF, Massarotti EM, Sparks JA, Jonsson AH, Brenner MB, Postow MA, Chan KK, Bass AR, Donlin LT, Rao DA. Clonally expanded CD38 hi cytotoxic CD8 T cells define the T cell infiltrate in checkpoint inhibitor-associated arthritis. Sci Immunol 2023; 8:eadd1591. [PMID: 37506196 PMCID: PMC10557056 DOI: 10.1126/sciimmunol.add1591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Immune checkpoint inhibitor (ICI) therapies used to treat cancer, such as anti-PD-1 antibodies, can induce autoimmune conditions in some individuals. The T cell mechanisms mediating such iatrogenic autoimmunity and their overlap with spontaneous autoimmune diseases remain unclear. Here, we compared T cells from the joints of 20 patients with an inflammatory arthritis induced by ICI therapy (ICI-arthritis) with two archetypal autoimmune arthritides, rheumatoid arthritis (RA) and psoriatic arthritis (PsA). Single-cell transcriptomic and antigen receptor repertoire analyses highlighted clonal expansion of an activated effector CD8 T cell population in the joints and blood of patients with ICI-arthritis. These cells were identified as CD38hiCD127- CD8 T cells and were uniquely enriched in ICI-arthritis joints compared with RA and PsA and also displayed an elevated interferon signature. In vitro, type I interferon induced CD8 T cells to acquire the ICI-associated CD38hi phenotype and enhanced cytotoxic function. In a cohort of patients with advanced melanoma, ICI therapy markedly expanded circulating CD38hiCD127- T cells, which were frequently bound by the therapeutic anti-PD-1 drug. In patients with ICI-arthritis, drug-bound CD8 T cells in circulation showed marked clonal overlap with drug-bound CD8 T cells from synovial fluid. These results suggest that ICI therapy directly targets CD8 T cells in patients who develop ICI-arthritis and induces an autoimmune pathology that is distinct from prototypical spontaneous autoimmune arthritides.
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Affiliation(s)
- Runci Wang
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Shanghai Institute of Rheumatology / Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China
| | - Anvita Singaraju
- HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Kathryne E. Marks
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lorien Shakib
- HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Garrett Dunlap
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Ifeoluwakiisi Adejoorin
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stinne R. Greisen
- Department of Biomedicine, Aarhus University / Department of Rheumatology, Aarhus University Hospital, Aarhus, Denmark
| | - Lin Chen
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Aidan K. Tirpack
- Medical School at Campbell University School of Osteopathic Medicine, Lillington, NC 27546, USA
| | - Carlos Aude
- Division of Rheumatology, Hospital for Special Surgery / Weill Cornell Medicine, New York, NY 10021, USA
| | - Miriam R. Fein
- HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA
| | - Derrick J. Todd
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lindsey MacFarlane
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Susan M. Goodman
- Division of Rheumatology, Hospital for Special Surgery / Weill Cornell Medicine, New York, NY 10021, USA
| | - Edward F. DiCarlo
- Division of Pathology, Hospital for Special Surgery / Weill Cornell Medicine, New York, NY 10021, USA
| | - Elena M. Massarotti
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey A. Sparks
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - A. Helena Jonsson
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael B. Brenner
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael A. Postow
- Melanoma Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Karmela K. Chan
- Division of Rheumatology, Hospital for Special Surgery / Weill Cornell Medicine, New York, NY 10021, USA
| | - Anne R. Bass
- Division of Rheumatology, Hospital for Special Surgery / Weill Cornell Medicine, New York, NY 10021, USA
| | - Laura T. Donlin
- HSS Research Institute, Hospital for Special Surgery, New York, NY 10021, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Deepak A. Rao
- Division of Rheumatology, Inflammation, Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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Rodríguez-Carrio J, Burska A, Conaghan PG, Dik WA, Biesen R, Eloranta ML, Cavalli G, Visser M, Boumpas DT, Bertsias G, Wahren-Herlenius M, Rehwinkel J, Frémond ML, Crow MK, Rönnblom L, Versnel MA, Vital EM. 2022 EULAR points to consider for the measurement, reporting and application of IFN-I pathway activation assays in clinical research and practice. Ann Rheum Dis 2023; 82:754-762. [PMID: 36858821 DOI: 10.1136/ard-2022-223628] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/04/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND Type I interferons (IFN-Is) play a role in a broad range of rheumatic and musculoskeletal diseases (RMDs), and compelling evidence suggests that their measurement could have clinical value, although testing has not progressed into clinical settings. OBJECTIVE To develop evidence-based points to consider (PtC) for the measurement and reporting of IFN-I assays in clinical research and to determine their potential clinical utility. METHODS EULAR standardised operating procedures were followed. A task force including rheumatologists, immunologists, translational scientists and a patient partner was formed. Two systematic reviews were conducted to address methodological and clinical questions. PtC were formulated based on the retrieved evidence and expert opinion. Level of evidence and agreement was determined. RESULTS Two overarching principles and 11 PtC were defined. The first set (PtC 1-4) concerned terminology, assay characteristics and reporting practices to enable more consistent reporting and facilitate translation and collaborations. The second set (PtC 5-11) addressed clinical applications for diagnosis and outcome assessments, including disease activity, prognosis and prediction of treatment response. The mean level of agreement was generally high, mainly in the first PtC set and for clinical applications in systemic lupus erythematosus. Harmonisation of assay methodology and clinical validation were key points for the research agenda. CONCLUSIONS IFN-I assays have a high potential for implementation in the clinical management of RMDs. Uptake of these PtC will facilitate the progress of IFN-I assays into clinical practice and may be also of interest beyond rheumatology.
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Affiliation(s)
- Javier Rodríguez-Carrio
- Department of Functional Biology, University of Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Agata Burska
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
| | - Philip G Conaghan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
| | - Willem A Dik
- Erasmus MC, University Medical Center Rotterdam, Laboratory Medical Immunology, Department of Immunology, Rotterdam, The Netherlands
| | - Robert Biesen
- Charité University Medicine Berlin, Department of Rheumatology, Berlin, Germany
| | - Maija-Leena Eloranta
- Uppsala University, Department of Medical Sciences, Rheumatology, Uppsala, Sweden
| | - Giulio Cavalli
- Vita-Salute San Raffaele University, Unit of Immunology, Rheumatology, Allergy and Rare Diseases, Milan, Italy
| | - Marianne Visser
- EULAR PARE Patient Research Partner, Amsterdam, The Netherlands
| | - Dimitrios T Boumpas
- Medicine, University of Crete, Medical School, Department of Internal Medicine, Heraklion, Greece
| | - George Bertsias
- University of Crete, Medical School, Department of Rheumatology-Clinical Immunology, Heraklion, Greece
| | - Marie Wahren-Herlenius
- Karolinska Institutet, Division of Rheumatology, Stockholm, Sweden
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Marie-Louise Frémond
- Université de Paris Cité, Hôpital Necker-Enfants Malades, Immuno-Hématologie et Rhumatologie pédiatriques, Paris, France
| | - Mary K Crow
- Hospital for Special Surgery, Weill Cornell Medical College, Mary Kirkland Center for Lupus Research, New York, New York, USA
| | - Lars Rönnblom
- Uppsala University, Department of Medical Sciences, Rheumatology, Uppsala, Sweden
| | - Marjan A Versnel
- Erasmus MC, University Medical Center Rotterdam, Department of Immunology, Rotterdam, The Netherlands
| | - Edward M Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
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5
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Burska A, Rodríguez-Carrio J, Biesen R, Dik WA, Eloranta ML, Cavalli G, Visser M, Boumpas DT, Bertsias G, Wahren-Herlenius M, Rehwinkel J, Frémond ML, Crow MK, Ronnblom L, Conaghan PG, Versnel M, Vital E. Type I interferon pathway assays in studies of rheumatic and musculoskeletal diseases: a systematic literature review informing EULAR points to consider. RMD Open 2023; 9:e002876. [PMID: 36863752 PMCID: PMC9990675 DOI: 10.1136/rmdopen-2022-002876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/08/2023] [Indexed: 03/04/2023] Open
Abstract
OBJECTIVES To systematically review the literature for assay methods that aim to evaluate type I interferon (IFN-I) pathway activation and to harmonise-related terminology. METHODS Three databases were searched for reports of IFN-I and rheumatic musculoskeletal diseases. Information about the performance metrics of assays measuring IFN-I and measures of truth were extracted and summarised. A EULAR task force panel assessed feasibility and developed consensus terminology. RESULTS Of 10 037 abstracts, 276 fulfilled eligibility criteria for data extraction. Some reported more than one technique to measure IFN-I pathway activation. Hence, 276 papers generated data on 412 methods. IFN-I pathway activation was measured using: qPCR (n=121), immunoassays (n=101), microarray (n=69), reporter cell assay (n=38), DNA methylation (n=14), flow cytometry (n=14), cytopathic effect assay (n=11), RNA sequencing (n=9), plaque reduction assay (n=8), Nanostring (n=5), bisulphite sequencing (n=3). Principles of each assay are summarised for content validity. Concurrent validity (correlation with other IFN assays) was presented for n=150/412 assays. Reliability data were variable and provided for 13 assays. Gene expression and immunoassays were considered most feasible. Consensus terminology to define different aspects of IFN-I research and practice was produced. CONCLUSIONS Diverse methods have been reported as IFN-I assays and these differ in what elements or aspects of IFN-I pathway activation they measure and how. No 'gold standard' represents the entirety of the IFN pathway, some may not be specific for IFN-I. Data on reliability or comparing assays were limited, and feasibility is a challenge for many assays. Consensus terminology should improve consistency of reporting.
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Affiliation(s)
- Agata Burska
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
| | - Javier Rodríguez-Carrio
- University of Oviedo, Area of Immunology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Robert Biesen
- Charité University Medicine Berlin, Department of Rheumatology, Berlin, Germany
| | - Willem A Dik
- Erasmus MC, University Medical Center Rotterdam, Laboratory Medical Immunology, Department of Immunology, Rotterdam, Netherlands Immunology, Rotterdam, The Netherlands
| | - Maija-Leena Eloranta
- Uppsala University, Department of Medical Sciences, Rheumatology, Uppsala, Sweden
| | - Giulio Cavalli
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, Vita-Salute San Raffaele University, Milan, Italy
- EULAR, PARE Patient Research Partners, Amsterdam, Netherlands
| | - Marianne Visser
- University of Crete, Medical School, Department of Internal Medicine, Heraklion, Greece
| | - Dimitrios T Boumpas
- University of Crete, Medical School, Department of Rheumatology-Clinical Immunology, Heraklion, Greece
| | - George Bertsias
- University of Crete, Medical School, Department of Rheumatology-Clinical Immunology, Heraklion, Greece
| | - Marie Wahren-Herlenius
- Karolinska Institutet, Division of Rheumatology, Stockholm, Sweden
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Norway
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, UK
| | - Marie-Louise Frémond
- Université de Paris Cité, Hôpital Necker-Enfants Malades, Immuno-Hématologie et Rhumatologie pédiatriques, Paris, France
| | - Mary K Crow
- Hospital for Special Surgery, Weill Cornell Medical College, Mary Kirkland Center for Lupus Research, New York, USA
| | - Lars Ronnblom
- Uppsala University, Department of Medical Sciences, Rheumatology, Uppsala, Sweden
| | - P G Conaghan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
| | - Marjan Versnel
- Erasmus MC, Department of Immunology, Rotterdam, The Netherlands
| | - Ed Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
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6
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Rodríguez-Carrio J, Burska A, Conaghan PG, Dik WA, Biesen R, Eloranta ML, Cavalli G, Visser M, Boumpas DT, Bertsias G, Wahren-Herlenius M, Rehwinkel J, Frémond ML, Crow MK, Ronnblom L, Vital E, Versnel M. Association between type I interferon pathway activation and clinical outcomes in rheumatic and musculoskeletal diseases: a systematic literature review informing EULAR points to consider. RMD Open 2023; 9:e002864. [PMID: 36882218 PMCID: PMC10008483 DOI: 10.1136/rmdopen-2022-002864] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/13/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Type I interferons (IFN-I) contribute to a broad range of rheumatic and musculoskeletal diseases (RMDs). Compelling evidence suggests that the measurement of IFN-I pathway activation may have clinical value. Although several IFN-I pathway assays have been proposed, the exact clinical applications are unclear. We summarise the evidence on the potential clinical utility of assays measuring IFN-I pathway activation. METHODS A systematic literature review was conducted across three databases to evaluate the use of IFN-I assays in diagnosis and monitor disease activity, prognosis, response to treatment and responsiveness to change in several RMDs. RESULTS Of 366 screened, 276 studies were selected that reported the use of assays reflecting IFN-I pathway activation for disease diagnosis (n=188), assessment of disease activity (n=122), prognosis (n=20), response to treatment (n=23) and assay responsiveness (n=59). Immunoassays, quantitative PCR (qPCR) and microarrays were reported most frequently, while systemic lupus erythematosus (SLE), rheumatoid arthritis, myositis, systemic sclerosis and primary Sjögren's syndrome were the most studied RMDs. The literature demonstrated significant heterogeneity in techniques, analytical conditions, risk of bias and application in diseases. Inadequate study designs and technical heterogeneity were the main limitations. IFN-I pathway activation was associated with disease activity and flare occurrence in SLE, but their incremental value was uncertain. IFN-I pathway activation may predict response to IFN-I targeting therapies and may predict response to different treatments. CONCLUSIONS Evidence indicates potential clinical value of assays measuring IFN-I pathway activation in several RMDs, but assay harmonisation and clinical validation are urged. This review informs the EULAR points to consider for the measurement and reporting of IFN-I pathway assays.
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Affiliation(s)
- Javier Rodríguez-Carrio
- Area of Immunology, University of Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Agata Burska
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
| | - P G Conaghan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
| | - Willem A Dik
- Laboratory Medical Immunology, department of Immunology, Erasmus MC University Medical Center Rotterdam, The Netherlands
| | - Robert Biesen
- Department of Rheumatology, Charité University Medicine Berlin, Berlin, Germany
| | - Maija-Leena Eloranta
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Giulio Cavalli
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, Vita-Salute San Raffaele University, Milan, Italy
| | - Marianne Visser
- EULAR, PARE Patient Research Partners, Amsterdam, The Netherlands
| | - Dimitrios T Boumpas
- Department of Internal Medicine, University of Crete, Medical School, Heraklion, Greece
| | - George Bertsias
- Department of Rheumatology-Clinical Immunology, University of Crete, Medical School, Heraklion, Greece
| | - Marie Wahren-Herlenius
- Karolinska Institutet, Division of Rheumatology, Stockholm, Sweden
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Norway
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, UK
| | - Marie-Louise Frémond
- Université de Paris Cité, Hôpital Necker-Enfants Malades, Immuno-Hématologie et Rhumatologie pédiatriques, Paris, France
| | - Mary K Crow
- Hospital for Special Surgery, Weill Cornell Medical College, Mary Kirkland Center for Lupus Research, New York, USA
| | - Lars Ronnblom
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Ed Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
| | - Marjan Versnel
- Department of Immunology, Erasmus MC University Medical Center Rotterdam, The Netherlands
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Zeng Y, Chen HQ, Zhang Z, Fan J, Li JZ, Zhou SM, Wang N, Yan SP, Cao J, Liu JY, Zhou ZY, Liu WB. IFI44L as a novel epigenetic silencing tumor suppressor promotes apoptosis through JAK/STAT1 pathway during lung carcinogenesis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 319:120943. [PMID: 36584854 DOI: 10.1016/j.envpol.2022.120943] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/06/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Numerous evidence showed that the occurrence and development of lung cancer is closely related to environmental pollution. Therefore, new environmental response predictive markers are urgently needed for early diagnosis and screening of lung cancer. Interferon-induced protein 44-like (IFI44L) has been shown to be related in a variety of tumors, but its function and mechanism during lung carcinogenesis still have remained largely unknown. In this study, gene expression and methylation status were analyzed through online tools and malignant transformation models. Differentially expressed cell models and xenograft tumor models were established and used to clarify the gene function. RT-qPCR, western blotting, immunohistochemistry, and co-immunoprecipitation (Co-IP) were used to explore the mechanism. Results showed that IFI44L was dramatically downexpressed during lung carcinogenesis, and its low expression may be attributed to DNA methylation. Overexpression of IFI44L obviously inhibited cell growth and promoted apoptosis. After knockdown of IFI44L expression, the proliferation ability was remarkably increased and the apoptosis was significantly reduced. Functional enrichment showed that IFI44L was involved in apoptosis and JAK/STAT1 signaling pathway, and was highly correlated with downstream molecules. After overexpression of IFI44L, the expression of P-STAT1 and downstream molecules XAF1, OAS1, OAS2 and OAS3 were significantly increased. After knockdown of STAT1 expression, the pro-apoptotic effect of IFI44L was reduced. Co-IP results showed that IFI44L had protein interaction with STAT1. Results proved that IFI44L promoted STAT1 phosphorylation and activated the JAK/STAT1 signaling pathway by directly binding to STAT1 protein, thereby leading to cell apoptosis. Our study revealed that IFI44L promotes cell apoptosis and exerts tumor suppressors by activating the JAK/STAT1 signaling pathway. It further suggests that IFI44L has clinical therapeutic potential and may be a promising biomarker during lung carcinogenesis.
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Affiliation(s)
- Yong Zeng
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Hong-Qiang Chen
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Zhe Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Jun Fan
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Jing-Zhi Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; School of Public Health, Xinxiang Medical University, Xinxiang, Henan, 453003, PR China
| | - Shi-Meng Zhou
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; School of Public Health, China Medical University, Shenyang, Liaoning, 110122, PR China
| | - Na Wang
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, PR China
| | - Su-Peng Yan
- Department of Sanitary Equipment and Metrology, School of Biomedical Engineering and Medical Imaging, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jin-Yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Zi-Yuan Zhou
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Wen-Bin Liu
- Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.
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8
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Zheng Q, Wang D, Lin R, Lv Q, Wang W. IFI44 is an immune evasion biomarker for SARS-CoV-2 and Staphylococcus aureus infection in patients with RA. Front Immunol 2022; 13:1013322. [PMID: 36189314 PMCID: PMC9520788 DOI: 10.3389/fimmu.2022.1013322] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 08/29/2022] [Indexed: 12/04/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic of severe coronavirus disease 2019 (COVID-19). Staphylococcus aureus is one of the most common pathogenic bacteria in humans, rheumatoid arthritis (RA) is among the most prevalent autoimmune conditions. RA is a significant risk factor for SARS-CoV-2 and S. aureus infections, although the mechanism of RA and SARS-CoV-2 infection in conjunction with S. aureus infection has not been elucidated. The purpose of this study is to investigate the biomarkers and disease targets between RA and SARS-CoV-2 and S. aureus infections using bioinformatics analysis, to search for the molecular mechanisms of SARS-CoV-2 and S. aureus immune escape and potential drug targets in the RA population, and to provide new directions for further analysis and targeted development of clinical treatments. Methods The RA dataset (GSE93272) and the S. aureus bacteremia (SAB) dataset (GSE33341) were used to obtain differentially expressed gene sets, respectively, and the common differentially expressed genes (DEGs) were determined through the intersection. Functional enrichment analysis utilizing GO, KEGG, and ClueGO methods. The PPI network was created utilizing the STRING database, and the top 10 hub genes were identified and further examined for functional enrichment using Metascape and GeneMANIA. The top 10 hub genes were intersected with the SARS-CoV-2 gene pool to identify five hub genes shared by RA, COVID-19, and SAB, and functional enrichment analysis was conducted using Metascape and GeneMANIA. Using the NetworkAnalyst platform, TF-hub gene and miRNA-hub gene networks were built for these five hub genes. The hub gene was verified utilizing GSE17755, GSE55235, and GSE13670, and its effectiveness was assessed utilizing ROC curves. CIBERSORT was applied to examine immune cell infiltration and the link between the hub gene and immune cells. Results A total of 199 DEGs were extracted from the GSE93272 and GSE33341 datasets. KEGG analysis of enrichment pathways were NLR signaling pathway, cell membrane DNA sensing pathway, oxidative phosphorylation, and viral infection. Positive/negative regulation of the immune system, regulation of the interferon-I (IFN-I; IFN-α/β) pathway, and associated pathways of the immunological response to viruses were enriched in GO and ClueGO analyses. PPI network and Cytoscape platform identified the top 10 hub genes: RSAD2, IFIT3, GBP1, RTP4, IFI44, OAS1, IFI44L, ISG15, HERC5, and IFIT5. The pathways are mainly enriched in response to viral and bacterial infection, IFN signaling, and 1,25-dihydroxy vitamin D3. IFI44, OAS1, IFI44L, ISG15, and HERC5 are the five hub genes shared by RA, COVID-19, and SAB. The pathways are primarily enriched for response to viral and bacterial infections. The TF-hub gene network and miRNA-hub gene network identified YY1 as a key TF and hsa-mir-1-3p and hsa-mir-146a-5p as two important miRNAs related to IFI44. IFI44 was identified as a hub gene by validating GSE17755, GSE55235, and GSE13670. Immune cell infiltration analysis showed a strong positive correlation between activated dendritic cells and IFI44 expression. Conclusions IFI144 was discovered as a shared biomarker and disease target for RA, COVID-19, and SAB by this study. IFI44 negatively regulates the IFN signaling pathway to promote viral replication and bacterial proliferation and is an important molecular target for SARS-CoV-2 and S. aureus immune escape in RA. Dendritic cells play an important role in this process. 1,25-Dihydroxy vitamin D3 may be an important therapeutic agent in treating RA with SARS-CoV-2 and S. aureus infections.
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Affiliation(s)
- Qingcong Zheng
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Du Wang
- Arthritis Clinical and Research Center, Peking University People’s Hospital, Beijing, China
| | - Rongjie Lin
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Qi Lv
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
| | - Wanming Wang
- Department of Orthopedics, 900th Hospital of Joint Logistics Support Force, Fuzhou, China
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9
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Srimadh Bhagavatham SK, Pulukool SK, Pradhan SS, R S, Ashok Naik A, V M DD, Sivaramakrishnan V. Systems biology approach delineates critical pathways associated with disease progression in rheumatoid arthritis. J Biomol Struct Dyn 2022:1-22. [PMID: 36047508 DOI: 10.1080/07391102.2022.2115555] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Rheumatoid Arthritis (RA) is a chronic systemic autoimmune disease leading to inflammation, cartilage cell death, synoviocyte proliferation, and increased and impaired differentiation of osteoclasts and osteoblasts leading to joint erosions and deformities. Transcriptomics, proteomics, and metabolomics datasets were analyzed to identify the critical pathways that drive the RA pathophysiology. Single nucleotide polymorphisms (SNPs) associated with RA were analyzed for the functional implications, clinical outcomes, and blood parameters later validated by literature. SNPs associated with RA were grouped into pathways that drive the immune response and cytokine production. Further gene set enrichment analysis (GSEA) was performed on gene expression omnibus (GEO) data sets of peripheral blood mononuclear cells (PBMCs), synovial macrophages, and synovial biopsies from RA patients showed enrichment of Th1, Th2, Th17 differentiation, viral and bacterial infections, metabolic signalling and immunological pathways with potential implications for RA. The proteomics data analysis presented pathways with genes involved in immunological signaling and metabolic pathways, including vitamin B12 and folate metabolism. Metabolomics datasets analysis showed significant pathways like amino-acyl tRNA biosynthesis, metabolism of amino acids (arginine, alanine aspartate, glutamate, glutamine, phenylalanine, and tryptophan), and nucleotide metabolism. Furthermore, our commonality analysis of multi-omics datasets identified common pathways with potential implications for joint remodeling in RA. Disease-modifying anti-rheumatic drugs (DMARDs) and biologics treatments were found to modulate many of the pathways that were deregulated in RA. Overall, our analysis identified molecular signatures associated with the observed symptoms, joint erosions, potential biomarkers, and therapeutic targets in RA. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sujith Kumar Pulukool
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Saiswaroop R
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Ashwin Ashok Naik
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, A.P., India
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10
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Song S, Zhao R, Qiao J, Liu J, Cheng T, Zhang SX, Li XF. Predictive value of drug efficacy by M6A modification patterns in rheumatoid arthritis patients. Front Immunol 2022; 13:940918. [PMID: 36052084 PMCID: PMC9427021 DOI: 10.3389/fimmu.2022.940918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022] Open
Abstract
Background Rheumatoid arthritis is a highly heterogeneous autoimmune disease characterized by unpredictable disease flares and significant differences in therapeutic response to available treatments. One possible reason for poor efficacy is that it cannot be treated accurately due to no optimal stratification for RA patients. Objective This study aims to construct an RA classification model by m6A characters and further predict response to medication. Methods Twenty m6A regulators were used to construct a random forest diagnosis model, and RNA-seq analysis was employed for external validation. The RNA modification patterns mediated by 20 m6A regulators were systematically evaluated in 1191 RA samples and explored different molecular clusters associated with other immune microenvironment characteristics and biological pathways. Then, we established an m6A score model to quantify the m6A modification patterns. The model was applied to patients at baseline to test the association between m6Ascore and infliximab responsiveness. Results The m6A diagnosis model showed good discriminatory ability in distinguishing RA. Patients with RA were classified into three clusters with distinct molecular and cellular signatures. Cluster A displayed strongly activated inflammatory cells and pathways. Specific innate lymphocytes occupied cluster B. Cluster C was mainly enriched in prominent adaptive lymphocytes and NK-mediated cytotoxicity signatures with the highest m6A score. Patients with a low m6Ascore exhibited significantly infliximab therapeutic benefits compared with those with a high m6Ascore (p< 0.05). Conclusion Our study is the first to provide a comprehensive analysis of m6A modifications in RA, which provides an innovative patient stratification framework and potentially enables improved therapeutic decisions.
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Affiliation(s)
- Shan Song
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, Shanxi, China
| | - Rong Zhao
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, Shanxi, China
| | - Jun Qiao
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, Shanxi, China
| | - Jia Liu
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, Shanxi, China
| | - Ting Cheng
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, Shanxi, China
| | - Sheng-Xiao Zhang
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, Shanxi, China
| | - Xiao-Feng Li
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, Shanxi, China
- *Correspondence: Xiao-Feng Li,
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11
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Iwasaki T, Watanabe R, Ito H, Fujii T, Okuma K, Oku T, Hirayama Y, Ohmura K, Murata K, Murakami K, Yoshitomi H, Tanaka M, Matsuda S, Matsuda F, Morinobu A, Hashimoto M. Dynamics of Type I and Type II Interferon Signature Determines Responsiveness to Anti-TNF Therapy in Rheumatoid Arthritis. Front Immunol 2022; 13:901437. [PMID: 35734167 PMCID: PMC9208293 DOI: 10.3389/fimmu.2022.901437] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022] Open
Abstract
The factors influencing long-term responses to a tumor necrosis factor inhibitor (TNFi) in rheumatoid arthritis (RA) patients currently remain unknown. Therefore, we herein conducted a multi-omics analysis of TNFi responses in a Japanese RA cohort. Blood samples were collected from 27 biological disease-modifying antirheumatic drug (DMARD)-naive RA patients at the initiation of and after three months of treatment with TNFi. Treatment responses were evaluated at one year. Differences in gene expression levels in peripheral blood mononuclear cells (PBMCs), plasma protein levels, drug concentrations, and the presence/absence of anti-drug antibodies were investigated, and a cell phenotypic analysis of PBMCs was performed using flow cytometry. After one year of treatment, thirteen patients achieved clinical remission (responders), while the others did not or switched to other biologics (non-responders). Differentially expressed genes related to treatment responses were enriched for the interferon (IFN) pathway. The expression of type I IFN signaling-related genes was higher in non-responders than in responders before and after treatment (P = 0.03, 0.005, respectively). The expression of type II IFN signaling-related genes did not significantly differ before treatment; however, it increased in non-responders and decreased in responders, with a significant difference being observed after three months of treatment (P = 1.2×10-3). The total number of lymphocytes and C-X-C Motif Chemokine Ligand 10 (CXCL10) protein levels were associated with the type I IFN signature (P = 6.7×10-7, 6.4×10-3, respectively). Hepatocyte growth factor (HGF) protein levels before treatment predicted fold increases in type II IFN (P = 0.03). These IFN signature-related indices (the number of lymphocytes, CXCL10, and HGF) significantly differed between responders and non-responders (P = 0.01, 0.01, and 0.04, respectively). A single-cell analysis revealed that the type I IFN signature was more highly enriched in monocytes than in other cell types. A deconvolution analysis of bulk-RNA sequence data identified CD4+ and CD8+ T cells as the main sources of the type II IFN signature in non-responders. Collectively, the present results demonstrated that the dynamics of the type I and II IFN pathways affected long-term responses to TNFi, providing information on its biological background and potential for clinical applications.
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Affiliation(s)
- Takeshi Iwasaki
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryu Watanabe
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Immunology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
- *Correspondence: Ryu Watanabe, ; Motomu Hashimoto,
| | - Hiromu Ito
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Orthopaedic Surgery, Kurashiki Central Hospital, Okayama, Japan
| | - Takayuki Fujii
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Okuma
- Center for Innovation in Immunoregulative Technology and Therapeutics, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Candidate Discovery Science Labs, Astellas Pharma Inc., Ibaraki, Japan
| | - Takuma Oku
- Center for Innovation in Immunoregulative Technology and Therapeutics, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Candidate Discovery Science Labs, Astellas Pharma Inc., Ibaraki, Japan
| | - Yoshitaka Hirayama
- Center for Innovation in Immunoregulative Technology and Therapeutics, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Candidate Discovery Science Labs, Astellas Pharma Inc., Ibaraki, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichi Murata
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Orthopaedic Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kosaku Murakami
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroyuki Yoshitomi
- Department of Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masao Tanaka
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shuichi Matsuda
- Department of Orthopaedic Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akio Morinobu
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Motomu Hashimoto
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Immunology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
- *Correspondence: Ryu Watanabe, ; Motomu Hashimoto,
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12
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Roodenrijs NMT, Welsing PMJ, van Roon J, Schoneveld JLM, van der Goes MC, Nagy G, Townsend MJ, van Laar JM. Mechanisms underlying DMARD inefficacy in difficult-to-treat rheumatoid arthritis: a narrative review with systematic literature search. Rheumatology (Oxford) 2022; 61:3552-3566. [PMID: 35238332 PMCID: PMC9434144 DOI: 10.1093/rheumatology/keac114] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 12/03/2022] Open
Abstract
Management of RA patients has significantly improved over the past decades. However, a substantial proportion of patients is difficult-to-treat (D2T), remaining symptomatic after failing biological and/or targeted synthetic DMARDs. Multiple factors can contribute to D2T RA, including treatment non-adherence, comorbidities and co-existing mimicking diseases (e.g. fibromyalgia). Additionally, currently available biological and/or targeted synthetic DMARDs may be truly ineffective (‘true’ refractory RA) and/or lead to unacceptable side effects. In this narrative review based on a systematic literature search, an overview of underlying (immune) mechanisms is presented. Potential scenarios are discussed including the influence of different levels of gene expression and clinical characteristics. Although the exact underlying mechanisms remain largely unknown, the heterogeneity between individual patients supports the assumption that D2T RA is a syndrome involving different pathogenic mechanisms.
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Affiliation(s)
- Nadia M T Roodenrijs
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Paco M J Welsing
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Joel van Roon
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Jan L M Schoneveld
- Department of Rheumatology, Bravis Hospital, Roosendaal, the Netherlands
| | - Marlies C van der Goes
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, the Netherlands.,Department of Rheumatology, Meander Medical Center, Amersfoort, the Netherlands
| | - György Nagy
- Department of Rheumatology & Clinical Immunology, Semmelweis University, Budapest, Hungary.,Department of Genetics, Cell and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Michael J Townsend
- Biomarker Discovery OMNI, Genentech Research & Early Development, South San Francisco, USA
| | - Jacob M van Laar
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, the Netherlands
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13
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Roberson EDO, Mesa RA, Morgan GA, Cao L, Marin W, Pachman LM. Transcriptomes of peripheral blood mononuclear cells from juvenile dermatomyositis patients show elevated inflammation even when clinically inactive. Sci Rep 2022; 12:275. [PMID: 34997119 PMCID: PMC8741808 DOI: 10.1038/s41598-021-04302-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
In juvenile dermatomyositis (JDM), the most common pediatric inflammatory myopathy, weakness is accompanied by a characteristic rash that often becomes chronic and is associated with vascular damage. We hoped to understand the molecular underpinnings of JDM, particularly when untreated, which would facilitate the identification of novel mechanisms and clinical targets that might disrupt disease progression. We studied the RNA-Seq data from untreated JDM peripheral blood mononuclear cells (PBMCs; n = 11), PBMCs from a subset of the same patients when clinically inactive (n = 8/11), and separate samples of untreated JDM skin and muscle (n = 4 each). All JDM samples were compared to non-inflammatory control tissues. The untreated JDM PBMCs showed a strong signature for type1 interferon response, along with IL-1, IL-10, and NF-κB. Surprisingly, PBMCs from clinically inactive JDM individuals had persistent immune activation that was enriched for IL-1 signaling. JDM skin and muscle both showed evidence for type 1 interferon activation and genes related to antigen presentation and decreased expression of cellular respiration genes. Additionally, we found that PBMC gene expression correlates with disease activity scores (DAS; skin, muscle, and total domains) and with nailfold capillary end row loop number (an indicator of microvascular damage). This included otoferlin, which was significantly increased in untreated JDM PBMCs and correlated with all 3 DAS domains. Overall, these data demonstrate that PBMC transcriptomes are informative of molecular disruptions in JDM and provide transcriptional evidence of chronic inflammation despite clinical quiescence.
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Affiliation(s)
- Elisha D O Roberson
- Division of Rheumatology, Department of Medicine, Washington University, 660 South Euclid Avenue, MSC 8045-0020-10, St. Louis, MO, 63110, USA. .,Department of Genetics, Washington University, St. Louis, MO, USA.
| | - Rosana A Mesa
- Division of Rheumatology, Department of Medicine, Washington University, 660 South Euclid Avenue, MSC 8045-0020-10, St. Louis, MO, 63110, USA
| | - Gabrielle A Morgan
- Division of Pediatric Rheumatology, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 East Chicago Avenue, Box 50, Chicago, IL, 60611, USA
| | - Li Cao
- Division of Rheumatology, Department of Medicine, Washington University, 660 South Euclid Avenue, MSC 8045-0020-10, St. Louis, MO, 63110, USA
| | - Wilfredo Marin
- Cure JM Center of Excellence in Juvenile Myositis (JM) Research and Care, Stanley Manne Children's Research Institute, Chicago, IL, USA
| | - Lauren M Pachman
- Division of Pediatric Rheumatology, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 East Chicago Avenue, Box 50, Chicago, IL, 60611, USA. .,Cure JM Center of Excellence in Juvenile Myositis (JM) Research and Care, Stanley Manne Children's Research Institute, Chicago, IL, USA. .,Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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14
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Cooles FAH, Isaacs JD. The interferon gene signature as a clinically relevant biomarker in autoimmune rheumatic disease. THE LANCET. RHEUMATOLOGY 2022; 4:e61-e72. [PMID: 38288732 DOI: 10.1016/s2665-9913(21)00254-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 12/19/2022]
Abstract
The interferon gene signature (IGS) is derived from the expression of interferon-regulated genes and is classically increased in response to type I interferon exposure. A raised whole blood IGS has increasingly been reported in rheumatic diseases as sequencing technology has advanced. Although its role remains unclear, we explore how a raised IGS can function as a clinically relevant biomarker, independent of whether it is a bystander effect or a key pathological process. For example, a raised IGS can act as a diagnostic biomarker when predicting rheumatoid arthritis in patients with arthralgia and anti-citrullinated protein antibodies, or predicting systemic lupus erythematous (SLE) in those with antinuclear antibodies; a theragnostic biomarker when predicting response for patients receiving disease modifying therapy, such as rituximab in rheumatoid arthritis; a biomarker of disease activity (early rheumatoid arthritis, dermatomyositis, systemic sclerosis, SLE); or finally a predictor of clinical characteristics, such as lupus nephritis in SLE or disease burden in primary Sjögren's syndrome. A high IGS does not uniformly predict worse clinical phenotypes across all diseases, as demonstrated by a reduced disease burden in primary Sjögren's syndrome, nor does it predict a universally poorer response to all therapies, as shown in rheumatoid arthritis. This dichotomy highlights both the complexity of type I interferon signalling in vivo and the current lack of standardisation when calculating the IGS. The IGS as a biomarker warrants further exploration, with beneficial clinical applications anticipated in multiple rheumatic diseases.
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Affiliation(s)
- Faye A H Cooles
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - John D Isaacs
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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15
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Willemsen J, Neuhoff MT, Hoyler T, Noir E, Tessier C, Sarret S, Thorsen TN, Littlewood-Evans A, Zhang J, Hasan M, Rush JS, Guerini D, Siegel RM. TNF leads to mtDNA release and cGAS/STING-dependent interferon responses that support inflammatory arthritis. Cell Rep 2021; 37:109977. [PMID: 34758308 DOI: 10.1016/j.celrep.2021.109977] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/30/2021] [Accepted: 10/20/2021] [Indexed: 02/07/2023] Open
Abstract
Tumor necrosis factor (TNF) is a key driver of several inflammatory diseases, such as rheumatoid arthritis, inflammatory bowel disease, and psoriasis, in which affected tissues show an interferon-stimulated gene signature. Here, we demonstrate that TNF triggers a type-I interferon response that is dependent on the cyclic guanosine monophosphate-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. We show that TNF inhibits PINK1-mediated mitophagy and leads to altered mitochondrial function and to an increase in cytosolic mtDNA levels. Using cGAS-chromatin immunoprecipitation (ChIP), we demonstrate that cytosolic mtDNA binds to cGAS after TNF treatment. Furthermore, TNF induces a cGAS-STING-dependent transcriptional response that mimics that of macrophages from rheumatoid arthritis patients. Finally, in an inflammatory arthritis mouse model, cGAS deficiency blocked interferon responses and reduced inflammatory cell infiltration and joint swelling. These findings elucidate a molecular mechanism linking TNF to type-I interferon signaling and suggest a potential benefit for therapeutic targeting of cGAS/STING in TNF-driven diseases.
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Affiliation(s)
- Joschka Willemsen
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland.
| | - Marie-Therese Neuhoff
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | - Thomas Hoyler
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | - Emma Noir
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | - Clemence Tessier
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | - Sophie Sarret
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | - Tara N Thorsen
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | | | - Juan Zhang
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | - Maroof Hasan
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | - James S Rush
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | - Danilo Guerini
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
| | - Richard M Siegel
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel 4002, Switzerland
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16
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Han L, Tu S, Shen P, Yan J, Huang Y, Ba X, Li T, Lin W, Li H, Yu K, Guo J, Huang Y, Qin K, Wang Y, Chen Z. A comprehensive transcriptomic analysis of alternate interferon signaling pathways in peripheral blood mononuclear cells in rheumatoid arthritis. Aging (Albany NY) 2021; 13:20511-20533. [PMID: 34432649 PMCID: PMC8436925 DOI: 10.18632/aging.203432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/03/2021] [Indexed: 01/13/2023]
Abstract
Interferon (IFN) signaling pathways play crucial roles in the pathogenesis of rheumatoid arthritis (RA). Prior studies have mainly studied mixed alterations in the IFN signaling pathway in RA, but these studies have not been sufficient to elucidate how imbalanced IFN signaling subtly influences immune cells. Single-cell RNA (scRNA) sequencing makes it possible to better understand the alternations in the interferon signaling pathways in RA. In the present study, we found that IFN signaling pathways were activated in natural killer (NK) cells, monocytes, T cells, B cells, and most immune cell subclasses in RA. We then explored and analyzed the connections between abnormal IFN signaling pathways and cellular functional changes in RA. Single-Cell rEgulatory Network Inference and Clustering (SCENIC) analysis and gene regulatory network (GRN) construction were also performed to identify key transcription factors in RA. Finally, we also investigated altered IFN signaling pathways in multiple RA peripheral blood samples, which indicated that abnormal IFN signaling pathways were universally observed in RA. Our study contributes to a better understanding of the delicate and precise regulation of IFN signaling in the immune system in RA. Furthermore, common alternations in IFN signaling pathway-related transcription factors could help to identify novel therapeutic targets for RA treatment.
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Affiliation(s)
- Liang Han
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shenghao Tu
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Pan Shen
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiahui Yan
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yao Huang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Ba
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tingting Li
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weiji Lin
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huihui Li
- Department of Cardiology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kun Yu
- Department of Cardiology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Guo
- Wuhan Institute of Biotechnology, Wuhan Biobank, Wuhan 430000, China
| | - Ying Huang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kai Qin
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Wang
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhe Chen
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
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17
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Krošel M, Gabathuler M, Maciukiewicz M, Moser L, Lee GI, Marks M, Tomšič M, Distler O, Ospelt C, Klein K. Individual functions of the histone acetyl transferases CBP and p300 in regulating the inflammatory response of synovial fibroblasts. J Autoimmun 2021; 123:102709. [PMID: 34304080 DOI: 10.1016/j.jaut.2021.102709] [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] [Received: 05/21/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/28/2022]
Abstract
Chromatin remodeling, and a persistent histone 3 lysine 27 acetylation (H3K27ac) in particular, are associated with a sustained inflammatory response of synovial fibroblasts (SF) in rheumatoid arthritis (RA). Here we investigated individual functions of the writers of H3K27ac marks, the homologues histone acetyl transferases (HAT) CBP and p300, in controlling the constitutive and inflammatory gene expression in RA SF. We applied a silencing strategy, followed by RNA-sequencing and pathway analysis, complemented with the treatment of SF with inhibitors targeting the HAT (C646) or bromo domains (I-CBP) of CBP and p300. We showed that CBP and p300 undertook overlapping and, in particular at gene levels, distinct regulatory functions in SF. p300 is the major HAT for H3K27ac in SF and regulated more diverse pathways than CBP. Whereas both factors regulated genes associated with extracellular matrix remodeling, adhesion and proliferation, p300 specifically controlled developmental genes associated with limb development. Silencing of CBP specifically down regulated the TNF-induced expression of interferon-signature genes. In contrast, silencing of p300 resulted in anti- and pro-inflammatory effects. Integration of data sets derived from RNA-sequencing and chromatin immunoprecipitation sequencing for H3K27ac revealed that changes in gene expression after CBP or p300 silencing could be only partially explained by changes in levels of H3K27ac. Inhibition of CBP/p300 using HAT and bromo domain inhibitors strongly mirrored effects obtained by silencing of p300, including anti- and pro-inflammatory effects, indicating that such inhibitors are not sufficient to be used as anti-inflammatory drugs.
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Affiliation(s)
- Monika Krošel
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland; Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Marcel Gabathuler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Malgorzata Maciukiewicz
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Larissa Moser
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Gideon Isaac Lee
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | | | - Matija Tomšič
- Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland.
| | - Kerstin Klein
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, Switzerland; Department of BioMedical Research, University of Bern, Bern, Switzerland; Department of Rheumatology and Immunology, University Hospital Bern, Bern, Switzerland.
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18
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Stockfelt M, Lundell AC, Hetland ML, Østergaard M, Uhlig T, Heiberg MS, Haavardsholm EA, Nurmohamed MT, Lampa J, Nordström D, Petersen KH, Gudbjornsson B, Gröndal G, Aldridge J, Andersson K, Blennow K, Zetterberg H, van Vollenhoven R, Rudin A. Plasma interferon-alpha is associated with double-positivity for autoantibodies but is not a predictor of remission in early rheumatoid arthritis-a spin-off study of the NORD-STAR randomized clinical trial. Arthritis Res Ther 2021; 23:189. [PMID: 34256800 PMCID: PMC8278690 DOI: 10.1186/s13075-021-02556-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The type I interferon (IFN) gene signature is present in a subgroup of patients with early rheumatoid arthritis (RA). Protein levels of IFNα have not been measured in RA and it is unknown whether they associate with clinical characteristics or treatment effect. METHODS Patients with early untreated RA (n = 347) were randomized to methotrexate combined with prednisone, certolizumab-pegol, abatacept, or tocilizumab. Plasma IFNα protein levels were determined by single molecular array (Simoa) before and 24 weeks after treatment initiation and were related to demographic and clinical factors including clinical disease activity index, disease activity score in 28 joints, swollen and tender joint counts, and patient global assessment. RESULTS IFNα protein positivity was found in 26% of the patients, and of these, 92% were double-positive for rheumatoid factor (RF) and anti-citrullinated protein antibodies (ACPA). IFNα protein levels were reduced 24 weeks after treatment initiation, and the absolute change was similar irrespective of treatment. IFNα protein positivity was associated neither with disease activity nor with achievement of CDAI remission 24 weeks after randomization. CONCLUSION IFNα protein positivity is present in a subgroup of patients with early RA and associates with double-positivity for autoantibodies but not with disease activity. Pre-treatment IFNα positivity did not predict remission in any of the treatment arms, suggesting that the IFNα system is distinct from the pathways of TNF, IL-6, and T-cell activation in early RA. A spin-off study of the NORD-STAR randomized clinical trial, NCT01491815 (ClinicalTrials), registered 12/08/2011, https://clinicaltrials.gov/ct2/show/NCT01491815 .
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Affiliation(s)
- Marit Stockfelt
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Guldhedsgatan 10A, S-405 30, Gothenburg, Sweden.
- Rheumatology Clinic, Sahlgrenska University Hospital, Gothenburg, Sweden.
| | - Anna-Carin Lundell
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Guldhedsgatan 10A, S-405 30, Gothenburg, Sweden
| | - Merete Lund Hetland
- Copenhagen Center for Arthritis Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Østergaard
- Copenhagen Center for Arthritis Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Till Uhlig
- Division of Rheumatology and Research, Diakonhjemmet Hospital, Oslo, Norway
| | | | - Espen A Haavardsholm
- Division of Rheumatology and Research, Diakonhjemmet Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Michael T Nurmohamed
- Amsterdam Rheumatology and Immunology Center, Reade, Amsterdam, The Netherlands
- Department of Rheumatology and Amsterdam Rheumatology Center, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Jon Lampa
- Department of Medicine, Rheumatology Unit, Center for Molecular Medicine (CMM), Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Dan Nordström
- Department of Medicine and Rheumatology, Helsinki University and University Hospital, Helsinki, Finland
| | - Kim Hørslev Petersen
- Danish Hospital for Rheumatic Diseases, University Hospital of Southern Denmark, Sønderborg, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Bjorn Gudbjornsson
- Centre for Rheumatology Research, Landspitali University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Gerdur Gröndal
- Centre for Rheumatology Research, Landspitali University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jonathan Aldridge
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Guldhedsgatan 10A, S-405 30, Gothenburg, Sweden
| | - Kerstin Andersson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Guldhedsgatan 10A, S-405 30, Gothenburg, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- UK Dementia Research Institute at UCL, London, UK
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Ronald van Vollenhoven
- Department of Rheumatology and Amsterdam Rheumatology Center, Amsterdam University Medical Centres, Amsterdam, The Netherlands
- Department of Medicine, Rheumatology Unit, Center for Molecular Medicine (CMM), Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Rudin
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Guldhedsgatan 10A, S-405 30, Gothenburg, Sweden
- Rheumatology Clinic, Sahlgrenska University Hospital, Gothenburg, Sweden
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19
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Martorell-Marugán J, López-Domínguez R, García-Moreno A, Toro-Domínguez D, Villatoro-García JA, Barturen G, Martín-Gómez A, Troule K, Gómez-López G, Al-Shahrour F, González-Rumayor V, Peña-Chilet M, Dopazo J, Sáez-Rodríguez J, Alarcón-Riquelme ME, Carmona-Sáez P. A comprehensive database for integrated analysis of omics data in autoimmune diseases. BMC Bioinformatics 2021; 22:343. [PMID: 34167460 PMCID: PMC8223391 DOI: 10.1186/s12859-021-04268-4] [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: 11/08/2020] [Accepted: 06/14/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Autoimmune diseases are heterogeneous pathologies with difficult diagnosis and few therapeutic options. In the last decade, several omics studies have provided significant insights into the molecular mechanisms of these diseases. Nevertheless, data from different cohorts and pathologies are stored independently in public repositories and a unified resource is imperative to assist researchers in this field. RESULTS Here, we present Autoimmune Diseases Explorer ( https://adex.genyo.es ), a database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most common autoimmune diseases. The database provides, in an easy-to-use environment, advanced data analysis and statistical methods for exploring omics datasets, including meta-analysis, differential expression or pathway analysis. CONCLUSIONS This is the first omics database focused on autoimmune diseases. This resource incorporates homogeneously processed data to facilitate integrative analyses among studies.
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Affiliation(s)
- Jordi Martorell-Marugán
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Atrys Health S.A., Barcelona, Spain
| | - Raúl López-Domínguez
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
| | - Adrián García-Moreno
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
| | - Daniel Toro-Domínguez
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Genetics of Complex Diseases, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
| | - Juan Antonio Villatoro-García
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Department of Statistics, University of Granada, 18071, Granada, Spain
| | - Guillermo Barturen
- Genetics of Complex Diseases, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
| | - Adoración Martín-Gómez
- Nephrology Units, AADEA: Asociación Andaluza de Enfermedades Autoinmunes, Hospital de Poniente, 04700, Almería, Spain
| | - Kevin Troule
- Bioinformatics Unit, Spanish National Cancer Center, CNIO, Madrid, Spain
| | | | - Fátima Al-Shahrour
- Bioinformatics Unit, Spanish National Cancer Center, CNIO, Madrid, Spain
| | | | - María Peña-Chilet
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocío, 41013, Seville, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Seville, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocío, 41013, Seville, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013, Seville, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Seville, Spain
- INB-ELIXIR-es, FPS, Hospital Virgen del Rocío, 42013, Seville, Spain
| | - Julio Sáez-Rodríguez
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, 52074, Aachen, Germany
- European Molecular Biology Laboratory-The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
- Institute for Computational Biomedicine, Bioquant Heidelberg, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, 69120, Heidelberg, Germany
| | - Marta E Alarcón-Riquelme
- Genetics of Complex Diseases, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain
- Unit of Chronic Inflammatory Diseases, Institute of Environmental Medicine, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Pedro Carmona-Sáez
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016, Granada, Spain.
- Department of Statistics, University of Granada, 18071, Granada, Spain.
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20
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Apel F, Andreeva L, Knackstedt LS, Streeck R, Frese CK, Goosmann C, Hopfner KP, Zychlinsky A. The cytosolic DNA sensor cGAS recognizes neutrophil extracellular traps. Sci Signal 2021; 14:14/673/eaax7942. [PMID: 33688080 DOI: 10.1126/scisignal.aax7942] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neutrophil extracellular traps (NETs) are structures consisting of chromatin and antimicrobial molecules that are released by neutrophils during a form of regulated cell death called NETosis. NETs trap invading pathogens, promote coagulation, and activate myeloid cells to produce type I interferons (IFNs), proinflammatory cytokines that regulate the immune system. Here, we showed that macrophages and other myeloid cells phagocytosed NETs. Once in phagosomes, NETs translocated to the cytosol, where the DNA backbones of these structures activated the innate immune sensor cyclic GMP-AMP synthase (cGAS) and induced type I IFN production. The NET-associated serine protease neutrophil elastase (NE) mediated the activation of this pathway. We showed that NET induction in mice treated with the lectin concanavalin A, a model of autoimmune hepatitis, resulted in cGAS-dependent stimulation of an IFN response, suggesting that NETs activated cGAS in vivo. Thus, our findings suggest that cGAS is a sensor of NETs, mediating immune cell activation during infection.
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Affiliation(s)
- Falko Apel
- Max Planck Institute for Infection Biology, Department of Cellular Microbiology, Charitéplatz 1, 10117 Berlin, Germany.,Department of Biology, Humboldt University, Charitéplatz 1, 10117 Berlin, Germany
| | - Liudmila Andreeva
- Gene Center, Ludwig-Maximillians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lorenz Sebastian Knackstedt
- Max Planck Institute for Infection Biology, Department of Cellular Microbiology, Charitéplatz 1, 10117 Berlin, Germany.,Department of Biology, Humboldt University, Charitéplatz 1, 10117 Berlin, Germany.,T-Knife GmbH, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Robert Streeck
- Max Planck Institute for Infection Biology, Department of Cellular Microbiology, Charitéplatz 1, 10117 Berlin, Germany.,Department of Biology, Humboldt University, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian Karl Frese
- Max Planck Unit for the Science of Pathogens, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian Goosmann
- Max Planck Institute for Infection Biology, Department of Cellular Microbiology, Charitéplatz 1, 10117 Berlin, Germany.,Department of Biology, Humboldt University, Charitéplatz 1, 10117 Berlin, Germany
| | - Karl-Peter Hopfner
- Gene Center, Ludwig-Maximillians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Arturo Zychlinsky
- Max Planck Institute for Infection Biology, Department of Cellular Microbiology, Charitéplatz 1, 10117 Berlin, Germany. .,Department of Biology, Humboldt University, Charitéplatz 1, 10117 Berlin, Germany
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21
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Avdeeva AS, Tchetina EV, Cherkasova MV, Markova GA, Artyuhov AS, Dashinimaev EB, Nasonov EL. The expression of interferon-stimulated genes (interferon “signature”) in patients with rheumatoid arthritis (Preliminary results). ACTA ACUST UNITED AC 2021. [DOI: 10.47360/1995-4484-2020-673-677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | | | | | - A. S. Artyuhov
- Research Institute of Translational Medicine, N.I. Pirogov Russian National Research Medical University
| | - E. B. Dashinimaev
- Research Institute of Translational Medicine, N.I. Pirogov Russian National Research Medical University; Koltzov Institute of Developmental Biology of Russian Academy of Sciences
| | - E. L. Nasonov
- V.A. Nasonova Research Institute of Rheumatology; I.M. Sechenov First Moscow State Medical University (Sechenovskiy University)
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22
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Mustelin T, Ukadike KC. How Retroviruses and Retrotransposons in Our Genome May Contribute to Autoimmunity in Rheumatological Conditions. Front Immunol 2020; 11:593891. [PMID: 33281822 PMCID: PMC7691656 DOI: 10.3389/fimmu.2020.593891] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/19/2020] [Indexed: 12/14/2022] Open
Abstract
More than 200 human disorders include various manifestations of autoimmunity. The molecular events that lead to these diseases are still incompletely understood and their causes remain largely unknown. Numerous potential triggers of autoimmunity have been proposed over the years, but very few of them have been conclusively confirmed or firmly refuted. Viruses have topped the lists of suspects for decades, and it seems that many viruses, including those of the Herpesviridae family, indeed can influence disease initiation and/or promote exacerbations by a number of mechanisms that include prolonged anti-viral immunity, immune subverting factors, and mechanisms, and perhaps “molecular mimicry”. However, no specific virus has yet been established as being truly causative. Here, we discuss a different, but perhaps mechanistically related possibility, namely that retrotransposons or retroviruses that infected us in the past and left a lasting copy of themselves in our genome still can provoke an escalating immune response that leads to autoimmune disease. Many of these loci still encode for retroviral proteins that have retained some, or all, of their original functions. Importantly, these endogenous proviruses cannot be eliminated by the immune system the way it can eliminate exogenous viruses. Hence, if not properly controlled, they may drive a frustrated and escalating chronic, or episodic, immune response to the point of a frank autoimmune disorder. Here, we discuss the evidence and the proposed mechanisms, and assess the therapeutic options that emerge from the current understanding of this field.
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Affiliation(s)
- Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Kennedy C Ukadike
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
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Differential CpG DNA methylation in peripheral naïve CD4 + T-cells in early rheumatoid arthritis patients. Clin Epigenetics 2020; 12:54. [PMID: 32264938 PMCID: PMC7137446 DOI: 10.1186/s13148-020-00837-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/08/2020] [Indexed: 12/15/2022] Open
Abstract
Background The genetic risk associated with rheumatoid arthritis (RA) includes genes regulating DNA methylation, one of the hallmarks of epigenetic re-programing, as well as many T-cell genes, with a strong MHC association, pointing to immunogenetic mechanisms as disease triggers leading to chronicity. The aim of our study was to explore DNA methylation in early, drug-naïve RA patients, towards a better understanding of early events in pathogenesis. Result Monocytes, naïve and memory CD4+ T-cells were sorted from 6 healthy controls and 10 RA patients. DNA methylation was assessed using a genome-wide Illumina 450K CpG promoter array. Differential methylation was confirmed using bisulfite sequencing for a specific gene promoter, ELISA for several cytokines and flow cytometry for cell surface markers. Differentially methylated (DM) CpGs were observed in 1047 genes in naïve CD4+ T-cells, 913 in memory cells and was minimal in monocytes with only 177 genes. Naive CD4+ T-cells were further investigated as presenting differential methylation in the promoter of > 500 genes associated with several disease-relevant pathways, including many cytokines and their receptors. We confirmed hypomethylation of a region of the TNF-alpha gene in early RA and differential expression of 3 cytokines (IL21, IL34 and RANKL). Using a bioinformatics package (DMRcate) and an in-house analysis based on differences in β values, we established lists of DM genes between health and RA. Publicly available gene expression data were interrogated to confirm differential expression of over 70 DM genes. The lists of DM genes were further investigated based on a functional relationship database analysis, which pointed to an IL6/JAK1/STAT3 node, related to TNF-signalling and engagement in Th17 cell differentiation amongst many pathways. Five DM genes for cell surface markers (CD4, IL6R, IL2RA/CD25, CD62L, CXCR4) were investigated towards identifying subpopulations of CD4+ T-cells undergoing these modifications and pointed to a subset of naïve T-cells, with high levels of CD4, IL2R, and CXCR4, but reduction and loss of IL6R and CD62L, respectively. Conclusion Our data provided novel conceptual advances in the understanding of early RA pathogenesis, with implications for early treatment and prevention.
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Shan S, Zhou Y, Yu J, Yang Q, Pan D, Wang Y, Li L, Zhu J, Zhang Y, Huang S, Li Z, Ning Z, Xin L, Lu X. Therapeutic treatment of a novel selective JAK3/JAK1/TBK1 inhibitor, CS12192, in rat and mouse models of rheumatoid arthritis. Int Immunopharmacol 2019; 77:105914. [DOI: 10.1016/j.intimp.2019.105914] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/06/2019] [Accepted: 09/12/2019] [Indexed: 10/25/2022]
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Using the Immunophenotype to Predict Response to Biologic Drugs in Rheumatoid Arthritis. J Pers Med 2019; 9:jpm9040046. [PMID: 31581724 PMCID: PMC6963853 DOI: 10.3390/jpm9040046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 01/09/2023] Open
Abstract
Tumour necrosis factor (TNF)-α is a key mediator of inflammation in rheumatoid arthritis, and its discovery led to the development of highly successful anti-TNF therapy. Subsequently, other biologic drugs targeting immune pathways, namely interleukin-6 blockade, B cell depletion, and T cell co-stimulation blockade, have been developed. Not all patients respond to a biologic drug, leading to a knowledge gap between biologic therapies available and the confident prediction of response. So far, genetic studies have failed to uncover clinically informative biomarkers to predict response. Given that the targets of biologics are immune pathways, immunological study has become all the more pertinent. Furthermore, advances in single-cell technology have enabled the characterization of many leucocyte subsets. Studying the blood immunophenotype may therefore, define biomarker profiles relevant to each individual patient's disease and treatment outcome. This review summarises our current understanding of how immune biomarkers might be able to predict treatment response to biologic drugs.
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Slight-Webb S, Bourn RL, Holers VM, James JA. Shared and unique immune alterations in pre-clinical autoimmunity. Curr Opin Immunol 2019; 61:60-68. [PMID: 31557691 DOI: 10.1016/j.coi.2019.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/01/2019] [Accepted: 08/26/2019] [Indexed: 02/08/2023]
Abstract
Progression from health to a classified autoimmune disease is an evolving process that can happen rapidly in some diseases, but usually takes years to develop. Specific immune alterations predate pathogenic autoimmunity and can be used as disease biomarkers to identify high-risk individuals for prevention studies applied in the pre-clinical state. Here we discuss recent findings that illuminate specific immune pathways that are altered in the earliest phases of pre-clinical autoimmunity as well as those mediators more closely associated with later clinically apparent and classified disease onset.
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Affiliation(s)
- Samantha Slight-Webb
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Rebecka L Bourn
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - V Michael Holers
- Medicine and Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, United States
| | - Judith A James
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States; Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States.
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27
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Petrackova A, Horak P, Radvansky M, Skacelova M, Fillerova R, Kudelka M, Smrzova A, Mrazek F, Kriegova E. Cross-Disease Innate Gene Signature: Emerging Diversity and Abundance in RA Comparing to SLE and SSc. J Immunol Res 2019; 2019:3575803. [PMID: 31396542 PMCID: PMC6664489 DOI: 10.1155/2019/3575803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022] Open
Abstract
Overactivation of the innate immune system together with the impaired downstream pathway of type I interferon-responding genes is a hallmark of rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic sclerosis (SSc). To date, limited data on the cross-disease innate gene signature exists among those diseases. We compared therefore an innate gene signature of Toll-like receptors (TLRs), seven key members of the interleukin (IL)1/IL1R family, and CXCL8/IL8 in peripheral blood mononuclear cells from well-defined patients with active stages of RA (n = 36, DAS28 ≥ 3.2), SLE (n = 28, SLEDAI > 6), and SSc (n = 22, revised EUSTAR index > 2.25). Emerging diversity and abundance of the innate signature in RA patients were detected: RA was characterized by the upregulation of TLR3, TLR5, IL1RAP/IL1R3, IL18R1, and SIGIRR/IL1R8 when compared to SSc (P corr < 0.02) and of TLR2, TLR5, and SIGIRR/IL1R8 when compared to SLE (P corr < 0.02). Applying the association rule analysis, six rules (combinations and expression of genes describing disease) were identified for RA (most frequently included high TLR3 and/or IL1RAP/IL1R3) and three rules for SLE (low IL1RN and IL18R1) and SSc (low TLR5 and IL18R1). This first cross-disease study identified emerging heterogeneity in the innate signature of RA patients with many upregulated innate genes compared to that of SLE and SSc.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Arthritis, Rheumatoid/blood
- Arthritis, Rheumatoid/genetics
- Arthritis, Rheumatoid/immunology
- Female
- Humans
- Immunity, Innate/genetics
- Interleukin-1/genetics
- Interleukin-1/metabolism
- Interleukin-8/genetics
- Interleukin-8/metabolism
- Leukocytes, Mononuclear/metabolism
- Lupus Erythematosus, Systemic/blood
- Lupus Erythematosus, Systemic/genetics
- Lupus Erythematosus, Systemic/immunology
- Male
- Middle Aged
- Receptors, Interleukin-1 Type I/genetics
- Receptors, Interleukin-1 Type I/metabolism
- Scleroderma, Systemic/blood
- Scleroderma, Systemic/genetics
- Scleroderma, Systemic/immunology
- Toll-Like Receptors/genetics
- Toll-Like Receptors/metabolism
- Transcriptome
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Affiliation(s)
- Anna Petrackova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital, Olomouc, Czech Republic
| | - Pavel Horak
- Department of Internal Medicine III-Nephrology, Rheumatology and Endocrinology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital, Olomouc, Czech Republic
| | - Martin Radvansky
- Faculty of Electrical Engineering and Computer Science, Department of Computer Science, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Martina Skacelova
- Department of Internal Medicine III-Nephrology, Rheumatology and Endocrinology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital, Olomouc, Czech Republic
| | - Regina Fillerova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital, Olomouc, Czech Republic
| | - Milos Kudelka
- Faculty of Electrical Engineering and Computer Science, Department of Computer Science, VSB-Technical University of Ostrava, Ostrava, Czech Republic
| | - Andrea Smrzova
- Department of Internal Medicine III-Nephrology, Rheumatology and Endocrinology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital, Olomouc, Czech Republic
| | - Frantisek Mrazek
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital, Olomouc, Czech Republic
| | - Eva Kriegova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital, Olomouc, Czech Republic
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Mustelin T, Lood C, Giltiay NV. Sources of Pathogenic Nucleic Acids in Systemic Lupus Erythematosus. Front Immunol 2019; 10:1028. [PMID: 31139185 PMCID: PMC6519310 DOI: 10.3389/fimmu.2019.01028] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
A hallmark of systemic lupus erythematosus (SLE), and several related autoimmune diseases, is the presence of autoantibodies against nucleic acids and nucleic acid-binding proteins, as well as elevated type I interferons (IFNs), which appear to be instrumental in disease pathogenesis. Here we discuss the sources and proposed mechanisms by which a range of cellular RNA and DNA species can become pathogenic and trigger the nucleic acid sensors that drive type I interferon production. Potentially SLE-promoting DNA may originate from pieces of chromatin, from mitochondria, or from reverse-transcribed cellular RNA, while pathogenic RNA may arise from mis-localized, mis-processed, ancient retroviral, or transposable element-derived transcripts. These nucleic acids may leak out from dying cells to be internalized and reacted to by immune cells or they may be generated and remain to be sensed intracellularly in immune or non-immune cells. The presence of aberrant DNA or RNA is normally counteracted by effective counter-mechanisms, the loss of which result in a serious type I IFN-driven disease called Aicardi-Goutières Syndrome. However, in SLE it remains unclear which mechanisms are most critical in precipitating disease: aberrant RNA or DNA, overly sensitive sensor mechanisms, or faulty counter-acting defenses. We propose that the clinical heterogeneity of SLE may be reflected, in part, by heterogeneity in which pathogenic nucleic acid molecules are present and which sensors and pathways they trigger in individual patients. Elucidation of these events may result in the recognition of distinct "endotypes" of SLE, each with its distinct therapeutic choices.
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Affiliation(s)
- Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
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Early Peritoneal CC Chemokine Production Correlates with Divergent Inflammatory Phenotypes and Susceptibility to Experimental Arthritis in Mice. J Immunol Res 2019; 2019:2641098. [PMID: 30937315 PMCID: PMC6413398 DOI: 10.1155/2019/2641098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/18/2018] [Indexed: 12/15/2022] Open
Abstract
The inflammatory and autoimmune events preceding clinical symptoms in rheumatoid arthritis (RA) and other autoimmune diseases are difficult to study in human patients. Therefore, animal models that share immunologic and clinical features with human RA, such as pristane-induced arthritis (PIA), are valuable tools for assessing the primordial events related to arthritis susceptibility. PIA-resistant HIII and susceptible LIII mice were injected i.p. with pristane, and peritoneal lavage fluid was harvested in the early (7 days) and late (35 days) preclinical phases of PIA. Chemokine and cytokine levels were measured in lavage supernatant with ELISA, peritoneal inflammatory leukocytes were immunophenotyped by flow cytometry, and gene expression was determined by qRT-PCR. Leukocyte recruitment was quantitatively and qualitatively divergent in the peritoneum of HIII and LIII mice, with an early increase of CC chemokines (CCL2/CCL3/CCL5/CCL12/CCL22) in the susceptible LIII strain. Also, cytokines such as IL-12p40, IL-23, and IL-18 were elevated in LIII mice while IL-6 was increased in HIII animals. The results show that an early peritoneal CC chemokine response is an important feature of arthritis susceptibility and defines potential biomarkers in this model.
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Rodríguez-Carrio J, López P, Alperi-López M, Caminal-Montero L, Ballina-García FJ, Suárez A. IRF4 and IRGs Delineate Clinically Relevant Gene Expression Signatures in Systemic Lupus Erythematosus and Rheumatoid Arthritis. Front Immunol 2019; 9:3085. [PMID: 30666255 PMCID: PMC6330328 DOI: 10.3389/fimmu.2018.03085] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/13/2018] [Indexed: 12/26/2022] Open
Abstract
Introduction: Overactivation of the type I interferon (IFN) signature has been observed in several systemic autoimmune conditions, such as Systemic Lupus Erythematosus (SLE) or Rheumatoid Arthritis (RA). Impaired control of Interferon-Responding Genes (IRGs) expression by their regulatory mechanisms, including Interferon Regulatory Factors (IRFs), may underlie these findings and it may explain the heterogeneity observed among these conditions. In the present study we aimed to evaluate the associations between IRF4 gene expression and those of IRGs in SLE and RA patients to gain insight about its links with the IFN signature as well as to explore the potential clinical relevance of these associations. Methods: The gene expression of IRF4 and IRGs (IFI44, IFI44L, IFI6, and MX1) in peripheral blood was analyzed in 75 SLE patients, 98 RA patients, and 28 healthy controls. A group of 13 biological-naïve RA patients was prospectively followed upon TNFα-blockade. The associations among IRF4 and IRGs were evaluated by principal component analyses (PCA), correlations and network analyses. Publicly available datasets were used for replication. Results: A broad activation of IRGs was observed in autoimmune patients, although certain heterogeneity can be distinguished, whereas IRF4 was only upregulated in RA. The differential expression of IRF4 in RA was then confirmed in publicly available gene expression datasets. PCA revealed different associations among IRF4 and IRGs in each condition, which was later confirmed by correlation and network analyses. Cluster analysis identified 3 gene expression signatures on the basis of IRF4 and IRGs expression which were differentially used by SLE and RA patients. Cluster III was associated with markers of disease severity in SLE patients. Cluster II, hallmarked by IRF4 upregulation, was linked to clinical stage and mild disease course in RA. TNFα-blockade led to changes in the association between IRF4 and IRGs, whereas increasing IRF4 expression was associated with a good clinical outcome in RA. Conclusions: The differential expression of IRF4 and IRGs observed in SLE and RA can delineate gene expression signatures associated with clinical features and treatment outcomes. These results support a clinically-relevant phenomenon of shaping of the IFN signature by IRF4 in autoimmune patients.
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Affiliation(s)
- Javier Rodríguez-Carrio
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Bone and Mineral Research Unit, REDinREN del ISCIII, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Patricia López
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Mercedes Alperi-López
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Rheumatology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Luis Caminal-Montero
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Internal Medicine, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Francisco J Ballina-García
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Rheumatology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Ana Suárez
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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31
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Rodríguez-Carrio J, Alperi-López M, López P, Ballina-García FJ, Suárez A. Profiling of B-Cell Factors and Their Decoy Receptors in Rheumatoid Arthritis: Association With Clinical Features and Treatment Outcomes. Front Immunol 2018; 9:2351. [PMID: 30369929 PMCID: PMC6194314 DOI: 10.3389/fimmu.2018.02351] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/24/2018] [Indexed: 12/27/2022] Open
Abstract
Introduction: B-cell activation is pivotal in rheumatoid arthritis (RA) pathogenesis and represents a relevant therapeutic target. The main aim of this study was to characterize the profiles of B-cell factors and their decoy receptors in RA and evaluate their clinical relevance. Methods: sBLyS, sAPRIL, sBCMA, sTACI, sBLyS-R, and several cytokines' serum levels were measured by immunoassays in 104 RA patients and 33 healthy controls (HC). An additional group of 42 systemic lupus erythematosus (SLE) patients were enrolled as disease controls. Whole blood IFI44, IFI44L, IFI6, and MX1 gene expression was measured and averaged into an IFN-score. BLyS membrane expression (mBLyS) was assessed on blood cell subsets by flow cytometry. Results: increased sAPRIL and sBCMA levels were found in RA, whereas BLyS was elevated in very early RA (VERA). No differences were observed for sTACI and sBLyS-R. An increased sBLyS/sBLyS-R ratio was associated with poor clinical outcome at 6 and 12 months in VERA, whereas a positive association with disease activity was observed in established disease. Increased mBLyS expression was found on monocytes, mDCs, neutrophils and B-cells in RA, to a similar extent that in SLE patients. Cluster analysis identified a specific B-cell factors profile overrepresented in RA and associated with autoantibodies, elevated proinflammatory cytokines (IFNα, MIP1α, TNFα, IL-37, and GM-CSF) and increased type-I IFN signature. Increasing sBCMA and sBLyS serum levels upon treatment and mBLyS expression at baseline on monocytes and mDCs, but not B-cells, were associated with poor clinical outcome upon TNFα-blockade. Conclusions: profound and complex alterations of soluble and membrane-bound B-cell factors are observed in RA associated with clinical outcomes, thus supporting its applicability to guide patient stratification along disease course.
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Affiliation(s)
- Javier Rodríguez-Carrio
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Mercedes Alperi-López
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain.,Department of Rheumatology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Patricia López
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Francisco J Ballina-García
- Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain.,Department of Rheumatology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Ana Suárez
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
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32
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Cooles FAH, Anderson AE, Skelton A, Pratt AG, Kurowska-Stolarska MS, McInnes I, Hilkens CMU, Isaacs JD. Phenotypic and Transcriptomic Analysis of Peripheral Blood Plasmacytoid and Conventional Dendritic Cells in Early Drug Naïve Rheumatoid Arthritis. Front Immunol 2018; 9:755. [PMID: 29867920 PMCID: PMC5968398 DOI: 10.3389/fimmu.2018.00755] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 03/27/2018] [Indexed: 12/27/2022] Open
Abstract
Objective Dendritic cells (DCs) are key orchestrators of immune function. To date, rheumatoid arthritis (RA) researchers have predominantly focused on a potential pathogenic role for CD1c+ DCs. In contrast, CD141+ DCs and plasmacytoid DCs (pDCs) have not been systematically examined, at least in early RA. In established RA, the role of pDCs is ambiguous and, since disease duration and treatment both impact RA pathophysiology, we examined pDCs, and CD1c+ and CD141+ conventional DCs (cDCs), in early, drug-naïve RA (eRA) patients. Methods We analyzed the frequency and phenotype of pDCs, CD1c+, and CD141+ DCs from eRA patients and compared findings with healthy controls. In parallel, we performed transcriptional analysis of >600 immunology-related genes (Nanostring) from peripheral blood pDCs, CD1c+ DCs, B cells, T cells, and monocytes. Results All DC subsets were reduced in eRA (n = 44) compared with healthy controls (n = 30) and, for pDCs, this was most marked in seropositive patients. CD141+ and CD1c+ DCs, but not pDCs, had a comparatively activated phenotype at baseline (increased CD86) and CD1c+ DC frequency inversely associated with disease activity. All DC frequencies remained static 12 months after initiation of immunomodulatory therapy despite a fall in activation markers (e.g., HLA-DR, CD40). There was no association between the whole blood interferon gene signature (IGS) and pDC or CD1c+ DC parameters but an inverse association between CD141+ DC frequency and IGS was noted. Furthermore, IFN-I and IFN-III mRNA transcripts were comparable between eRA pDC and other leukocyte subsets (B cells, CD4+, and CD8+ T cells and monocytes) with no obvious circulating cellular source of IFN-I or IFN-III. Transcriptomic analysis suggested increased pDC and CD1c+ DC proliferation in eRA; pDC differentially expressed genes also suggested enhanced tolerogenic function, whereas for CD1c+ DCs, pro-inflammatory transcripts were upregulated. Discussion This is the first detailed examination of DC subsets in eRA peripheral blood. Compared with CD1c+ DCs, pDCs are less activated and may be skewed toward tolerogenic functions. CD141+ DCs may be implicated in RA pathophysiology. Our findings justify further investigation of early RA DC biology.
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Affiliation(s)
- Faye A H Cooles
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Amy E Anderson
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew Skelton
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Arthur G Pratt
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mariola S Kurowska-Stolarska
- Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), University of Glasgow, Glasgow, United Kingdom
| | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), University of Glasgow, Glasgow, United Kingdom
| | - Catharien M U Hilkens
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John D Isaacs
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
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