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Sharma SD, Bluett J. Towards Personalized Medicine in Rheumatoid Arthritis. Open Access Rheumatol 2024; 16:89-114. [PMID: 38779469 PMCID: PMC11110814 DOI: 10.2147/oarrr.s372610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, incurable, multisystem, inflammatory disease characterized by synovitis and extra-articular features. Although several advanced therapies targeting inflammatory mechanisms underlying the disease are available, no advanced therapy is universally effective. Therefore, a ceiling of treatment response is currently accepted where no advanced therapy is superior to another. The current challenge for medical research is the discovery and integration of predictive markers of drug response that can be used to personalize medicine so that the patient is started on "the right drug at the right time". This review article summarizes our current understanding of predicting response to anti-rheumatic drugs in RA, obstacles impeding the development of personalized medicine approaches and future research priorities to overcome these barriers.
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Affiliation(s)
- Seema D Sharma
- Centre for Musculoskeletal Research, Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - James Bluett
- Centre for Musculoskeletal Research, Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
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2
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Yu CY, Lee HS, Joo YB, Cho SK, Choi CB, Sung YK, Kim TH, Jun JB, Yoo DH, Bae SC, Kim K, Bang SY. Transcriptomic network analysis reveals key drivers of response to anti-TNF biologics in patients with rheumatoid arthritis. Rheumatology (Oxford) 2024; 63:1422-1431. [PMID: 37572297 DOI: 10.1093/rheumatology/kead403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/08/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023] Open
Abstract
OBJECTIVE Anti-TNF biologics have been widely used to ameliorate disease activity in patients with RA. However, a large fraction of patients show a poor response to these agents. Moreover, no clinically applicable predictive biomarkers have been established. This study aimed to identify response-associated biomarkers using longitudinal transcriptomic data in two independent RA cohorts. METHODS RNA sequencing data from peripheral blood cell samples of Korean and Caucasian RA cohorts before and after initial treatment with anti-TNF biologics were analysed to assess treatment-induced expression changes that differed between highly reliable excellent responders and null responders. Weighted correlation network, immune cell composition, and key driver analyses were performed to understand response-associated transcriptomic networks and cell types and their correlation with disease activity indices. RESULTS In total, 305 response-associated genes showed significantly different treatment-induced expression changes between excellent and null responders. Co-expression network construction and subsequent key driver analysis revealed that 41 response-associated genes played a crucial role as key drivers of transcriptomic alteration in four response-associated networks involved in various immune pathways: type I IFN signalling, myeloid leucocyte activation, B cell activation, and NK cell/lymphocyte-mediated cytotoxicity. Transcriptomic response scores that we developed to estimate the individual-level degree of expression changes in the response-associated key driver genes were significantly correlated with the changes in clinical indices in independent patients with moderate or ambiguous response outcomes. CONCLUSION This study provides response-specific treatment-induced transcriptomic signatures by comparing the transcriptomic landscape between patients with excellent and null responses to anti-TNF drugs at both gene and network levels.
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Affiliation(s)
- Chae-Yeon Yu
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
| | - Young Bin Joo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
| | - Soo-Kyung Cho
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
| | - Chan-Bum Choi
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
| | - Yoon-Kyoung Sung
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
| | - Jae-Bum Jun
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
| | - Dae Hyun Yoo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases and Hanyang University Institute for Rheumatology, Seoul, Republic of Korea
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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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Metzemaekers M, Malengier-Devlies B, Gouwy M, De Somer L, Cunha FDQ, Opdenakker G, Proost P. Fast and furious: The neutrophil and its armamentarium in health and disease. Med Res Rev 2023; 43:1537-1606. [PMID: 37036061 DOI: 10.1002/med.21958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 12/27/2022] [Accepted: 03/24/2023] [Indexed: 04/11/2023]
Abstract
Neutrophils are powerful effector cells leading the first wave of acute host-protective responses. These innate leukocytes are endowed with oxidative and nonoxidative defence mechanisms, and play well-established roles in fighting invading pathogens. With microbicidal weaponry largely devoid of specificity and an all-too-well recognized toxicity potential, collateral damage may occur in neutrophil-rich diseases. However, emerging evidence suggests that neutrophils are more versatile, heterogeneous, and sophisticated cells than initially thought. At the crossroads of innate and adaptive immunity, neutrophils demonstrate their multifaceted functions in infectious and noninfectious pathologies including cancer, autoinflammation, and autoimmune diseases. Here, we discuss the kinetics of neutrophils and their products of activation from bench to bedside during health and disease, and provide an overview of the versatile functions of neutrophils as key modulators of immune responses and physiological processes. We focus specifically on those activities and concepts that have been validated with primary human cells.
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Affiliation(s)
- Mieke Metzemaekers
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Bert Malengier-Devlies
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Mieke Gouwy
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Lien De Somer
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- Division of Pediatric Rheumatology, University Hospital Leuven, Leuven, Belgium
- European Reference Network for Rare Immunodeficiency, Autoinflammatory and Autoimmune Diseases (RITA) at the University Hospital Leuven, Leuven, Belgium
| | | | - Ghislain Opdenakker
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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5
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Cui Y, Zhang H, Wang Z, Gong B, Al-Ward H, Deng Y, Fan O, Wang J, Zhu W, Sun YE. Exploring the shared molecular mechanisms between systemic lupus erythematosus and primary Sjögren's syndrome based on integrated bioinformatics and single-cell RNA-seq analysis. Front Immunol 2023; 14:1212330. [PMID: 37614232 PMCID: PMC10442653 DOI: 10.3389/fimmu.2023.1212330] [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: 04/26/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023] Open
Abstract
Background Systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) are common systemic autoimmune diseases that share a wide range of clinical manifestations and serological features. This study investigates genes, signaling pathways, and transcription factors (TFs) shared between SLE and pSS. Methods Gene expression profiles of SLE and pSS were obtained from the Gene Expression Omnibus (GEO). Weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) analysis were conducted to identify shared genes related to SLE and pSS. Overlapping genes were then subject to Gene Ontology (GO) and protein-protein interaction (PPI) network analyses. Cytoscape plugins cytoHubba and iRegulon were subsequently used to screen shared hub genes and predict TFs. In addition, gene set variation analysis (GSVA) and CIBERSORTx were used to calculate the correlations between hub genes and immune cells as well as related pathways. To confirm these results, hub genes and TFs were verified in microarray and single-cell RNA sequencing (scRNA-seq) datasets. Results Following WGCNA and limma analysis, 152 shared genes were identified. These genes were involved in interferon (IFN) response and cytokine-mediated signaling pathway. Moreover, we screened six shared genes, namely IFI44L, ISG15, IFIT1, USP18, RSAD2 and ITGB2, out of which three genes, namely IFI44L, ISG15 and ITGB2 were found to be highly expressed in both microarray and scRNA-seq datasets. IFN response and ITGB2 signaling pathway were identified as potentially relevant pathways. In addition, STAT1 and IRF7 were identified as common TFs in both diseases. Conclusion This study revealed IFI44L, ISG15 and ITGB2 as the shared genes and identified STAT1 and IRF7 as the common TFs of SLE and pSS. Notably, the IFN response and ITGB2 signaling pathway played vital roles in both diseases. Our study revealed common pathogenetic characteristics of SLE and pSS. The particular roles of these pivotal genes and mutually overlapping pathways may provide a basis for further mechanistic research.
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Affiliation(s)
- Yanling Cui
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Huina Zhang
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhen Wang
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bangdong Gong
- Division of Rheumatology, Tongji Hospital of Tongji University School of Medicine, Shanghai, China
| | - Hisham Al-Ward
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yaxuan Deng
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Orion Fan
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Junbang Wang
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wenmin Zhu
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yi Eve Sun
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
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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: 12] [Impact Index Per Article: 12.0] [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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7
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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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8
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Miyamoto T, Honda Y, Izawa K, Kanazawa N, Kadowaki S, Ohnishi H, Fujimoto M, Kambe N, Kase N, Shiba T, Nakagishi Y, Akizuki S, Murakami K, Bamba M, Nishida Y, Inui A, Fujisawa T, Nishida D, Iwata N, Otsubo Y, Ishimori S, Nishikori M, Tanizawa K, Nakamura T, Ueda T, Ohwada Y, Tsuyusaki Y, Shimizu M, Ebato T, Iwao K, Kubo A, Kawai T, Matsubayashi T, Miyazaki T, Kanayama T, Nishitani-Isa M, Nihira H, Abe J, Tanaka T, Hiejima E, Okada S, Ohara O, Saito MK, Takita J, Nishikomori R, Yasumi T. Assessment of type I interferon signatures in undifferentiated inflammatory diseases: A Japanese multicenter experience. Front Immunol 2022; 13:905960. [PMID: 36211342 PMCID: PMC9541620 DOI: 10.3389/fimmu.2022.905960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/01/2022] [Indexed: 11/28/2022] Open
Abstract
Purpose Upregulation of type I interferon (IFN) signaling has been increasingly detected in inflammatory diseases. Recently, upregulation of the IFN signature has been suggested as a potential biomarker of IFN-driven inflammatory diseases. Yet, it remains unclear to what extent type I IFN is involved in the pathogenesis of undifferentiated inflammatory diseases. This study aimed to quantify the type I IFN signature in clinically undiagnosed patients and assess clinical characteristics in those with a high IFN signature. Methods The type I IFN signature was measured in patients’ whole blood cells. Clinical and biological data were collected retrospectively, and an intensive genetic analysis was performed in undiagnosed patients with a high IFN signature. Results A total of 117 samples from 94 patients with inflammatory diseases, including 37 undiagnosed cases, were analyzed. Increased IFN signaling was observed in 19 undiagnosed patients, with 10 exhibiting clinical features commonly found in type I interferonopathies. Skin manifestations, observed in eight patients, were macroscopically and histologically similar to those found in proteasome-associated autoinflammatory syndrome. Genetic analysis identified novel mutations in the PSMB8 gene of one patient, and rare variants of unknown significance in genes linked to type I IFN signaling in four patients. A JAK inhibitor effectively treated the patient with the PSMB8 mutations. Patients with clinically quiescent idiopathic pulmonary hemosiderosis and A20 haploinsufficiency showed enhanced IFN signaling. Conclusions Half of the patients examined in this study, with undifferentiated inflammatory diseases, clinically quiescent A20 haploinsufficiency, or idiopathic pulmonary hemosiderosis, had an elevated type I IFN signature.
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Affiliation(s)
- Takayuki Miyamoto
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yoshitaka Honda
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Department of Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kazushi Izawa
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
- *Correspondence: Kazushi Izawa,
| | - Nobuo Kanazawa
- Department of Dermatology, Hyogo Medical University, Nishinomiya, Japan
| | - Saori Kadowaki
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Masakazu Fujimoto
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Naotomo Kambe
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Naoya Kase
- Department of Clinical Application, Center for iPS cell (Induced pluripotent stem cell) Research and Application, Kyoto University, Kyoto, Japan
| | - Takeshi Shiba
- Department of Pediatrics, Tenri Hospital, Tenri, Japan
| | - Yasuo Nakagishi
- Department of Pediatric Rheumatology, Hyogo Prefectural Kobe Children’s Hospital, Kobe, Japan
| | - Shuji Akizuki
- Division of Clinical Immunology and Cancer Immunotherapy, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosaku Murakami
- Division of Clinical Immunology and Cancer Immunotherapy, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Bamba
- Department of Pediatrics, Kawasaki Municipal Hospital, Kawasaki, Japan
| | - Yutaka Nishida
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Ayano Inui
- Department of Pediatric Hepatology and Gastroenterology, Saiseikai Yokohamashi Tobu Hospital, Yokohama, Japan
| | - Tomoo Fujisawa
- Department of Pediatric Hepatology and Gastroenterology, Saiseikai Yokohamashi Tobu Hospital, Yokohama, Japan
| | - Daisuke Nishida
- Department of Infection and Immunology, Aichi Children’s Health and Medical Center, Aichi, Japan
| | - Naomi Iwata
- Department of Infection and Immunology, Aichi Children’s Health and Medical Center, Aichi, Japan
| | - Yoshikazu Otsubo
- Department of Pediatrics, Sasebo City General Hospital, Sasebo, Japan
| | - Shingo Ishimori
- Department of Pediatrics, Takatsuki General Hospital, Takatsuki, Japan
| | - Momoko Nishikori
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kiminobu Tanizawa
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoyuki Nakamura
- Department of General Medicine, Osaka City Hospital Organization Osaka City General Hospital, Osaka, Japan
| | - Takeshi Ueda
- Department of Emergency and General Internal Medicine, Rakuwakai Marutamachi Hospital, Kyoto, Japan
| | - Yoko Ohwada
- Department of Pediatrics, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Yu Tsuyusaki
- Department of Neurology, Kanagawa Children’s Medical Center, Yokohama, Japan
| | - Masaki Shimizu
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takasuke Ebato
- Department of Pediatrics, Kitasato University, School of Medicine, Kanagawa, Japan
| | - Kousho Iwao
- Department of Internal Medicine, Division of Rheumatology, Infectious Diseases and Laboratory Medicine, University of Miyazaki, Miyazaki, Japan
| | - Akiharu Kubo
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Toshinao Kawai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | | | | | | | | | - Hiroshi Nihira
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Junya Abe
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Pediatrics, Kitano Hospital, Tazuke Kofukai Medical Research Institute, Osaka, Japan
| | - Takayuki Tanaka
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Pediatrics, Otsu Red Cross Hospital, Otsu, Japan
| | - Eitaro Hiejima
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Megumu K. Saito
- Department of Clinical Application, Center for iPS cell (Induced pluripotent stem cell) Research and Application, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
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9
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-Omic Approaches and Treatment Response in Rheumatoid Arthritis. Pharmaceutics 2022; 14:pharmaceutics14081648. [PMID: 36015273 PMCID: PMC9412998 DOI: 10.3390/pharmaceutics14081648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is an inflammatory disorder characterized by an aberrant activation of innate and adaptive immune cells. There are different drugs used for the management of RA, including disease-modifying antirheumatic drugs (DMARDs). However, a significant percentage of RA patients do not initially respond to DMARDs. This interindividual variation in drug response is caused by a combination of environmental, genetic and epigenetic factors. In this sense, recent -omic studies have evidenced different molecular signatures involved in this lack of response. The aim of this review is to provide an updated overview of the potential role of -omic approaches, specifically genomics, epigenomics, transcriptomics, and proteomics, to identify molecular biomarkers to predict the clinical efficacy of therapies currently used in this disorder. Despite the great effort carried out in recent years, to date, there are still no validated biomarkers of response to the drugs currently used in RA. -Omic studies have evidenced significant differences in the molecular profiles associated with treatment response for the different drugs used in RA as well as for different cell types. Therefore, global and cell type-specific -omic studies analyzing response to the complete therapeutical arsenal used in RA, including less studied therapies, such as sarilumab and JAK inhibitors, are greatly needed.
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10
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Gene Ontology Analysis Highlights Biological Processes Influencing Non-Response to Anti-TNF Therapy in Rheumatoid Arthritis. Biomedicines 2022; 10:biomedicines10081808. [PMID: 36009355 PMCID: PMC9404936 DOI: 10.3390/biomedicines10081808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/20/2022] Open
Abstract
Anti-TNF therapy has significantly improved disease control in rheumatoid arthritis, but a fraction of rheumatoid arthritis patients do not respond to anti-TNF therapy or lose response over time. Moreover, the mechanisms underlying non-response to anti-TNF therapy remain largely unknown. To date, many single biomarkers of response to anti-TNF therapy have been published but they have not yet been analyzed as a system of interacting nodes. The aim of our study is to systematically elucidate the biological processes underlying non-response to anti-TNF therapy in rheumatoid arthritis using the gene ontologies of previously published predictive biomarkers. Gene networks were constructed based on published biomarkers and then enriched gene ontology terms were elucidated in subgroups using gene ontology software tools. Our results highlight the novel role of proteasome-mediated protein catabolic processes (p = 2.91 × 10−15) and plasma lipoproteins (p = 4.55 × 10−11) in anti-TNF therapy response. The results of our gene ontology analysis help elucidate the biological processes underlying non-response to anti-TNF therapy in rheumatoid arthritis and encourage further study of the highlighted processes.
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11
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Nagafuchi Y, Yanaoka H, Fujio K. Lessons From Transcriptome Analysis of Autoimmune Diseases. Front Immunol 2022; 13:857269. [PMID: 35663941 PMCID: PMC9157483 DOI: 10.3389/fimmu.2022.857269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022] Open
Abstract
Various immune cell types, including monocytes, macrophages, and adaptive immune T and B cells, play major roles in inflammation in systemic autoimmune diseases. However, the precise contribution of these cells to autoimmunity remains elusive. Transcriptome analysis has added a new dimension to biology and medicine. It enables us to observe the dynamics of gene expression in different cell types in patients with diverse diseases as well as in healthy individuals, which cannot be achieved with genomic information alone. In this review, we summarize how transcriptome analysis has improved our understanding of the pathological roles of immune cells in autoimmune diseases with a focus on the ImmuNexUT database we reported. We will also discuss the common experimental and analytical design of transcriptome analyses. Recently, single-cell RNA-seq analysis has provided atlases of infiltrating immune cells, such as pro-inflammatory monocytes and macrophages, peripheral helper T cells, and age or autoimmune-associated B cells in various autoimmune disease lesions. With the integration of genomic data, expression quantitative trait locus (eQTL) analysis can help identify candidate causal genes and immune cells. Finally, we also mention how the information obtained from these analyses can be used practically to predict patient prognosis.
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Affiliation(s)
- Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruyuki Yanaoka
- Immuno-Rheumatology Center, St. Luke's International Hospital, St. Luke's International University, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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12
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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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13
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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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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: 77] [Impact Index Per Article: 25.7] [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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Current Understanding of the Neutrophil Transcriptome in Health and Disease. Cells 2021; 10:cells10092406. [PMID: 34572056 PMCID: PMC8469435 DOI: 10.3390/cells10092406] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022] Open
Abstract
Neutrophils are key cells of the innate immune system. It is now understood that this leukocyte population is diverse in both the basal composition and functional plasticity. Underlying this plasticity is a post-translational framework for rapidly achieving early activation states, but also a transcriptional capacity that is becoming increasingly recognized by immunologists. Growing interest in the contribution of neutrophils to health and disease has resulted in more efforts to describe their transcriptional activity. Whilst initial efforts focused predominantly on understanding the existing biology, investigations with advanced methods such as single cell RNA sequencing to understand interactions of the entire immune system are revealing higher flexibility in neutrophil transcription than previously thought possible and multiple transition states. It is now apparent that neutrophils utilise many forms of RNA in the regulation of their function. This review collates current knowledge on the nuclei structure and gene expression activity of human neutrophils across homeostasis and disease, before highlighting knowledge gaps that are research priority areas.
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17
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Tsuchiya H, Fujio K. Title Current Status of the Search for Biomarkers for Optimal Therapeutic Drug Selection for Patients with Rheumatoid Arthritis. Int J Mol Sci 2021; 22:ijms22179534. [PMID: 34502442 PMCID: PMC8431405 DOI: 10.3390/ijms22179534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/28/2021] [Accepted: 08/28/2021] [Indexed: 12/19/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by destructive synovitis. It is significantly associated with disability, impaired quality of life, and premature mortality. Recently, the development of biological agents (including tumor necrosis factor-α and interleukin-6 receptor inhibitors) and Janus kinase inhibitors have advanced the treatment of RA; however, it is still difficult to predict which drug will be effective for each patient. To break away from the current therapeutic approaches that could be described as a “lottery,” there is an urgent need to establish biomarkers that stratify patients in terms of expected therapeutic responsiveness. This review deals with recent progress from multi-faceted analyses of the synovial tissue in RA, which is now bringing new insights into diverse features at both the cellular and molecular levels and their potential links with particular clinical phenotypes.
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18
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Ge X, Frank-Bertoncelj M, Klein K, McGovern A, Kuret T, Houtman M, Burja B, Micheroli R, Shi C, Marks M, Filer A, Buckley CD, Orozco G, Distler O, Morris AP, Martin P, Eyre S, Ospelt C. Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability. Genome Biol 2021; 22:247. [PMID: 34433485 PMCID: PMC8385949 DOI: 10.1186/s13059-021-02460-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies have reported more than 100 risk loci for rheumatoid arthritis (RA). These loci are shown to be enriched in immune cell-specific enhancers, but the analysis so far has excluded stromal cells, such as synovial fibroblasts (FLS), despite their crucial involvement in the pathogenesis of RA. Here we integrate DNA architecture, 3D chromatin interactions, DNA accessibility, and gene expression in FLS, B cells, and T cells with genetic fine mapping of RA loci. RESULTS We identify putative causal variants, enhancers, genes, and cell types for 30-60% of RA loci and demonstrate that FLS account for up to 24% of RA heritability. TNF stimulation of FLS alters the organization of topologically associating domains, chromatin state, and the expression of putative causal genes such as TNFAIP3 and IFNAR1. Several putative causal genes constitute RA-relevant functional networks in FLS with roles in cellular proliferation and activation. Finally, we demonstrate that risk variants can have joint-specific effects on target gene expression in RA FLS, which may contribute to the development of the characteristic pattern of joint involvement in RA. CONCLUSION Overall, our research provides the first direct evidence for a causal role of FLS in the genetic susceptibility for RA accounting for up to a quarter of RA heritability.
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Affiliation(s)
- Xiangyu Ge
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Mojca Frank-Bertoncelj
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Kerstin Klein
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Amanda McGovern
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Tadeja Kuret
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia
| | - Miranda Houtman
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Blaž Burja
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia
| | - Raphael Micheroli
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Chenfu Shi
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Andrew Filer
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK
| | - Christopher D Buckley
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University Foundation Trust, Manchester, UK
| | - Oliver Distler
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul Martin
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University Foundation Trust, Manchester, UK
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University Foundation Trust, Manchester, UK
| | - Caroline Ospelt
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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19
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Harrison SR, Burska AN, Emery P, Marzo-Ortega H, Ponchel F. Interferon-related gene expression in response to TNF inhibitor treatment in ankylosing spondylitis patients: a pilot study. Rheumatology (Oxford) 2021; 60:3607-3616. [PMID: 33393636 DOI: 10.1093/rheumatology/keaa817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/07/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE Ankylosing spondylitis (AS) is a chronic inflammatory arthritis primarily affecting the spine and sacroiliac joints. TNF inhibitor (TNFi) drugs are recommended for patients not responding to NSAIDs; however, there is a significant need for biomarkers of response. IFN-regulated genes (IRGs) and other cytokines/chemokines are linked to autoimmune diseases and have been associated with treatment response. Our objective was to explore whether IRGs and cytokines/chemokines can be associated with response to TNFiagents in AS. METHODS Peripheral blood mononuclear cells were obtained from 26 AS patients who were to receive a TNFi (I, n = 15) or placebo (P, n = 11) at week 0 and week 22. Response (R)/non-response (NR) was defined as reduction in ASDAS ≥ 1.2 points or reduction in sacroiliac/vertebral MRI lesions. The expression of 96 genes was quantified using TaqMan assays. Finally, ELISA was used to measure IL-6 in serum samples from another 38 AS patients. RESULTS Analysis of gene expression in 26 baseline samples segregated patients into four groups defined by a signature of 15 genes (mainly IRGs). ASDAS response was associated with one group independently of treatment received. We then analysed response to the TNFi (n = 15) and identified a 12-gene signature associated with MRI response. A third IRG signature was also associated with a reduction in IRGs expression post-TNFi samples (n = 10 pairs). Finally, decreased circulating IL-6 was associated with BASDAI-R. CONCLUSION This pilot study suggests an association between IRG expression and response to TNFi in AS. These findings require validation in a larger cohort in order to construct predictive algorithms for patient stratification.
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Affiliation(s)
- Stephanie R Harrison
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK
| | - Agata N Burska
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK
| | - Paul Emery
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Helena Marzo-Ortega
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK.,NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Frederique Ponchel
- University of Leeds, Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK
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20
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Wajda A, Sivitskaya L, Paradowska-Gorycka A. Application of NGS Technology in Understanding the Pathology of Autoimmune Diseases. J Clin Med 2021; 10:3334. [PMID: 34362117 PMCID: PMC8348854 DOI: 10.3390/jcm10153334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
NGS technologies have transformed clinical diagnostics and broadly used from neonatal emergencies to adult conditions where the diagnosis cannot be made based on clinical symptoms. Autoimmune diseases reveal complicate molecular background and traditional methods could not fully capture them. Certainly, NGS technologies meet the needs of modern exploratory research, diagnostic and pharmacotherapy. Therefore, the main purpose of this review was to briefly present the application of NGS technology used in recent years in the understanding of autoimmune diseases paying particular attention to autoimmune connective tissue diseases. The main issues are presented in four parts: (a) panels, whole-genome and -exome sequencing (WGS and WES) in diagnostic, (b) Human leukocyte antigens (HLA) as a diagnostic tool, (c) RNAseq, (d) microRNA and (f) microbiome. Although all these areas of research are extensive, it seems that epigenetic impact on the development of systemic autoimmune diseases will set trends for future studies on this area.
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Affiliation(s)
- Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland
| | - Larysa Sivitskaya
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, 220072 Minsk, Belarus
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland
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21
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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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22
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Lu H, Zhang J, Jiang Z, Zhang M, Wang T, Zhao H, Zeng P. Detection of Genetic Overlap Between Rheumatoid Arthritis and Systemic Lupus Erythematosus Using GWAS Summary Statistics. Front Genet 2021; 12:656545. [PMID: 33815486 PMCID: PMC8012913 DOI: 10.3389/fgene.2021.656545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background Clinical and epidemiological studies have suggested systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are comorbidities and common genetic etiologies can partly explain such coexistence. However, shared genetic determinations underlying the two diseases remain largely unknown. Methods Our analysis relied on summary statistics available from genome-wide association studies of SLE (N = 23,210) and RA (N = 58,284). We first evaluated the genetic correlation between RA and SLE through the linkage disequilibrium score regression (LDSC). Then, we performed a multiple-tissue eQTL (expression quantitative trait loci) weighted integrative analysis for each of the two diseases and aggregated association evidence across these tissues via the recently proposed harmonic mean P-value (HMP) combination strategy, which can produce a single well-calibrated P-value for correlated test statistics. Afterwards, we conducted the pleiotropy-informed association using conjunction conditional FDR (ccFDR) to identify potential pleiotropic genes associated with both RA and SLE. Results We found there existed a significant positive genetic correlation (rg = 0.404, P = 6.01E-10) via LDSC between RA and SLE. Based on the multiple-tissue eQTL weighted integrative analysis and the HMP combination across various tissues, we discovered 14 potential pleiotropic genes by ccFDR, among which four were likely newly novel genes (i.e., INPP5B, OR5K2, RP11-2C24.5, and CTD-3105H18.4). The SNP effect sizes of these pleiotropic genes were typically positively dependent, with an average correlation of 0.579. Functionally, these genes were implicated in multiple auto-immune relevant pathways such as inositol phosphate metabolic process, membrane and glucagon signaling pathway. Conclusion This study reveals common genetic components between RA and SLE and provides candidate associated loci for understanding of molecular mechanism underlying the comorbidity of the two diseases.
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Affiliation(s)
- Haojie Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Jinhui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Zhou Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Meng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Ting Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Huashuo Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
| | - Ping Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, China.,Center for Medical Statistics and Data Analysis, School of Public Health, Xuzhou Medical University, Xuzhou, China
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23
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Oliver J, Nair N, Orozco G, Smith S, Hyrich KL, Morgan A, Isaacs J, Wilson AG, Barton A, Plant D. Transcriptome-wide study of TNF-inhibitor therapy in rheumatoid arthritis reveals early signature of successful treatment. Arthritis Res Ther 2021; 23:80. [PMID: 33691749 PMCID: PMC7948368 DOI: 10.1186/s13075-021-02451-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Despite the success of TNF-inhibitor therapy in rheumatoid arthritis treatment, up to 40% of patients fail to respond adequately. This study aimed to identify transcriptome-based biomarkers of adalimumab response in rheumatoid arthritis (RA) to aid timely switching in non-responder patients and provide a better mechanistic understanding of the pathways involved in response/non-response. METHODS The Affymetrix Human Transcriptome Array 2.0 (HTA) was used to measure the transcriptome in whole blood at pre-treatment and at 3 months in EULAR good- and non-responders to adalimumab therapy. Differential expression of transcripts was analysed at the transcript level using multiple linear regression. Differentially expressed genes were validated in independent samples using OpenArray™ RT-qPCR. RESULTS In total, 813 transcripts were differentially expressed between pre-treatment and 3 months in adalimumab good-responders. No significant differential expression was observed between good- and non-responders at either time-point and no significant changes were observed in non-responders between time-points. OpenArray™ RT-qPCR was performed for 104 differentially expressed transcripts in good-responders, selected based on magnitude of effect or p value or based on prior association with RA or the immune system, validating differential expression for 17 transcripts. CONCLUSIONS An early transcriptome signature of DAS28 response to adalimumab has been identified and replicated in independent datasets. Whilst treat-to-target approaches encourage early switching in non-responsive patients, registry evidence suggests that this does not always occur. The results herein could guide the development of a blood test to distinguish responders from non-responders at 3 months and support clinical decisions to switch non-responsive patients to an alternative therapy.
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Affiliation(s)
- James Oliver
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Nisha Nair
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Gisela Orozco
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Samantha Smith
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Kimme L Hyrich
- NIHR Manchester BRC, Manchester University Foundation Trust, Manchester, UK
- Versus Arthritis Centre for Epidemiology, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Ann Morgan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds and NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - John Isaacs
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, UK
| | - Anthony G Wilson
- UCD School of Medicine and Medical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Anne Barton
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
- NIHR Manchester BRC, Manchester University Foundation Trust, Manchester, UK
| | - Darren Plant
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK.
- NIHR Manchester BRC, Manchester University Foundation Trust, Manchester, UK.
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24
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Fresneda Alarcon M, McLaren Z, Wright HL. Neutrophils in the Pathogenesis of Rheumatoid Arthritis and Systemic Lupus Erythematosus: Same Foe Different M.O. Front Immunol 2021; 12:649693. [PMID: 33746988 PMCID: PMC7969658 DOI: 10.3389/fimmu.2021.649693] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 12/14/2022] Open
Abstract
Dysregulated neutrophil activation contributes to the pathogenesis of autoimmune diseases including rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). Neutrophil-derived reactive oxygen species (ROS) and granule proteases are implicated in damage to and destruction of host tissues in both conditions (cartilage in RA, vascular tissue in SLE) and also in the pathogenic post-translational modification of DNA and proteins. Neutrophil-derived cytokines and chemokines regulate both the innate and adaptive immune responses in RA and SLE, and neutrophil extracellular traps (NETs) expose nuclear neoepitopes (citrullinated proteins in RA, double-stranded DNA and nuclear proteins in SLE) to the immune system, initiating the production of auto-antibodies (ACPA in RA, anti-dsDNA and anti-acetylated/methylated histones in SLE). Neutrophil apoptosis is dysregulated in both conditions: in RA, delayed apoptosis within synovial joints contributes to chronic inflammation, immune cell recruitment and prolonged release of proteolytic enzymes, whereas in SLE enhanced apoptosis leads to increased apoptotic burden associated with development of anti-nuclear auto-antibodies. An unbalanced energy metabolism in SLE and RA neutrophils contributes to the pathology of both diseases; increased hypoxia and glycolysis in RA drives neutrophil activation and NET production, whereas decreased redox capacity increases ROS-mediated damage in SLE. Neutrophil low-density granulocytes (LDGs), present in high numbers in the blood of both RA and SLE patients, have opposing phenotypes contributing to clinical manifestations of each disease. In this review we will describe the complex and contrasting phenotype of neutrophils and LDGs in RA and SLE and discuss their discrete roles in the pathogenesis of each condition. We will also review our current understanding of transcriptomic and metabolomic regulation of neutrophil phenotype in RA and SLE and discuss opportunities for therapeutic targeting of neutrophil activation in inflammatory auto-immune disease.
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Affiliation(s)
- Michele Fresneda Alarcon
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Zoe McLaren
- Liverpool University Hospitals National Health Service (NHS) Foundation Trust, Liverpool, United Kingdom
| | - Helen Louise Wright
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
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25
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Esnault S, Khosravi M, Kelly EA, Liu LY, Bochkov YA, Tattersall MC, Jarjour NN. Increased IL-6 and Potential IL-6 trans-signalling in the airways after an allergen challenge. Clin Exp Allergy 2021; 51:564-573. [PMID: 33471392 DOI: 10.1111/cea.13832] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/22/2020] [Accepted: 01/16/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND In asthma, IL-6 is a potential cause of enhanced inflammation, tissue damage and airway dysfunction. IL-6 signalling is regulated by its receptor, which is composed of two proteins, IL-6R and GP130. In addition to their membrane form, these two proteins may be found as extracellular soluble forms. The interaction of IL-6 with soluble IL-6R (sIL-6R) can trigger IL-6 trans-signalling in cells lacking IL-6R. Conversely, the soluble form of GP130 (sGP130) competes with its membrane form to inhibit IL-6 trans-signalling. OBJECTIVES We aimed to analyse IL-6 trans-signalling proteins in the airways of subjects after an allergen challenge. METHODS We used a model of segmental bronchoprovocation with an allergen (SBP-Ag) in human subjects with allergy. Before and 48 h after SBP-Ag, bronchoalveolar lavages (BALs) allowed for the analysis of proteins in BAL fluids (BALFs) by ELISA, and membrane proteins on the surface of BAL cells by flow cytometry. In addition, we performed RNA sequencing (RNA-seq) and used proteomic data to further inform on the expression of the IL-6R subunits by eosinophils, bronchial epithelial cells and lung fibroblasts. Finally, we measured the effect of IL-6 trans-signalling on bronchial fibroblasts, in vitro. RESULTS IL-6, sIL-6R, sGP130 and the molar ratio of sIL-6R/sGP130 increased in the airways after SBP-Ag, suggesting the potential for enhanced IL-6 trans-signalling activity. BAL lymphocytes, monocytes and eosinophils displayed IL-6R on their surface and were all possible providers of sIL-6R, whereas GP130 was highly expressed in bronchial epithelial cells and lung fibroblasts. Finally, bronchial fibroblasts activated by IL-6 trans-signalling produced enhanced amounts of the chemokine, MCP-1 (CCL2). CONCLUSION AND CLINICAL RELEVANCE After a bronchial allergen challenge, we found augmentation of the elements of IL-6 trans-signalling. Allergen-induced IL-6 trans-signalling activity can activate fibroblasts to produce chemokines that can further enhance inflammation and lung dysfunction.
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Affiliation(s)
- Stephane Esnault
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, the University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Mehdi Khosravi
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, the University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Elizabeth A Kelly
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, the University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Lin Ying Liu
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, the University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Yury A Bochkov
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Matthew C Tattersall
- Department of Medicine, Division of Cardiovascular Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Nizar N Jarjour
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, the University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
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26
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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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27
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Ptacek J, Hawtin RE, Sun D, Louie B, Evensen E, Mittleman BB, Cesano A, Cavet G, Bingham CO, Cofield SS, Curtis JR, Danila MI, Raman C, Furie RA, Genovese MC, Robinson WH, Levesque MC, Moreland LW, Nigrovic PA, Shadick NA, O’Dell JR, Thiele GM, Clair EWS, Striebich CC, Hale MB, Khalili H, Batliwalla F, Aranow C, Mackay M, Diamond B, Nolan GP, Gregersen PK, Bridges SL. Diminished cytokine-induced Jak/STAT signaling is associated with rheumatoid arthritis and disease activity. PLoS One 2021; 16:e0244187. [PMID: 33444321 PMCID: PMC7808603 DOI: 10.1371/journal.pone.0244187] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/05/2020] [Indexed: 12/11/2022] Open
Abstract
Rheumatoid arthritis (RA) is a systemic and incurable autoimmune disease characterized by chronic inflammation in synovial lining of joints. To identify the signaling pathways involved in RA, its disease activity, and treatment response, we adapted a systems immunology approach to simultaneously quantify 42 signaling nodes in 21 immune cell subsets (e.g., IFNα→p-STAT5 in B cells) in peripheral blood mononuclear cells (PBMC) from 194 patients with longstanding RA (including 98 patients before and after treatment), and 41 healthy controls (HC). We found multiple differences between patients with RA compared to HC, predominantly in cytokine-induced Jak/STAT signaling in many immune cell subsets, suggesting pathways that may be associated with susceptibility to RA. We also found that high RA disease activity, compared to low disease activity, was associated with decreased (e.g., IFNα→p-STAT5, IL-10→p-STAT1) or increased (e.g., IL-6→STAT3) response to stimuli in multiple cell subsets. Finally, we compared signaling in patients with established, refractory RA before and six months after initiation of methotrexate (MTX) or TNF inhibitors (TNFi). We noted significant changes from pre-treatment to post-treatment in IFNα→p-STAT5 signaling and IL-10→p-STAT1 signaling in multiple cell subsets; these changes brought the aberrant RA signaling profiles toward those of HC. This large, comprehensive functional signaling pathway study provides novel insights into the pathogenesis of RA and shows the potential of quantification of cytokine-induced signaling as a biomarker of disease activity or treatment response.
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Affiliation(s)
- Jason Ptacek
- Nodality, Inc., South San Francisco, California, United States of America
| | - Rachael E. Hawtin
- Nodality, Inc., South San Francisco, California, United States of America
| | - Dongmei Sun
- University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
| | - Brent Louie
- Nodality, Inc., South San Francisco, California, United States of America
| | - Erik Evensen
- Nodality, Inc., South San Francisco, California, United States of America
| | | | - Alessandra Cesano
- Nodality, Inc., South San Francisco, California, United States of America
| | - Guy Cavet
- Nodality, Inc., South San Francisco, California, United States of America
| | - Clifton O. Bingham
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Stacey S. Cofield
- University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
| | - Jeffrey R. Curtis
- University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
| | - Maria I. Danila
- University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
| | - Chander Raman
- University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
| | - Richard A. Furie
- The Feinstein Institute for Medical Research and Northwell Health, Manhasset, New York, United States of America
| | - Mark C. Genovese
- Stanford University School of Medicine, Stanford, California, United States of America
| | - William H. Robinson
- Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Larry W. Moreland
- University of Colorado Anschutz Medical Campus, Boulder, Colorado, United States of America
| | - Peter A. Nigrovic
- Brigham and Women’s Hospital, Harvard University, Boston, Massachusetts, United States of America
| | - Nancy A. Shadick
- Brigham and Women’s Hospital, Harvard University, Boston, Massachusetts, United States of America
| | - James R. O’Dell
- University of Nebraska Medical Center, Lincoln, Nebraska, United States of America
| | - Geoffrey M. Thiele
- University of Nebraska Medical Center, Lincoln, Nebraska, United States of America
| | - E. William St Clair
- Duke University Medical Center, Durham, North Carolina, United States of America
| | | | - Matthew B. Hale
- Stanford University School of Medicine, Stanford, California, United States of America
| | - Houman Khalili
- The Feinstein Institute for Medical Research and Northwell Health, Manhasset, New York, United States of America
| | - Franak Batliwalla
- The Feinstein Institute for Medical Research and Northwell Health, Manhasset, New York, United States of America
| | - Cynthia Aranow
- The Feinstein Institute for Medical Research and Northwell Health, Manhasset, New York, United States of America
| | - Meggan Mackay
- The Feinstein Institute for Medical Research and Northwell Health, Manhasset, New York, United States of America
| | - Betty Diamond
- The Feinstein Institute for Medical Research and Northwell Health, Manhasset, New York, United States of America
| | - Garry P. Nolan
- Nodality, Inc., South San Francisco, California, United States of America
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research and Northwell Health, Manhasset, New York, United States of America
| | - S. Louis Bridges
- Hospital for Special Surgery and Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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Wright HL, Lyon M, Chapman EA, Moots RJ, Edwards SW. Rheumatoid Arthritis Synovial Fluid Neutrophils Drive Inflammation Through Production of Chemokines, Reactive Oxygen Species, and Neutrophil Extracellular Traps. Front Immunol 2021; 11:584116. [PMID: 33469455 PMCID: PMC7813679 DOI: 10.3389/fimmu.2020.584116] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disorder affecting synovial joints. Neutrophils are believed to play an important role in both the initiation and progression of RA, and large numbers of activated neutrophils are found within both synovial fluid (SF) and synovial tissue from RA joints. In this study we analyzed paired blood and SF neutrophils from patients with severe, active RA (DAS28>5.1, n=3) using RNA-seq. 772 genes were significantly different between blood and SF neutrophils. IPA analysis predicted that SF neutrophils had increased expression of chemokines and ROS production, delayed apoptosis, and activation of signaling cascades regulating the production of NETs. This activated phenotype was confirmed experimentally by incubating healthy control neutrophils in cell-free RA SF, which was able to delay apoptosis and induce ROS production in both unprimed and TNFα primed neutrophils (p<0.05). RA SF significantly increased neutrophil migration through 3μM transwell chambers (p<0.05) and also increased production of NETs by healthy control neutrophils (p<0.001), including exposure of myeloperoxidase (MPO) and citrullinated histone-H3-positive DNA NETs. IPA analysis predicted NET production was mediated by signaling networks including AKT, RAF1, SRC, and NF-κB. Our results expand the understanding of the molecular changes that take place in the neutrophil transcriptome during migration into inflamed joints in RA, and the altered phenotype in RA SF neutrophils. Specifically, RA SF neutrophils lose their migratory properties, residing within the joint to generate signals that promote joint damage, as well as inflammation via recruitment and activation of both innate and adaptive immune cells. We propose that this activated SF neutrophil phenotype contributes to the chronic inflammation and progressive damage to cartilage and bone observed in patients with RA.
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Affiliation(s)
- Helen L. Wright
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Max Lyon
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Elinor A. Chapman
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Robert J. Moots
- Department of Rheumatology, Aintree University Hospital, Liverpool, United Kingdom
- Faculty of Health, Social Care and Medicine, Edge Hill University, Ormskirk, United Kingdom
| | - Steven W. Edwards
- Faculty of Health, Social Care and Medicine, Edge Hill University, Ormskirk, United Kingdom
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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29
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Sepsis and Autoimmune Disease: Pathology, Systems Medicine, and Artificial Intelligence. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11643-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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30
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Pathi A, Wright M, Smed MK, Nelson JL, Olsen J, Hetland ML, Zoffmann V, Jawaheer D. The Rheumatoid Arthritis Gene Expression Signature Among Women Who Improve or Worsen During Pregnancy: A Pilot Study. J Rheumatol 2020; 48:985-991. [PMID: 33323535 DOI: 10.3899/jrheum.201128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To assess whether gene expression signatures associated with rheumatoid arthritis (RA) before pregnancy differ between women who improve or worsen during pregnancy, and to determine whether these expression signatures are altered during pregnancy when RA improves or worsens. METHODS Clinical data and blood samples were collected before pregnancy (T0) and at the third trimester (T3) from 11 women with RA and 5 healthy women. RA disease activity was assessed using the Clinical Disease Activity Index (CDAI). At each timepoint, RA-associated gene expression signatures were identified using differential expression analysis of RNA sequencing profiles between women with RA and healthy women. RESULTS Of the women with RA, 6 improved by T3 (RAimproved), 3 worsened (RAworsened),and 2 were excluded. At T0, mean CDAI scores were similar in both groups (RAimproved 11.2 ± 9.8; RAworsened 13.8 ± 6.7; Wilcoxon rank-sum test: P = 0.6). In the RAimproved group, 89 genes were differentially expressed at T0 (q < 0.05 and fold change ≥ 2) compared to healthy women. When RA improved at T3, 65 of 89 (73%) of these genes no longer displayed RA-associated expression. In the RAworsened group, a largely different RA gene expression signature (429 genes) was identified at T0. When RA disease activity worsened at T3, 207 of 429 (48%) genes lost their differential expression, while an additional 151 genes became newly differentially expressed. CONCLUSION In our pilot dataset, pre-pregnancy RA expression signatures differed between women who subsequently improved or worsened during pregnancy, suggesting that inherent genomic differences may influence how pregnancy affects disease activity. Further, these RA signatures were altered during pregnancy as disease activity changed.
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Affiliation(s)
- Amogh Pathi
- A. Pathi, BS, M. Wright, MS, Staff Research Associate II, Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Matthew Wright
- A. Pathi, BS, M. Wright, MS, Staff Research Associate II, Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Mette Kiel Smed
- M.K. Smed, RM, Study Coordinator, Juliane Marie Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - J Lee Nelson
- J.L. Nelson, MD, Professor, Fred Hutchinson Cancer Research Center, and University of Washington, Seattle, Washington, USA
| | - Jørn Olsen
- J. Olsen, MD, PhD, Professor, University of California Los Angeles, Los Angeles, California, USA, and Aarhus University Hospital, Aarhus, Denmark
| | - Merete Lund Hetland
- M.L. Hetland, DMSc, Professor, DANBIO Registry and Copenhagen Centre for Arthritis Research, Centre for Rheumatology and Spine Diseases VRR, Rigshospitalet, Copenhagen, and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Vibeke Zoffmann
- V. Zoffmann, RN, PhD, Professor, Juliane Marie Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, and Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Damini Jawaheer
- D. Jawaheer, PhD, Associate Scientist, Children's Hospital Oakland Research Institute, Oakland, and University of California San Francisco, San Francisco, California, USA.
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31
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Effects of Biological Therapies on Molecular Features of Rheumatoid Arthritis. Int J Mol Sci 2020; 21:ijms21239067. [PMID: 33260629 PMCID: PMC7731249 DOI: 10.3390/ijms21239067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/15/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune and chronic inflammatory disease primarily affecting the joints, and closely related to specific autoantibodies that mostly target modified self-epitopes. Relevant findings in the field of RA pathogenesis have been described. In particular, new insights come from studies on synovial fibroblasts and cells belonging to the innate and adaptive immune system, which documented the aberrant production of inflammatory mediators, oxidative stress and NETosis, along with relevant alterations of the genome and on the regulatory epigenetic mechanisms. In recent years, the advances in the understanding of RA pathogenesis by identifying key cells and cytokines allowed the development of new targeted disease-modifying antirheumatic drugs (DMARDs). These drugs considerably improved treatment outcomes for the majority of patients. Moreover, numerous studies demonstrated that the pharmacological therapy with biologic DMARDs (bDMARDs) promotes, in parallel to their clinical efficacy, significant improvement in all these altered molecular mechanisms. Thus, continuous updating of the knowledge of molecular processes associated with the pathogenesis of RA, and on the specific effects of bDMARDs in the correction of their dysregulation, are essential in the early and correct approach to the treatment of this complex autoimmune disorder. The present review details basic mechanisms related to the physiopathology of RA, along with the core mechanisms of response to bDMARDs.
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32
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Glennon-Alty L, Moots RJ, Edwards SW, Wright HL. Type I interferon regulates cytokine-delayed neutrophil apoptosis, reactive oxygen species production and chemokine expression. Clin Exp Immunol 2020; 203:151-159. [PMID: 32990354 PMCID: PMC7806414 DOI: 10.1111/cei.13525] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/21/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
Interferons (IFNs) are key regulators of a number of inflammatory conditions in which neutrophils play an important role in pathology, such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), where type I IFNs are implicated in disease pathology. However, IFNs are usually generated in vivo together with other cytokines that also have immunoregulatory functions, but such interactions are poorly defined experimentally. We measured the effects of type I (IFN-α) IFN, elevated in both RA and SLE, on the functions of healthy neutrophils incubated in vitro in the absence and presence of proinflammatory cytokines typically elevated in inflammatory diseases [tumour necrosis factor (TNF-α), granulocyte-macrophage colony-stimulating factor (GM-CSF)]. IFN-α alone had no effect on neutrophil apoptosis; however, it abrogated the anti-apoptotic effect of GM-CSF (18 h, P < 0·01). The enhanced stability of the anti-apoptotic protein myeloid cell leukaemia 1 (Mcl-1) and delayed activation of caspase activation normally regulated by GM-CSF were blocked by IFN-α: this effect was mediated, in part, by activation of p38 mitogen-activated protein kinase (MAPK). IFN-α alone also primed reactive oxygen species (ROS) production and maintained the transient priming effect of TNF-α for up to 4 h: it also down-regulated GM-CSF- and TNF-α-activated expression of chemokine (C-X-C motif) ligand (CXCL)1, CXCL2, CXCL3, CXCL8, CCL3 and CCL4 but, in contrast, increased the expression of CXCL10. These novel data identify complex regulatory signalling networks in which type I IFNs profoundly alter the response of neutrophils to inflammatory cytokines. This is likely to have important consequences in vivo and may explain the complexity and heterogeneity of inflammatory diseases such as RA, in which multiple cytokine cascades have been activated.
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Affiliation(s)
- L Glennon-Alty
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, Merseyside, UK.,Liverpool Health Partners, University of Liverpool, Liverpool, Merseyside, UK
| | - R J Moots
- Department of Rheumatology, Aintree University Hospital, Liverpool, UK
| | - S W Edwards
- Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Liverpool, Merseyside, UK
| | - H L Wright
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, Merseyside, UK
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Mavragani CP, Nezos A, Dovrolis N, Andreou NP, Legaki E, Sechi LA, Bamias G, Gazouli M. Type I and II Interferon Signatures Can Predict the Response to Anti-TNF Agents in Inflammatory Bowel Disease Patients: Involvement of the Microbiota. Inflamm Bowel Dis 2020; 26:1543-1553. [PMID: 32812029 DOI: 10.1093/ibd/izaa216] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Anti-TNF agents have been a cornerstone of IBD therapy; however, response to treatment has been variable, and clinically applicable biomarkers are urgently needed. We hypothesized that the type I and type II interferon (IFN) signatures may be a confounding factor for response to antitumor necrosis factor (TNF) treatment via interactions with the host and its gut microbiota. METHODS Peripheral blood from 30 IBD patients and 10 healthy controls was subjected to real-time quantitative real-time polymerase chain reaction for type I and type II IFN genes (IFNGs), both at baseline and after treatment with anti-TNF. Correlation between IFN signatures and microbiota composition was also determined for a subgroup of patients and controls. RESULTS At baseline, type I IFN score was significantly higher in IBD patients (P = 0.04 vs controls). Responders to subsequent anti-TNF treatment had significantly lower baseline scores for both type I and II IFN signatures (P < 0.005 vs nonresponders for both comparisons). During treatment with anti-TNF, the expression of type I and II IFNGs was significantly elevated in responders and decreased in nonresponders. In addition, changes in IFN signatures correlated to specific alterations in the abundance of several microbial taxa of the gut microbiome. CONCLUSIONS Baseline expression of type I and II IFN signatures and their kinetics during anti-TNF administration significantly correlate to treatment responses in IBD patients. Peripheral blood IFN signatures may serve as clinically meaningful biomarkers for the identification of subgroups of patients with favorable response to anti-TNF treatment. Additionally, the distinct synergies between different IFN types and microbiota might help drive therapeutic intervention.
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Affiliation(s)
- Clio P Mavragani
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Adrianos Nezos
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolas Dovrolis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Evangelia Legaki
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Leonardo A Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giorgos Bamias
- GI-Unit, 3rd Academic Department of Internal Medicine, Sotiria Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Burja B, Mertelj T, Frank-Bertoncelj M. Hi- JAKi-ng Synovial Fibroblasts in Inflammatory Arthritis With JAK Inhibitors. Front Med (Lausanne) 2020; 7:124. [PMID: 32432116 PMCID: PMC7214667 DOI: 10.3389/fmed.2020.00124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/20/2020] [Indexed: 12/23/2022] Open
Abstract
The Janus kinase (JAK)-Signal transducer and activator of transcription (STAT) pathway is one of the central signaling hubs in inflammatory, immune and cancer cells. Inhibiting the JAK-STAT pathway with JAK inhibitors (jakinibs) constitutes an important therapeutic strategy in cancer and chronic inflammatory diseases like rheumatoid arthritis (RA). FDA has approved different jakinibs for the treatment of RA, including tofacitinib, baricitinib and upadacitinib, and several jakinibs are being tested in clinical trials. Here, we reviewed published studies of jakinib effects on resolving synovial pathology in inflammatory arthritis. We discussed the results of jakinibs on structural joint damage in clinical trials and explored the effects of jakinibs across different in vitro, ex vivo, and in vivo synovial experimental models. We delved rigorously into experimental designs of in vitro fibroblast studies, deconvoluted jakinib efficacy in synovial fibroblasts across diverse experimental conditions and discussed their translatability in vivo. Synovial fibroblasts can readily activate the JAK-STAT signaling pathway in response to cytokine stimulation. We highlighted rather limited effects of jakinibs on the in vitro cultured synovial fibroblasts and inferred that direct and indirect (immune cell-dependent) actions of jakinibs are required to curb the fibroblast pathology in vivo. These actions have not been mimicked optimally in current in vitro experimental designs, where inflammatory stimuli do not naturally clear out with treatment as they do in vivo. While summarizing the broad knowledge of synovial jakinib effects, our review uniquely challenges future study designs to better mimick the jakinib actions in broader cell communities, as occurring in vivo in the inflamed synovium. This can deepen our understanding of collective synovial activities of jakinibs and their therapeutic limitations, thereby fostering jakinib development in arthritis.
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Affiliation(s)
- Blaž Burja
- Center of Experimental Rheumatology, University Hospital Zurich, Schlieren, Switzerland.,Department of Rheumatology, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tonja Mertelj
- Center of Experimental Rheumatology, University Hospital Zurich, Schlieren, Switzerland
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Abstract
Systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are two common autoimmune rheumatic diseases that vary in severity, clinical presentation, and disease course between individuals. Molecular and genetic studies of both diseases have identified candidate genes and molecular pathways that are linked to various disease outcomes and treatment responses. Currently, patients can be grouped into molecular subsets in each disease, and these molecular categories should enable precision medicine approaches to be applied in rheumatic diseases. In this article, we will review key lessons learned about disease heterogeneity and molecular characterization in rheumatology, which we hope will lead to personalized therapeutic strategies.
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Affiliation(s)
| | - Jaqueline L. Paredes
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
| | - Simone Appenzeller
- Rheumatology Unit, Department of Medicine, Faculty of Medical Science, State University of Campinas, Campinas, Brazil
| | - Timothy B. Niewold
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
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36
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Song W, Tang D, Chen D, Zheng F, Huang S, Xu Y, Yu H, He J, Hong X, Yin L, Liu D, Dai W, Dai Y. Advances in applying of multi-omics approaches in the research of systemic lupus erythematosus. Int Rev Immunol 2020; 39:163-173. [PMID: 32138562 DOI: 10.1080/08830185.2020.1736058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Wencong Song
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Donge Tang
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Deheng Chen
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Fengping Zheng
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Shaoying Huang
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Yong Xu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Haiyan Yu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Jingquan He
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Xiaoping Hong
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Lianghong Yin
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dongzhou Liu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, USA
| | - Yong Dai
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
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37
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Pin A, Monasta L, Taddio A, Piscianz E, Tommasini A, Tesser A. An Easy and Reliable Strategy for Making Type I Interferon Signature Analysis Comparable among Research Centers. Diagnostics (Basel) 2019; 9:E113. [PMID: 31487897 PMCID: PMC6787630 DOI: 10.3390/diagnostics9030113] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 01/13/2023] Open
Abstract
Interferon-stimulated genes (ISGs) are a set of genes whose transcription is induced by interferon (IFN). The measure of the expression of ISGs enables calculating an IFN score, which gives an indirect estimate of the exposition of cells to IFN-mediated inflammation. The measure of the IFN score is proposed for the screening of monogenic interferonopathies, like the Aicardi-Goutières syndrome, or to stratify subjects with systemic lupus erythematosus to receive IFN-targeted treatments. Apart from these scenarios, there is no agreement on the diagnostic value of the score in distinguishing IFN-related disorders from diseases dominated by other types of cytokines. Since the IFN score is currently measured in several research hospitals, merging experiences could help define the potential of scoring IFN inflammation in clinical practice. However, the IFN score calculated at different laboratories may be hardly comparable due to the distinct sets of IFN-stimulated genes assessed and to different controls used for data normalization. We developed a reliable approach to minimize the inter-laboratory variability, thereby providing shared strategies for the IFN signature analysis and allowing different centers to compare data and merge their experiences.
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Affiliation(s)
- Alessia Pin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Lorenzo Monasta
- Clinical Epidemiology and Public Health Research Unit, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", 34137 Trieste, Italy.
| | - Andrea Taddio
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy.
- Department of Paediatrics, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", 34137 Trieste, Italy.
| | - Elisa Piscianz
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", 34137 Trieste, Italy.
| | - Alberto Tommasini
- Department of Paediatrics, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", 34137 Trieste, Italy.
| | - Alessandra Tesser
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", 34137 Trieste, Italy.
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Bonelli M, Dalwigk K, Platzer A, Olmos Calvo I, Hayer S, Niederreiter B, Holinka J, Sevelda F, Pap T, Steiner G, Superti-Furga G, Smolen JS, Kiener HP, Karonitsch T. IRF1 is critical for the TNF-driven interferon response in rheumatoid fibroblast-like synoviocytes : JAKinibs suppress the interferon response in RA-FLSs. Exp Mol Med 2019; 51:1-11. [PMID: 31285419 PMCID: PMC6802656 DOI: 10.1038/s12276-019-0267-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 02/20/2019] [Accepted: 03/11/2019] [Indexed: 12/28/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by persistent synovial inflammation. The major drivers of synovial inflammation are cytokines and chemokines. Among these molecules, TNF activates fibroblast-like synoviocytes (FLSs), which leads to the production of inflammatory mediators. Here, we show that TNF regulates the expression of the transcription factor interferon regulatory factor 1 (IRF1) in human FLSs as well as in a TNF transgenic arthritis mouse model. Transcriptomic analyses of IRF1-deficient, TNF-stimulated FLSs define the interferon (IFN) pathway as a major target of IRF1. IRF1 expression is associated with the expression of IFNβ, which leads to the activation of the JAK-STAT pathway. Blocking the JAK-STAT pathway with the Janus kinase inhibitor (JAKinib) baricitinib or tofacitinib reduces the expression of IFN-regulated genes (IRGs) in TNF-activated FLSs. Therefore, we conclude that TNF induces a distinct inflammatory cascade, in which IRGs are key elements, in FLSs. The IFN-signature might be a promising biomarker for the efficient and personalized use of new treatment strategies for RA, such as JAKinibs.
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Affiliation(s)
- Michael Bonelli
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria
| | - Karolina Dalwigk
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria
| | - Alexander Platzer
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria
| | - Isabel Olmos Calvo
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria
| | - Silvia Hayer
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria
| | - Birgit Niederreiter
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria
| | - Johannes Holinka
- Department of Orthopaedics, Medical University of Vienna, 1090, Vienna, Austria
| | - Florian Sevelda
- Department of Orthopaedics, Medical University of Vienna, 1090, Vienna, Austria
| | - Thomas Pap
- Institute of Musculoskeletal Medicine, University Hospital Muenster, 48149, Muenster, Germany
| | - Günter Steiner
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria.,Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Josef S Smolen
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria
| | - Hans P Kiener
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria
| | - Thomas Karonitsch
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, 1090, Vienna, Austria.
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Crookenden MA, Moyes KM, Kuhn-Sherlock B, Lehnert K, Walker CG, Loor JJ, Mitchell MD, Murray A, Dukkipati VSR, Vailati-Riboni M, Heiser A, Roche JR. Transcriptomic analysis of circulating neutrophils in metabolically stressed peripartal grazing dairy cows. J Dairy Sci 2019; 102:7408-7420. [PMID: 31178180 DOI: 10.3168/jds.2019-16367] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/19/2019] [Indexed: 12/19/2022]
Abstract
The high metabolic demand during the transition into lactation places cows at greater risk of metabolic and infectious disease than at any other time in their lactation cycle. Additionally, a change occurs in the innate immune response during this period, which contributes to increased risk of disease. In the current study, we compared the transcriptomes of neutrophils from dairy cows divergent in their metabolic health post-calving. Cows (n = 5 per risk group) were selected from a parent experiment (n = 45 cows). Those with high or low concentrations of plasma nonesterified fatty acids, plasma β-hydroxybutyrate, and liver triacylglycerol in both wk 1 and 2 were deemed to be at "high risk" (HR) or "low risk" (LR) of metabolic dysfunction, respectively. Circulating neutrophils were isolated at 3 time points during the transition period (d 0 and wk 1 and 4 post-calving), and gene expression was analyzed using RNA sequencing. Differential gene expression between the risk groups was determined using edgeR (http://bioconductor.org), and pathway analysis was conducted using Ingenuity Pathway Analysis (Ingenuity Systems, Qiagen, Valencia, CA). Statistical analysis indicated no interaction between risk and week. Therefore, the overall effect of risk was analyzed across all time points. In total, 3,500 genes were differentially expressed between the HR and LR cows (false discovery rate < 0.05). Of these, 2,897 genes were identified by Ingenuity Pathway Analysis and used for pathway analysis. Of the relevant pathways identified, neutrophils isolated from HR cows showed downregulation of genes involved in the recruitment of granulocytes, interferon signaling, and apoptosis, and upregulation of genes involved in cell survival. The results indicate that metabolically stressed cows had reduced neutrophil function during the peripartum period, highlighting a potential relationship between subclinical metabolic disease and innate immune function that suggests that metabolic health negatively affects the innate immune system and may contribute to the state of immunosuppression during the peripartum period. In this way, the metabolic stress among the HR cows may reduce their ability to combat infection during the transition period.
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Affiliation(s)
- M A Crookenden
- DairyNZ Ltd., Hamilton, New Zealand 3284; School of Biological Sciences, University of Auckland, New Zealand 1010.
| | - K M Moyes
- Department of Animal and Avian Sciences, University of Maryland, College Park 20742
| | | | - K Lehnert
- School of Biological Sciences, University of Auckland, New Zealand 1010
| | - C G Walker
- DairyNZ Ltd., Hamilton, New Zealand 3284
| | - J J Loor
- Department of Animal Sciences, University of Illinois, Urbana 61801
| | - M D Mitchell
- University of Queensland, Centre for Clinical Research, Herston, Australia 4029
| | - A Murray
- Institute of Veterinary, Animal, and Biomedical Sciences, Massey University, Palmerston North, New Zealand 4442
| | - V S R Dukkipati
- Institute of Veterinary, Animal, and Biomedical Sciences, Massey University, Palmerston North, New Zealand 4442
| | - M Vailati-Riboni
- Department of Animal Sciences, University of Illinois, Urbana 61801
| | - A Heiser
- Institute of Veterinary, Animal, and Biomedical Sciences, Massey University, Palmerston North, New Zealand 4442; AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand 4442
| | - J R Roche
- DairyNZ Ltd., Hamilton, New Zealand 3284; School of Biological Sciences, University of Auckland, New Zealand 1010
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de Jong TD, Snoek T, Mantel E, van der Laken CJ, van Vollenhoven RF, Lems WF. Dynamics of the Type I Interferon Response During Immunosuppressive Therapy in Rheumatoid Arthritis. Front Immunol 2019; 10:902. [PMID: 31068954 PMCID: PMC6491736 DOI: 10.3389/fimmu.2019.00902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Objective: The type I interferon (IFN) response in rheumatoid arthritis (RA) has been extensively studied in relation to therapy with biological DMARDs (bDMARDs). However, the effect of conventional synthetic (cs)DMARDs and glucocorticoids (GCs) on IFN response gene (IRG) expression remains largely unknown, even though csDMARDS are used throughout all disease phases, including simultaneously with biologic therapy. This study was aimed to determine the dynamics of IFN response upon immunosuppressive treatment. Methods: Whole blood was collected in PAXgene tubes from 35 RA patients who received either COBRA therapy (combination of prednisone, initially 60 mg, methotrexate and sulfasalazine) (n = 14) or COBRA-light therapy (prednisone, initially 30 mg, and methotrexate) (n = 21). Expression of 10 IRGs was determined by real-time PCR at baseline (T0), after 4 weeks (T4), and 13 weeks (T13) of treatment. IRG selection was based on the differential presence of transcription factor binding sites (TFBS), in order to study the therapy effect on different pathway components involved in IFN signaling. Results: Seven of the 10 IRGs displayed significant changes during treatment (p ≤ 0.016). These 7 IRGs all displayed a particularly pronounced decrease between T0 and T4 (≥1.6-fold, p ≤ 0.0059). The differences between IRG sensitivity to the treatment appeared related to the presence of TFBS for STAT1 and IRF proteins within the genes. The extent of the decreases between T0 and T4 was similar for the COBRA- and COBRA-light-treated group, despite the differences in drug combination and doses in those groups. Between T4 and T13, however, IRG expression in the COBRA-light-treated group displayed a significant increase, whereas it remained stable or decreased even further in most COBRA-treated patients (comparison of mean fold changes, p = 0.011). A significant association between IRG dynamics and clinical response to therapy was not detected. Conclusions: Immunosuppressive treatment with csDMARDs, in this case a combination of prednisolone, methotrexate and sulfasalazine, substantially downregulates the IFN response in RA patients. The dynamics of this downregulation were partly dependent on the presence of TFBS within the IRGs and the combination and dosages of agents, but they were irrespective of the clinical response to therapy.
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Affiliation(s)
- Tamarah D de Jong
- Amsterdam UMC, Vrije Universiteit Amsterdam, Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam, Netherlands
| | - Tanja Snoek
- Amsterdam UMC, Vrije Universiteit Amsterdam, Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam, Netherlands
| | - Elise Mantel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam, Netherlands
| | - Conny J van der Laken
- Amsterdam UMC, Vrije Universiteit Amsterdam, Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam, Netherlands
| | - Ronald F van Vollenhoven
- Amsterdam UMC, Vrije Universiteit Amsterdam, Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam, Netherlands
| | - Willem F Lems
- Amsterdam UMC, Vrije Universiteit Amsterdam, Rheumatology, Amsterdam Rheumatology and Immunology Center, Amsterdam, Netherlands
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Schubert C, Allhoff M, Tillmann S, Maié T, Costa IG, Lipka DB, Schemionek M, Feldberg K, Baumeister J, Brümmendorf TH, Chatain N, Koschmieder S. Differential roles of STAT1 and STAT2 in the sensitivity of JAK2V617F- vs. BCR-ABL-positive cells to interferon alpha. J Hematol Oncol 2019; 12:36. [PMID: 30940163 PMCID: PMC6444528 DOI: 10.1186/s13045-019-0722-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 03/13/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Interferon alpha (IFNa) monotherapy is recommended as the standard therapy in polycythemia vera (PV) but not in chronic myeloid leukemia (CML). Here, we investigated the mechanisms of IFNa efficacy in JAK2V617F- vs. BCR-ABL-positive cells. METHODS Gene expression microarrays and RT-qPCR of PV vs. CML patient PBMCs and CD34+ cells and of the murine cell line 32D expressing JAK2V617F or BCR-ABL were used to analyze and compare interferon-stimulated gene (ISG) expression. Furthermore, using CRISPR/Cas9n technology, targeted disruption of STAT1 or STAT2, respectively, was performed in 32D-BCR-ABL and 32D-JAK2V617F cells to evaluate the role of these transcription factors for IFNa efficacy. The knockout cell lines were reconstituted with STAT1, STAT2, STAT1Y701F, or STAT2Y689F to analyze the importance of wild-type and phosphomutant STATs for the IFNa response. ChIP-seq and ChIP were performed to correlate histone marks with ISG expression. RESULTS Microarray analysis and RT-qPCR revealed significant upregulation of ISGs in 32D-JAK2V617F but downregulation in 32D-BCR-ABL cells, and these effects were reversed by tyrosine kinase inhibitor (TKI) treatment. Similar expression patterns were confirmed in human cell lines, primary PV and CML patient PBMCs and CD34+ cells, demonstrating that these effects are operational in patients. IFNa treatment increased Stat1, Stat2, and Irf9 mRNA as well as pY-STAT1 in all cell lines; however, viability was specifically decreased in 32D-JAK2V617F. STAT1 or STAT2 knockout and reconstitution with wild-type or phospho-deficient STAT mutants demonstrated the necessity of STAT2 for IFNa-induced STAT1 phosphorylation in BCR-ABL- but not in JAK2V617F-expressing cells. STAT1 was essential for IFNa activity in both BCR-ABL- and JAK2V617F-positive cells. Furthermore, ChIP experiments demonstrate higher repressive and lower active chromatin marks at the promoters of ISGs in BCR-ABL-expressing cells. CONCLUSIONS JAK2V617F but not BCR-ABL sensitizes MPN cells to interferon, and this effect was dependent on STAT1. Moreover, STAT2 is a survival factor in BCR-ABL- and JAK2V617F-positive cells but an IFNa-sensitizing factor solely in 32D-JAK2V617F cells by upregulation of STAT1 expression.
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Affiliation(s)
- Claudia Schubert
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr 30, 52074, Aachen, Germany
| | - Manuel Allhoff
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Stefan Tillmann
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr 30, 52074, Aachen, Germany
| | - Tiago Maié
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Daniel B Lipka
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mirle Schemionek
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr 30, 52074, Aachen, Germany
| | - Kristina Feldberg
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr 30, 52074, Aachen, Germany
| | - Julian Baumeister
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr 30, 52074, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr 30, 52074, Aachen, Germany
| | - Nicolas Chatain
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr 30, 52074, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstr 30, 52074, Aachen, Germany.
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Plant D, Maciejewski M, Smith S, Nair N, Hyrich K, Ziemek D, Barton A, Verstappen S. Profiling of Gene Expression Biomarkers as a Classifier of Methotrexate Nonresponse in Patients With Rheumatoid Arthritis. Arthritis Rheumatol 2019; 71:678-684. [PMID: 30615300 PMCID: PMC9328381 DOI: 10.1002/art.40810] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/04/2018] [Indexed: 12/16/2022]
Abstract
Objective Approximately 30–40% of rheumatoid arthritis (RA) patients who are initially started on low‐dose methotrexate (MTX) will not benefit from the treatment. To date, no reliable biomarkers of MTX inefficacy in RA have been identified. The aim of this study was to analyze whole blood samples from RA patients at 2 time points (pretreatment and 4 weeks following initiation of MTX), to identify gene expression biomarkers of the MTX response. Methods RA patients who were about to commence treatment with MTX were selected from the Rheumatoid Arthritis Medication Study. Using European League Against Rheumatism (EULAR) response criteria, 42 patients were categorized as good responders and 43 as nonresponders at 6 months following the initation of MTX treatment. Data on whole blood transcript expression were generated, and supervised machine learning methods were used to predict a EULAR nonresponse. Models in which transcript levels were included were compared to models in which clinical covariates alone (e.g., baseline disease activity, sex) were included. Gene network and ontology analysis was also performed. Results Based on the ratio of transcript values (i.e., the difference in log2‐transformed expression values between 4 weeks of treatment and pretreatment), a highly predictive classifier of MTX nonresponse was developed using L2‐regularized logistic regression (mean ± SEM area under the receiver operating characteristic [ROC] curve [AUC] 0.78 ± 0.11). This classifier was superior to models that included clinical covariates (ROC AUC 0.63 ± 0.06). Pathway analysis of gene networks revealed significant overrepresentation of type I interferon signaling pathway genes in nonresponders at pretreatment (P = 2.8 × 10−25) and at 4 weeks after treatment initiation (P = 4.9 × 10−28). Conclusion Testing for changes in gene expression between pretreatment and 4 weeks post–treatment initiation may provide an early classifier of the MTX treatment response in RA patients who are unlikely to benefit from MTX over 6 months. Such patients should, therefore, have their treatment escalated more rapidly, which would thus potentially impact treatment pathways. These findings emphasize the importance of a role for early treatment biomarker monitoring in RA patients started on MTX.
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Affiliation(s)
- Darren Plant
- Manchester University NHS Foundation Trust, Manchester, UK
| | | | | | - Nisha Nair
- University of Manchester, Manchester, UK
| | | | - Kimme Hyrich
- Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Anne Barton
- Manchester University NHS Foundation Trust, Manchester, UK
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Chapman EA, Lyon M, Simpson D, Mason D, Beynon RJ, Moots RJ, Wright HL. Caught in a Trap? Proteomic Analysis of Neutrophil Extracellular Traps in Rheumatoid Arthritis and Systemic Lupus Erythematosus. Front Immunol 2019; 10:423. [PMID: 30915077 PMCID: PMC6421309 DOI: 10.3389/fimmu.2019.00423] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/18/2019] [Indexed: 12/22/2022] Open
Abstract
Neutrophil Extracellular Traps (NETs) are implicated in the development of auto-immunity in diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) through the externalization of intracellular neoepitopes e.g., dsDNA and nuclear proteins in SLE and citrullinated peptides in RA. The aim of this work was to use quantitative proteomics to identify and measure NET proteins produced by neutrophils from healthy controls, and from patients with RA and SLE to determine if NETs can be differentially-generated to expose different sets of neoepitopes. Ultra-pure neutrophils (>99%) from healthy individuals (n = 3) and patients with RA or SLE (n = 6 each) were incubated ± PMA (50 nM, PKC super-activator) or A23187 (3.8 μM, calcium ionophore) for 4 h. NETs were liberated by nuclease digestion and concentrated onto Strataclean beads prior to on-bead digestion with trypsin. Data-dependent LC-MS/MS analyses were conducted on a QExactive HF quadrupole-Orbitrap mass spectrometer, and label-free protein quantification was carried out using Progenesis QI. PMA-induced NETs were decorated with annexins, azurocidin and histone H3, whereas A23187-induced NETs were decorated with granule proteins including CAMP/LL37, CRISP3, lipocalin and MMP8, histones H1.0, H1.4, and H1.5, interleukin-8, protein-arginine deiminase-4 (PADI4), and α-enolase. Four proteins were significantly different between PMA-NETs from RA and SLE neutrophils (p < 0.05): RNASE2 was higher in RA, whereas MPO, leukocyte elastase inhibitor and thymidine phosphorylase were higher in SLE. For A23187-NETs, six NET proteins were higher in RA (p < 0.05), including CAMP/LL37, CRISP3, interleukin-8, MMP8; Thirteen proteins were higher in SLE, including histones H1.0, H2B, and H4. This work provides the first, direct comparison of NOX2-dependent (PMA) and NOX2-independent (A23187) NETs using quantitative proteomics, and the first direct comparison of RA and SLE NETs using quantitative proteomics. We show that it is the nature of the stimulant rather than neutrophil physiology that determines NET protein profiles in disease, since stimulation of NETosis in either a NOX2-dependent or a NOX2-independent manner generates broadly similar NET proteins irrespective of the disease background. We also use our proteomics pipeline to identify an extensive range of post-translationally modified proteins in RA and SLE, including histones and granule proteins, many of which are known targets of auto-antibodies in each disease.
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Affiliation(s)
- Elinor A Chapman
- Department of Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Max Lyon
- Department of Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Deborah Simpson
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Centre for Proteome Research, University of Liverpool, Liverpool, United Kingdom
| | - David Mason
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Centre for Cell Imaging, University of Liverpool, Liverpool, United Kingdom
| | - Robert J Beynon
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,Centre for Proteome Research, University of Liverpool, Liverpool, United Kingdom
| | - Robert J Moots
- Department of Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom.,University of Liverpool and Aintree University Hospital, Members of Liverpool Health Partners, Liverpool, United Kingdom
| | - Helen L Wright
- Department of Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
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Lequerré T, Rottenberg P, Derambure C, Cosette P, Vittecoq O. Predictors of treatment response in rheumatoid arthritis. Joint Bone Spine 2019; 86:151-158. [DOI: 10.1016/j.jbspin.2018.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2018] [Indexed: 12/13/2022]
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45
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Li X, Wu D, Cooper NGF, Rai SN. Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model. Stat Appl Genet Mol Biol 2019; 18:/j/sagmb.ahead-of-print/sagmb-2018-0021/sagmb-2018-0021.xml. [PMID: 30667368 DOI: 10.1515/sagmb-2018-0021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
High throughput RNA sequencing (RNA-seq) technology is increasingly used in disease-related biomarker studies. A negative binomial distribution has become the popular choice for modeling read counts of genes in RNA-seq data due to over-dispersed read counts. In this study, we propose two explicit sample size calculation methods for RNA-seq data using a negative binomial regression model. To derive these new sample size formulas, the common dispersion parameter and the size factor as an offset via a natural logarithm link function are incorporated. A two-sided Wald test statistic derived from the coefficient parameter is used for testing a single gene at a nominal significance level 0.05 and multiple genes at a false discovery rate 0.05. The variance for the Wald test is computed from the variance-covariance matrix with the parameters estimated from the maximum likelihood estimates under the unrestricted and constrained scenarios. The performance and a side-by-side comparison of our new formulas with three existing methods with a Wald test, a likelihood ratio test or an exact test are evaluated via simulation studies. Since other methods are much computationally extensive, we recommend our M1 method for quick and direct estimation of sample sizes in an experimental design. Finally, we illustrate sample sizes estimation using an existing breast cancer RNA-seq data.
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Affiliation(s)
- Xiaohong Li
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY 40202, USA.,Department of Anatomical Sciences and Neurobiology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Dongfeng Wu
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY 40202, USA
| | - Nigel G F Cooper
- Department of Anatomical Sciences and Neurobiology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Shesh N Rai
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY 40202, USA
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Acosta-Herrera M, Kerick M, González-Serna D, Wijmenga C, Franke A, Gregersen PK, Padyukov L, Worthington J, Vyse TJ, Alarcón-Riquelme ME, Mayes MD, Martin J. Genome-wide meta-analysis reveals shared new loci in systemic seropositive rheumatic diseases. Ann Rheum Dis 2018; 78:311-319. [PMID: 30573655 DOI: 10.1136/annrheumdis-2018-214127] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/18/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Immune-mediated inflammatory diseases (IMIDs) are heterogeneous and complex conditions with overlapping clinical symptoms and elevated familial aggregation, which suggests the existence of a shared genetic component. In order to identify this genetic background in a systematic fashion, we performed the first cross-disease genome-wide meta-analysis in systemic seropositive rheumatic diseases, namely, systemic sclerosis, systemic lupus erythematosus, rheumatoid arthritis and idiopathic inflammatory myopathies. METHODS We meta-analysed ~6.5 million single nucleotide polymorphisms in 11 678 cases and 19 704 non-affected controls of European descent populations. The functional roles of the associated variants were interrogated using publicly available databases. RESULTS Our analysis revealed five shared genome-wide significant independent loci that had not been previously associated with these diseases: NAB1, KPNA4-ARL14, DGQK, LIMK1 and PRR12. All of these loci are related with immune processes such as interferon and epidermal growth factor signalling, response to methotrexate, cytoskeleton dynamics and coagulation cascade. Remarkably, several of the associated loci are known key players in autoimmunity, which supports the validity of our results. All the associated variants showed significant functional enrichment in DNase hypersensitivity sites, chromatin states and histone marks in relevant immune cells, including shared expression quantitative trait loci. Additionally, our results were significantly enriched in drugs that are being tested for the treatment of the diseases under study. CONCLUSIONS We have identified shared new risk loci with functional value across diseases and pinpoint new potential candidate loci that could be further investigated. Our results highlight the potential of drug repositioning among related systemic seropositive rheumatic IMIDs.
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Affiliation(s)
| | - Martin Kerick
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, PTS Granada, Granada, Spain
| | - David González-Serna
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, PTS Granada, Granada, Spain
| | | | | | - Cisca Wijmenga
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Peter K Gregersen
- Robert S Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Manhasset, New York, USA
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jane Worthington
- Manchester NIHR Biomedical Research Centre, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Timothy James Vyse
- Division of Genetics and Molecular Medicine, King's College London, London, UK.,Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK
| | - Marta Eugenia Alarcón-Riquelme
- Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Maureen D Mayes
- Department of Internal Medicine, Division of Rheumatology, The University of Texas Health Science Center-Houston, Houston, Texas, USA
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, PTS Granada, Granada, Spain
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Chokesuwattanaskul S, Phelan MM, Edwards SW, Wright HL. A robust intracellular metabolite extraction protocol for human neutrophil metabolic profiling. PLoS One 2018; 13:e0209270. [PMID: 30571714 PMCID: PMC6301625 DOI: 10.1371/journal.pone.0209270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/03/2018] [Indexed: 01/31/2023] Open
Abstract
Neutrophils are phagocytic innate immune cells that play essential roles in host defence, but are also implicated in inflammatory diseases such as rheumatoid arthritis (RA) where they contribute to systemic inflammation and joint damage. Transcriptomic analysis of neutrophils has revealed significant changes in gene expression in neutrophils activated in vitro by cytokines and in vivo during inflammation in RA. However, there are no reports on the global metabolomic changes that occur as a consequence of this activation. The aim of this study was to establish protocols for the study of changes in the metabolome of human neutrophils using 1H NMR spectroscopy. Sample preparation and spectral analysis protocols were optimised using neutrophils isolated by Ficoll-Paque, with decreased washing steps and inclusion of a heat-shock step to quench metabolite turnover. Cells were incubated ± PMA for 15 min in HEPES-free media and samples were analysed by NMR using a 700 MHz NMR Avance IIIHD Bruker NMR spectrometer equipped with a TCI cryoprobe. Chenomx, Bruker TopSpin and AMIX software were used to process spectra and identify metabolites. Principal Component Analysis (PCA) and signalling pathway analysis was carried out using Metaboanalyst. Cell number and number of scans (NS) were optimised as >3.6 million cells and 512 NS. 327 spectral bins were defined in the neutrophil spectra, of which 287 (87.7%) were assigned to 110 metabolites that included: amino acids, peptides and analogues; carbohydrates, carbonyls and alcohols; nucleotides, nucleosides and analogues; lipids and lipid-like molecules; benzenoids; and other organic compounds. 43 metabolites changed at least 1.5 fold (increase or decrease) after the addition of PMA for 5 or 15 min. Pathway analysis revealed that PMA affected nicotinate and nicotinamide metabolism, aminoacyl-tRNA biosynthesis and glycolysis, suggesting a redirection of glucose metabolism from glycolysis to the pentose phosphate pathway and production of NADPH for activation of the NADPH oxidase and subsequent respiratory burst. We have developed protocols for the study of human neutrophils by 1H NMR spectroscopy. Importantly, this methodology has sufficient sensitivity and reproducibility to detect changes in metabolite abundance from cell numbers typically collected from clinical samples or experiments with multiple assay conditions.
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Affiliation(s)
- Susama Chokesuwattanaskul
- Biochemistry Department, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Marie M. Phelan
- Biochemistry Department, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- HLS Technology Directorate, University of Liverpool, Liverpool, United Kingdom
| | - Steven W. Edwards
- Biochemistry Department, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Helen L. Wright
- Department of Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
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Brown RA, Henderlight M, Do T, Yasin S, Grom AA, DeLay M, Thornton S, Schulert GS. Neutrophils From Children With Systemic Juvenile Idiopathic Arthritis Exhibit Persistent Proinflammatory Activation Despite Long-Standing Clinically Inactive Disease. Front Immunol 2018; 9:2995. [PMID: 30619348 PMCID: PMC6305285 DOI: 10.3389/fimmu.2018.02995] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/04/2018] [Indexed: 01/09/2023] Open
Abstract
Background: Systemic juvenile idiopathic arthritis (SJIA) is a chronic childhood arthropathy with features of autoinflammation. Early inflammatory SJIA is associated with expansion and activation of neutrophils with a sepsis-like phenotype, but neutrophil phenotypes present in longstanding and clinically inactive disease (CID) are unknown. The objective of this study was to examine activated neutrophil subsets, S100 alarmin release, and gene expression signatures in children with a spectrum of SJIA disease activity. Methods: Highly-purified neutrophils were isolated using a two-step procedure of density-gradient centrifugation followed by magnetic-bead based negative selection prior to flow cytometry or cell culture to quantify S100 protein release. Whole transcriptome gene expression profiles were compared in neutrophils from children with both active SJIA and CID. Results: Patients with SJIA and active systemic features demonstrated a higher proportion of CD16+CD62Llo neutrophil population compared to controls. This neutrophil subset was not seen in patients with CID or patients with active arthritis not exhibiting systemic features. Using imaging flow cytometry, CD16+CD62Llo neutrophils from patients with active SJIA and features of macrophage activation syndrome (MAS) had increased nuclear hypersegmentation compared to CD16+CD62L+ neutrophils. Serum levels of S100A8/A9 and S100A12 were strongly correlated with peripheral blood neutrophil counts. Neutrophils from active SJIA patients did not show enhanced resting S100 protein release; however, regardless of disease activity, neutrophils from SJIA patients did show enhanced S100A8/A9 release upon PMA stimulation compared to control neutrophils. Furthermore, whole transcriptome analysis of highly purified neutrophils from children with active SJIA identified 214 differentially expressed genes (DEG) compared to neutrophils from healthy controls. The most significantly upregulated gene pathway was Immune System Process, including AIM2, IL18RAP, and NLRC4. Interestingly, this gene set showed intermediate levels of expression in neutrophils from patients with long-standing CID yet persistent serum IL-18 elevation. Indeed, all patient samples regardless of disease activity demonstrated elevated inflammatory gene expression, including inflammasome components and S100A8. Conclusion: We identify features of neutrophil activation in SJIA patients with both active disease and CID, including a proinflammatory gene expression signature, reflecting persistent innate immune activation. Taken together, these studies expand understanding of neutrophil function in chronic autoinflammatory disorders such as SJIA.
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Affiliation(s)
- Rachel A Brown
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Maggie Henderlight
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Thuy Do
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Shima Yasin
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Alexei A Grom
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Monica DeLay
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Sherry Thornton
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Grant S Schulert
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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JAK2V617F but not CALR mutations confer increased molecular responses to interferon-α via JAK1/STAT1 activation. Leukemia 2018; 33:995-1010. [PMID: 30470838 DOI: 10.1038/s41375-018-0295-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023]
Abstract
Pegylated interferon-α (peg-IFNa) treatment induces molecular responses (MR) in patients with myeloproliferative neoplasms (MPNs), including partial MR (PMR) in 30-40% of patients. Here, we compared the efficacy of IFNa treatment in JAK2V617F- vs. calreticulin (CALR)-mutated cells and investigated the mechanisms of differential response. Retrospective analysis of MPN patients treated with peg-IFNa demonstrated that patients harboring the JAK2V617F mutation were more likely to achieve PMR than those with mutated CALR (p = 0.004), while there was no significant difference in hematological response. In vitro experiments confirmed an upregulation of IFN-stimulated genes in JAK2V617F-positive 32D cells as well as patient samples (peripheral blood mononuclear cells and CD34+ hematopoietic stem cells) compared to their CALR-mutated counterparts, and higher IFNa doses were needed to achieve the same IFNa response in CALR- as in JAK2V617F-mutant 32D cells. Additionally, Janus-activated kinase-1 (JAK1) and signal transducers and activators of transcription 1 (STAT1) showed constitutive phosphorylation in JAK2V617F-mutated but not CALR-mutated cells, indicating priming towards an IFNa response. Moreover, IFN-induced growth arrest was counteracted by selective JAK1 inhibition but enhanced by JAK2 inhibition. In conclusion, our data suggest that, clinically, higher doses of IFNa are needed in CALR-mutated vs. JAK2V617F-positive patients and we suggest a model of JAK2V617F-JAK1/STAT1 crosstalk leading to a priming of JAK2V617F-positive cells to IFNa resulting in differential sensitivity.
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Sumitomo S, Nagafuchi Y, Tsuchida Y, Tsuchiya H, Ota M, Ishigaki K, Suzuki A, Kochi Y, Fujio K, Yamamoto K. Transcriptome analysis of peripheral blood from patients with rheumatoid arthritis: a systematic review. Inflamm Regen 2018; 38:21. [PMID: 30410636 PMCID: PMC6217768 DOI: 10.1186/s41232-018-0078-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022] Open
Abstract
In the era of precision medicine, transcriptome analysis of whole gene expression is an essential technology. While DNA microarray has a limited dynamic range and a problem of background hybridization, RNA sequencing (RNA-seq) has a broader dynamic range and a lower background signal that increase the sensitivity and reproducibility. While transcriptome analyses in rheumatoid arthritis (RA) have generally focused on whole peripheral blood mononuclear cells (PBMC), analyses of detailed cell subsets have an increased need for understanding the pathophysiology of disease because the involvement of CD4+ T cells in the pathogenesis of RA has been established. Transcriptome analysis of detailed CD4+ T cell subsets or neutrophils shed new light on the pathophysiology of RA. There are several analyses about the effect of biological treatment. Many studies report the association between type I interferon signature gene expression and response to therapy.
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Affiliation(s)
- Shuji Sumitomo
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Yasuo Nagafuchi
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Yumi Tsuchida
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Haruka Tsuchiya
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Mineto Ota
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Kazuyoshi Ishigaki
- 2Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
| | - Akari Suzuki
- 3Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
| | - Yuta Kochi
- 3Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
| | - Keishi Fujio
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Kazuhiko Yamamoto
- 4Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
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