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Szűcs G, Szekanecz Z, Szamosi S. Can we define difficult-to-treat systemic sclerosis? Expert Rev Clin Immunol 2024; 20:1065-1081. [PMID: 38711393 DOI: 10.1080/1744666x.2024.2352450] [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: 01/17/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
INTRODUCTION Systemic sclerosis (SSc) is a chronic autoimmune rheumatic disease characterized by microvascular alterations, immunopathology, and widespread fibrosis involving various organs. It is considered difficult to treat due to several reasons: complex pathogenesis, heterogeneity, late diagnosis, limited treatment options for certain organ manifestations, lack of personalized medicine. AREAS COVERED This review presents the heterogeneity, survival and organ manifestations with their risk factors of systemic sclerosis and their current treatment options, while drawing attention to difficult-to-treat forms of the disease, based on literature indexed in PubMed. EXPERT OPINION Despite recent advances in the management of SSc over the last decades, the disease presents significant morbidity and mortality. Although available treatment protocols brought significant advancements in terms of survival in SSc-associated interstitial lung disease and pulmonary arterial hypertension, less success has been achieved in the treatment of Raynaud's phenomenon and digital ulcers and the results are modest in case of heart, gastrointestinal, and renal manifestations. There are patients who do not respond to treatment and deteriorate even with adequate therapy. They can be considered difficult-to treat (D2T) cases. We have created a possible score system based on the individual organ manifestations and highlighted treatment options for the D2T SSc category.
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Affiliation(s)
- Gabriella Szűcs
- Department of Rheumatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltán Szekanecz
- Department of Rheumatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilvia Szamosi
- Department of Rheumatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Le Maître M, Guerrier T, Collet A, Derhourhi M, Meneboo JP, Toussaint B, Bonnefond A, Villenet C, Sebda S, Bongiovanni A, Tardivel M, Simon M, Jendoubi M, Daunou B, Largy A, Figeac M, Dubucquoi S, Launay D. Characteristics and impact of infiltration of B-cells from systemic sclerosis patients in a 3D healthy skin model. Front Immunol 2024; 15:1373464. [PMID: 39185406 PMCID: PMC11341436 DOI: 10.3389/fimmu.2024.1373464] [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: 01/19/2024] [Accepted: 07/23/2024] [Indexed: 08/27/2024] Open
Abstract
Introduction In systemic sclerosis (SSc), B-cells are activated and present in the skin and lung of patients where they can interact with fibroblasts. The precise impact and mechanisms of the interaction of B-cells and fibroblasts at the tissular level are poorly studied. Objective We investigated the impact and mechanisms of B-cell/fibroblast interactions in cocultures between B-cells from patients with SSc and 3-dimensional reconstituted healthy skin model including fibroblasts, keratinocytes and extracellular matrix. Methods The quantification and description of the B-cell infiltration in 3D cocultures were performed using cells imagery strategy and cytometry. The effect of coculture on the transcriptome of B-cells and fibroblasts was studied with bulk and single-cell RNA sequencing approaches. The mechanisms of this interaction were studied by blocking key cytokines like IL-6 and TNF. Results We showed a significant infiltration of B-cells in the 3D healthy skin model. The amount but not the depth of infiltration was higher with B-cells from SSc patients and with activated B-cells. B-cell infiltrates were mainly composed of naïve and memory cells, whose frequencies differed depending on B-cells origin and activation state: infiltrated B-cells from patients with SSc showed an activated profile and an overexpression of immunoglobulin genes compared to circulating B-cells before infiltration. Our study has shown for the first time that activated B-cells modified the transcriptomic profile of both healthy and SSc fibroblasts, toward a pro-inflammatory (TNF and IL-17 signaling) and interferon profile, with a key role of the TNF pathway. Conclusion B-cells and 3D skin cocultures allowed the modelization of B-cells infiltration in tissues observed in SSc, uncovering an influence of the underlying disease and the activation state of B-cells. We showed a pro-inflammatory effect on skin fibroblasts and pro-activation effect on infiltrating B-cells during coculture. This reinforces the role of B-cells in SSc and provide potential targets for future therapeutic approach in this disease.
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Affiliation(s)
- Mathilde Le Maître
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Thomas Guerrier
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Aurore Collet
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- CHU Lille, Institut d’Immunologie, Pôle de Biologie Pathologie Génétique, Lille, France
| | - Mehdi Derhourhi
- Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- Université de Lille, Lille, France
| | - Jean-Pascal Meneboo
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Bénédicte Toussaint
- Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- Université de Lille, Lille, France
| | - Amélie Bonnefond
- Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France
- Université de Lille, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Céline Villenet
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Shéhérazade Sebda
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Antonino Bongiovanni
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Meryem Tardivel
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Myriam Simon
- Service de Médecine Interne et d’Immunologie Clinique, Centre de Référence Des Maladies Auto-Immunes et Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), CHU Lille, Lille, France
| | - Manel Jendoubi
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Blanche Daunou
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Alexis Largy
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Martin Figeac
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - Sylvain Dubucquoi
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- CHU Lille, Institut d’Immunologie, Pôle de Biologie Pathologie Génétique, Lille, France
| | - David Launay
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- Service de Médecine Interne et d’Immunologie Clinique, Centre de Référence Des Maladies Auto-Immunes et Systémiques Rares du Nord et Nord-Ouest de France (CeRAINO), CHU Lille, Lille, France
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Zhu H, Luo H, Skaug B, Tabib T, Li YN, Tao Y, Matei AE, Lyons MA, Schett G, Lafyatis R, Assassi S, Distler JHW. Fibroblast Subpopulations in Systemic Sclerosis: Functional Implications of Individual Subpopulations and Correlations with Clinical Features. J Invest Dermatol 2024; 144:1251-1261.e13. [PMID: 38147960 PMCID: PMC11116078 DOI: 10.1016/j.jid.2023.09.288] [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: 03/14/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 12/28/2023]
Abstract
Fibroblasts constitute a heterogeneous population of cells. In this study, we integrated single-cell RNA-sequencing and bulk RNA-sequencing data as well as clinical information to study the role of individual fibroblast populations in systemic sclerosis (SSc). SSc skin demonstrated an increased abundance of COMP+, COL11A1+, MYOC+, CCL19+, SFRP4/SFRP2+, and PRSS23/SFRP2+ fibroblasts signatures and decreased proportions of CXCL12+ and PI16+ fibroblast signatures in the Prospective Registry of Early Systemic Sclerosis and Genetics versus Environment in Scleroderma Outcome Study cohorts. Numerical differences were confirmed by multicolor immunofluorescence for selected fibroblast populations. COMP+, COL11A1+, SFRP4/SFRP2+, PRSS23/SFRP2+, and PI16+ fibroblasts were similarly altered between normal wound healing and patients with SSc. The proportions of profibrotic COMP+, COL11A1+, SFRP4/SFRP2+, and PRSS23/SFRP2+ and proinflammatory CCL19+ fibroblast signatures were positively correlated with clinical and histopathological parameters of skin fibrosis, whereas signatures of CXCL12+ and PI16+ fibroblasts were inversely correlated. Incorporating the proportions of COMP+, COL11A1+, SFRP4/SFRP2+, and PRSS23/SFRP2+ fibroblast signatures into machine learning models improved the classification of patients with SSc into those with progressive versus stable skin fibrosis. In summary, the profound imbalance of fibroblast subpopulations in SSc may drive the progression of skin fibrosis. Specific targeting of disease-relevant fibroblast populations may offer opportunities for the treatment of SSc and other fibrotic diseases.
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Affiliation(s)
- Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China; Department of Internal Medicine 3, Friedrich-Alexander University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| | - Hui Luo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Brian Skaug
- Division of Rheumatology, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yi-Nan Li
- Department of Internal Medicine 3, Friedrich-Alexander University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany; Department of Rheumatology, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Hiller Research Center, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Yongguang Tao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Alexandru-Emil Matei
- Department of Internal Medicine 3, Friedrich-Alexander University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany; Department of Rheumatology, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Hiller Research Center, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marka A Lyons
- Division of Rheumatology, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Georg Schett
- Department of Internal Medicine 3, Friedrich-Alexander University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shervin Assassi
- Division of Rheumatology, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jörg H W Distler
- Department of Internal Medicine 3, Friedrich-Alexander University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany; Department of Rheumatology, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Hiller Research Center, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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Zhao Y, Xu W, Gao W, Li X, Liu B, Yan S, Ma Z, Yang Q. Phenotypes of patients with systemic sclerosis in the Chinese Han population: a cluster analysis. Clin Rheumatol 2024; 43:1635-1646. [PMID: 38485877 DOI: 10.1007/s10067-024-06936-1] [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: 10/30/2023] [Revised: 02/22/2024] [Accepted: 03/10/2024] [Indexed: 04/16/2024]
Abstract
OBJECTIVE Systemic sclerosis (SSc) is a heterogeneous connective tissue disease that is commonly subdivided into limited cutaneous SSc (lcSSc) and diffuse cutaneous SSc (dcSSc) based on the extent of skin involvement. This subclassification may not reflect the full range of clinical phenotypic variation. This study aimed to investigate clinical features and aggregation of patients with SSc in Chinese based on SSc manifestations and organ involvements, in order to achieve precise treatment of SSc early prevention of complications. METHODS In total 287 SSc patients were included in this study. A cluster analysis was applied according to 13 clinical and serologic variables to determine subgroups of patients. Survival rates between obtained clusters and risk factors affecting prognosis were also compared. RESULT In this study, six clusters were observed: cluster 1 (n = 66) represented the skin type, with all patients showing skin thickening. In cluster 2 (n = 56), most patients had vascular and articular involvement. Cluster 3 (n = 14) individuals mostly had cardiac and pulmonary involvement. In cluster 4 (n = 52), the gastrointestinal type, 50 patients presented with stomach symptoms and 28 patients presented with esophageal symptoms. In cluster 5 (n = 50), patients barely had any major organ involvement. Cluster 6 (n = 49) included 46% of all patients presenting with renal crisis. CONCLUSION The results of our cluster analysis study implied that limiting SSc patient subgroups to those based only on skin involvement might not capture the full heterogeneity of the disease. Organ damage and antibody profiles should be considered when identifying homogeneous patient groups with a specific prognosis. Key Points • Provides a new method of categorizing SSc patients. • Can better explain disease progression and guide subsequent treatment.
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Affiliation(s)
- Yaqi Zhao
- Department of Rheumatology and Immunology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Wei Xu
- Department of Rheumatology and Immunology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Wenfeng Gao
- Department of Rheumatology and Immunology, the Affiliated Hospital of Weifang Medical College, Weifang, Shandong, China
| | - Xinya Li
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Baocheng Liu
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Suyan Yan
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Zhenzhen Ma
- Department of Rheumatology and Immunology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
| | - Qingrui Yang
- Department of Rheumatology and Immunology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
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Rosenstein RK, Rose JJ, Brooks SR, Tsai WL, Gadina M, Pavletic SZ, Nagao K, Cowen EW. Identification of Fibroinflammatory and Fibrotic Transcriptomic Subsets of Human Cutaneous Sclerotic Chronic Graft-Versus-Host Disease. JID INNOVATIONS 2024; 4:100246. [PMID: 38357212 PMCID: PMC10864809 DOI: 10.1016/j.xjidi.2023.100246] [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: 12/14/2022] [Revised: 10/23/2023] [Accepted: 11/06/2023] [Indexed: 02/16/2024] Open
Abstract
Cutaneous sclerotic chronic graft-versus-host disease (cGVHD) is a common and highly morbid complication of allogeneic hematopoietic stem cell transplantation. Our goals were to identify signals active in the skin of patients with sclerotic cGVHD in an effort to better understand how to treat this manifestation and to explore the heterogeneity of the disease. We identified genes that are significantly upregulated in the skin of patients with sclerotic cGVHD (n = 17) compared with those in the skin of patients who underwent allogeneic hematopoietic stem cell transplantation without cutaneous cGVHD (n = 9) by bulk RNA sequencing. Sclerotic cGVHD was most associated with T helper 1, phagocytic, and fibrotic pathways. In addition, different transcriptomic groups of affected patients were discovered: those with fibrotic and inflammatory/T helper 1 gene expression (the fibroinflammatory group) and those with predominantly fibrotic/TGFβ-associated expression (the fibrotic group). Further study will help elucidate whether these gene expression findings can be used to tailor treatment decisions. Multiple proteins encoded by highly induced genes in the skin (SFRP4, SERPINE2, COMP) were also highly induced in the plasma of patients with sclerotic cGVHD (n = 16) compared with those in plasma of control patients who underwent allogeneic hematopoietic stem cell transplantation without sclerotic cGVHD (n = 17), suggesting these TGFβ and Wnt pathway mediators as candidate blood biomarkers of the disease.
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Affiliation(s)
- Rachel K. Rosenstein
- Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Department of Medicine, Hackensack University Medical Center, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | | | - Stephen R. Brooks
- Biodata Mining and Discovery Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Wanxia L. Tsai
- Translational Immunology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Massimo Gadina
- Translational Immunology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Steven Z. Pavletic
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Keisuke Nagao
- Cutaneous Leukocyte Biology Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward W. Cowen
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Sun T, Vander Heiden JA, Gao X, Yin J, Uttarwar S, Liang WC, Jia G, Yadav R, Huang Z, Mitra M, Halpern W, Bender HS, Brightbill HD, Wu Y, Lupardus P, Ramalingam T, Arron JR. Isoform-selective TGF-β3 inhibition for systemic sclerosis. MED 2024; 5:132-147.e7. [PMID: 38272035 DOI: 10.1016/j.medj.2023.12.011] [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: 06/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Transforming growth factor β (TGF-β) is implicated as a key mediator of pathological fibrosis, but its pleiotropic activity in a range of homeostatic functions presents challenges to its safe and effective therapeutic targeting. There are three isoforms of TGF-β, TGF-β1, TGF-β2, and TGF-β3, which bind to a common receptor complex composed of TGF-βR1 and TGF-βR2 to induce similar intracellular signals in vitro. We have recently shown that the cellular expression patterns and activation thresholds of TGF-β2 and TGF-β3 are distinct from those of TGF-β1 and that selective short-term TGF-β2 and TGF-β3 inhibition can attenuate fibrosis in vivo without promoting excessive inflammation. Isoform-selective inhibition of TGF-β may therefore provide a therapeutic opportunity for patients with chronic fibrotic disorders. METHODS Transcriptomic profiling of skin biopsies from patients with systemic sclerosis (SSc) from multiple clinical trials was performed to evaluate the role of TGF-β3 in this disease. Antibody humanization, biochemical characterization, crystallization, and pre-clinical experiments were performed to further characterize an anti-TGF-β3 antibody. FINDINGS In the skin of patients with SSc, TGF-β3 expression is uniquely correlated with biomarkers of TGF-β signaling and disease severity. Crystallographic studies establish a structural basis for selective TGF-β3 inhibition with a potent and selective monoclonal antibody that attenuates fibrosis effectively in vivo at clinically translatable exposures. Toxicology studies suggest that, as opposed to pan-TGF-β inhibitors, this anti-TGF-β3 antibody has a favorable safety profile for chronic administration. CONCLUSION We establish a rationale for targeting TGF-β3 in SSc with a favorable therapeutic index. FUNDING This study was funded by Genentech, Inc.
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Affiliation(s)
- Tianhe Sun
- Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Jason A Vander Heiden
- Department of OMNI Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xia Gao
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jianping Yin
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Salil Uttarwar
- Department of OMNI Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wei-Ching Liang
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Guiquan Jia
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rajbharan Yadav
- Department of Preclinical and Translational Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zhiyu Huang
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mayurranjan Mitra
- Department of DevSci Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wendy Halpern
- Department of DevSci SA Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hannah S Bender
- Department of Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hans D Brightbill
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yan Wu
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Patrick Lupardus
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Thirumalai Ramalingam
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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Komura K, Yanaba K, Bouaziz JD, Yoshizaki A, Hasegawa M, Varga J, Takehara K, Matsushita T. Perspective to precision medicine in scleroderma. Front Immunol 2024; 14:1298665. [PMID: 38304250 PMCID: PMC10830793 DOI: 10.3389/fimmu.2023.1298665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024] Open
Abstract
Systemic sclerosis (SSc) is a rare and heterogeneous disease with no relevant environmental trigger or significant responsible gene. It has been and will continue to be difficult to identify large enough patients to conduct classic population-based epidemiologic exposure/non-exposure studies with adequate power to ascertain environmental and genetic risk factors for these entities. The complexity of pathogenesis and heterogeneity are likely to require personalized/precision medicine for SSc. Since several potential drugs are currently available for specific patients if not whole SSc, classification of SSc seems to form the foundation for a better therapeutic strategy. To date, SSc has been classified based on the extent/severity of the affected area as well as some disease markers, including the autoantibody profile. However, such an analysis should also lead to improvements in the design of appropriately stratified clinical trials to determine the effects and prediction of targeted therapies. An approach based on drug response preclinically conducted using patients' own fibroblasts in vitro, can provide a precise disease marker/therapeutic selection for clinical practice. Because scleroderma dermal fibroblasts have a persistent hyper-productive phenotype occurring not only in person, but also in cell culture conditions. Thus, an accumulating approach based on disease markers ensures progression and de-escalation to re-establish a better life with a personally optimized drug environment after the onset of SSc.
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Affiliation(s)
- Kazuhiro Komura
- Department of Dermatology, Kanazawa Red Cross Hospital, Japanese Red Cross Society, Kanazawa, Japan
- Northwestern Scleroderma Program, Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Koichi Yanaba
- Department of Dermatology, Jikei University, Tokyo, Japan
| | | | - Ayumi Yoshizaki
- Department of Dermatology, University of Tokyo, Tokyo, Japan
| | | | - John Varga
- Northwestern Scleroderma Program, Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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Jia G, Ramalingam TR, Heiden JV, Gao X, DePianto D, Morshead KB, Modrusan Z, Ramamoorthi N, Wolters P, Lin C, Khanna D, Arron JR. An interleukin 6 responsive plasma cell signature is associated with disease progression in systemic sclerosis interstitial lung disease. iScience 2023; 26:108133. [PMID: 37867940 PMCID: PMC10585397 DOI: 10.1016/j.isci.2023.108133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/14/2023] [Accepted: 09/30/2023] [Indexed: 10/24/2023] Open
Abstract
Systemic sclerosis (SSc) interstitial lung disease (ILD) is among the leading causes of SSc-related morbidity and mortality. Tocilizumab (TCZ, anti-IL6RA) has demonstrated a reduced rate of pulmonary function decline in two phase 2/3 trials (faSScinate and focuSSced) in SSc-ILD patients. We performed transcriptome analysis of skin biopsy samples collected in the studies to decipher gene networks that were potentially associated with clinical responses to TCZ treatment. One module correlated with disease progression showed pharmacodynamic changes with TCZ treatment, and was characterized by plasma cell (PC) genes. PC signature gene expression levels were also significantly increased in both fibrotic SSc and IPF lungs compared to controls. scRNAseq analyses confirmed that PC signature genes were co-expressed in CD38 and CD138 expressing PC subsets in SSc lungs. These data provide insights into the potential role of PC in disease progression and mechanisms of action of TCZ in fibrotic interstitial lung diseases.
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Affiliation(s)
- Guiquan Jia
- Genentech Inc, South San Francisco, CA 94080, USA
| | | | | | - Xia Gao
- Genentech Inc, South San Francisco, CA 94080, USA
| | | | | | | | | | | | - Celia Lin
- Genentech Inc, South San Francisco, CA 94080, USA
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Berkowitz JS, Tabib T, Xiao H, Sadej GM, Khanna D, Fuschiotti P, Lafyatis RA, Das J. Cell Type-Specific Biomarkers of Systemic Sclerosis Disease Severity Capture Cell-Intrinsic and Cell-Extrinsic Circuits. Arthritis Rheumatol 2023; 75:1819-1830. [PMID: 37096444 PMCID: PMC10543405 DOI: 10.1002/art.42536] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/04/2023] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
Abstract
OBJECTIVE Systemic sclerosis (SSc) is a multifactorial autoimmune fibrotic disorder involving complex rewiring of cell-intrinsic and cell-extrinsic signaling coexpression networks involving a range of cell types. However, the rewired circuits as well as corresponding cell-cell interactions remain poorly understood. To address this, we used a predictive machine learning framework to analyze single-cell RNA-sequencing data from 24 SSc patients across the severity spectrum as quantified by the modified Rodnan skin score (MRSS). METHODS We used a least absolute shrinkage and selection operator (LASSO)-based predictive machine learning approach on the single-cell RNA-sequencing data set to identify predictive biomarkers of SSc severity, both across and within cell types. The use of L1 regularization helps prevent overfitting on high-dimensional data. Correlation network analyses were coupled to the LASSO model to identify cell-intrinsic and cell-extrinsic co-correlates of the identified biomarkers of SSc severity. RESULTS We found that the uncovered cell type-specific predictive biomarkers of MRSS included previously implicated genes in fibroblast and myeloid cell subsets (e.g., SFPR2+ fibroblasts and monocytes), as well as novel gene biomarkers of MRSS, especially in keratinocytes. Correlation network analyses revealed novel cross-talk between immune pathways and implicated keratinocytes in addition to fibroblast and myeloid cells as key cell types involved in SSc pathogenesis. We then validated the uncovered association of key gene expression and protein markers in keratinocytes, KRT6A and S100A8, with SSc skin disease severity. CONCLUSION Our global systems analyses reveal previously uncharacterized cell-intrinsic and cell-extrinsic signaling coexpression networks underlying SSc severity that involve keratinocytes, myeloid cells, and fibroblasts.
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Affiliation(s)
- Jacob S Berkowitz
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gabrielle M. Sadej
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dinesh Khanna
- Division of Rheumatology, Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Patrizia Fuschiotti
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A. Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Benfaremo D, Agarbati S, Mozzicafreddo M, Paolini C, Svegliati S, Moroncini G. Skin Gene Expression Profiles in Systemic Sclerosis: From Clinical Stratification to Precision Medicine. Int J Mol Sci 2023; 24:12548. [PMID: 37628728 PMCID: PMC10454358 DOI: 10.3390/ijms241612548] [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: 07/13/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Systemic sclerosis, also known as scleroderma or SSc, is a condition characterized by significant heterogeneity in clinical presentation, disease progression, and response to treatment. Consequently, the design of clinical trials to successfully identify effective therapeutic interventions poses a major challenge. Recent advancements in skin molecular profiling technologies and stratification techniques have enabled the identification of patient subgroups that may be relevant for personalized treatment approaches. This narrative review aims at providing an overview of the current status of skin gene expression analysis using computational biology approaches and highlights the benefits of stratifying patients upon their skin gene signatures. Such stratification has the potential to lead toward a precision medicine approach in the management of SSc.
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Affiliation(s)
- Devis Benfaremo
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy; (D.B.); (S.A.); (M.M.); (C.P.); (S.S.)
- Clinica Medica, Department of Internal Medicine, Marche University Hospital, 60126 Ancona, Italy
| | - Silvia Agarbati
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy; (D.B.); (S.A.); (M.M.); (C.P.); (S.S.)
| | - Matteo Mozzicafreddo
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy; (D.B.); (S.A.); (M.M.); (C.P.); (S.S.)
| | - Chiara Paolini
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy; (D.B.); (S.A.); (M.M.); (C.P.); (S.S.)
| | - Silvia Svegliati
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy; (D.B.); (S.A.); (M.M.); (C.P.); (S.S.)
- Clinica Medica, Department of Internal Medicine, Marche University Hospital, 60126 Ancona, Italy
| | - Gianluca Moroncini
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy; (D.B.); (S.A.); (M.M.); (C.P.); (S.S.)
- Clinica Medica, Department of Internal Medicine, Marche University Hospital, 60126 Ancona, Italy
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11
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Yang M, Goh V, Lee J, Espinoza M, Yuan Y, Carns M, Aren K, Chung L, Khanna D, McMahan ZH, Agrawal R, Nelson LB, Shah SJ, Whitfield ML, Hinchcliff M. Clinical Phenotypes of Patients With Systemic Sclerosis With Distinct Molecular Signatures in Skin. Arthritis Care Res (Hoboken) 2023; 75:1469-1480. [PMID: 35997480 PMCID: PMC9947190 DOI: 10.1002/acr.24998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 07/21/2022] [Accepted: 08/16/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Systemic sclerosis (SSc) patients are classified according to degree of skin fibrosis (limited and diffuse cutaneous [lc and dc]) and serum autoantibodies. We undertook the present multicenter study to determine whether intrinsic subset (IS) classification based upon skin gene expression yields additional valuable clinical information. METHODS SSc patients and healthy participants (HPs) were classified into Normal-like, Limited, Fibroproliferative, and Inflammatory ISs using a previously trained classifier. Clinical data were obtained (serum autoantibodies, pulmonary function testing, modified Rodnan skin thickness scores [mRSS], and high-resolution chest computed tomography [HRCT]). Statistical analyses were performed to compare patients classified by IS, traditional cutaneous classification, and serum autoantibodies. RESULTS A total of 223 participants (165 SSc [115 dcSSc and 50 lcSSc] and 58 HPs) were classified. Inflammatory IS patients had higher mRSS (22.1 ± 9.9; P < 0.001) than other ISs and dcSSc patients (19.4 ± 9.4; P = 0.05) despite similar disease duration (median [interquartile range] months 14.9 [19.9] vs. 18.4 [31.6]; P = 0.48). In multivariable modeling, no significant association between mRSS and RNA polymerase III (P = 0.07) or anti-topoisomerase I (Scl-70) (P = 0.09) was found. Radiographic interstitial lung disease (ILD) was more prevalent in Fibroproliferative IS compared with other ISs (91%; P = 0.04) with similar prevalence between lcSSc and dcSSc (67% vs. 76%; P = 0.73). Positive Scl-70 antibody was the strongest ILD predictor (P < 0.001). Interestingly, all lcSSc/Fibroproliferative patients demonstrated radiographic ILD. CONCLUSIONS Classification by IS identifies patients with distinct clinical phenotypes versus traditional cutaneous or autoantibody classification. IS classification identifies subgroups of SSc patients with more radiographic ILD (Fibroproliferative), higher mRSS (Inflammatory), and milder phenotype (Normal-like) and may provide additional clinically useful information to current SSc classification systems.
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Affiliation(s)
- Monica Yang
- Department of Medicine, Division of Rheumatology, University of California San Francisco, San Francisco, California
| | - Vivien Goh
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jungwha Lee
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Monica Espinoza
- Department of Biomedical Data Science, Geisel School of Medicine Dartmouth, Lebanon, New Hampshire
| | - Yiwei Yuan
- Department of Biomedical Data Science, Geisel School of Medicine Dartmouth, Lebanon, New Hampshire
| | - Mary Carns
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kathleen Aren
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lorinda Chung
- Department of Internal Medicine, Stanford University, Palo Alto, California
| | - Dinesh Khanna
- University of Michigan Scleroderma Program, Ann Arbor, Michigan
| | - Zsuzsanna H. McMahan
- Department of Internal Medicine, Division of Rheumatology, Johns Hopkins University, Baltimore, Maryland
| | - Rishi Agrawal
- Department of Radiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lauren Beussink Nelson
- Department of Internal Medicine, Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sanjiv J Shah
- Department of Internal Medicine, Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Michael L. Whitfield
- Department of Biomedical Data Science, Geisel School of Medicine Dartmouth, Lebanon, New Hampshire
| | - Monique Hinchcliff
- Department of Internal Medicine, Section of Rheumatology, Allergy & Immunology, Yale School of Medicine, New Haven, Connecticut
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12
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Lescoat A, Roofeh D, Kuwana M, Lafyatis R, Allanore Y, Khanna D. Therapeutic Approaches to Systemic Sclerosis: Recent Approvals and Future Candidate Therapies. Clin Rev Allergy Immunol 2023; 64:239-261. [PMID: 34468946 PMCID: PMC9034469 DOI: 10.1007/s12016-021-08891-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 02/06/2023]
Abstract
Systemic sclerosis is the rheumatic disease with the highest individual mortality. The severity of the disease is determined by the extent of fibrotic changes to cutaneous and internal organ tissues, the most life-threatening visceral manifestations being interstitial lung disease, SSc-associated-pulmonary arterial hypertension and myocardial involvement. The heterogeneity of the disease has initially hindered the design of successful clinical trials, but considerations on classification criteria have improved patient selection in trials, allowing the identification of more homogeneous groups of patients based on progressive visceral manifestations or the extent of skin involvement with a focus of patients with early disease. Two major subsets of systemic sclerosis are classically described: limited cutaneous systemic sclerosis characterized by distal skin fibrosis and the diffuse subset with distal and proximal skin thickening. Beyond this dichotomic subgrouping of systemic sclerosis, new phenotypic considerations based on antibody subtypes have provided a better understanding of the heterogeneity of the disease, anti-Scl70 antibodies being associated with progressive interstitial lung disease regardless of cutaneous involvement. Two targeted therapies, tocilizumab (a monoclonal antibody targeting interleukin-6 receptors (IL-6R)) and nintedanib (a tyrosine kinase inhibitor), have recently been approved by the American Food & Drug Administration to limit the decline of lung function in patients with SSc-associated interstitial lung disease, demonstrating that such better understanding of the disease pathogenesis with the identification of key targets can lead to therapeutic advances in the management of some visceral manifestations of the disease. This review will provide a brief overview of the pathogenesis of SSc and will present a selection of therapies recently approved or evaluated in this context. Therapies evaluated and approved in SSc-ILD will be emphasized and a review of recent phase II trials in diffuse cutaneous systemic sclerosis will be proposed. We will also discuss selected therapeutic pathways currently under investigation in systemic sclerosis that still lack clinical data in this context but that may show promising results in the future based on preclinical data.
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Affiliation(s)
- Alain Lescoat
- Department of Internal Medicine and Clinical Immunology, Rennes University Hospital, Rennes, France
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Michigan Scleroderma Program, University of Michigan, Ann Arbor, MI, USA
| | - David Roofeh
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Michigan Scleroderma Program, University of Michigan, Ann Arbor, MI, USA
| | - Masataka Kuwana
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, Tokyo, Japan
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yannick Allanore
- INSERM U1016 and CNRS UMR8104, Institut Cochin, Paris, France
- Université de Paris, Université Paris Descartes, Paris, France
- Service de Rhumatologie, Hôpital Cochin, AP-HP.CUP, Paris, France
| | - Dinesh Khanna
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
- Michigan Scleroderma Program, University of Michigan, Ann Arbor, MI, USA.
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13
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Makinde HKM, Dunn JLM, Gadhvi G, Carns M, Aren K, Chung AH, Muhammad LN, Song J, Cuda CM, Dominguez S, Pandolfino JE, Dematte D’Amico JE, Budinger GS, Assassi S, Frech TM, Khanna D, Shaeffer A, Perlman H, Hinchcliff M, Winter DR. Three Distinct Transcriptional Profiles of Monocytes Associate with Disease Activity in Scleroderma Patients. Arthritis Rheumatol 2023; 75:595-608. [PMID: 36281773 PMCID: PMC10165944 DOI: 10.1002/art.42380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/23/2022] [Accepted: 10/06/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Patients with diffuse cutaneous systemic sclerosis (dcSSc) display a complex clinical phenotype. Transcriptional profiling of whole blood or tissue from patients are affected by changes in cellular composition that drive gene expression and an inability to detect minority cell populations. We undertook this study to focus on the 2 main subtypes of circulating monocytes, classical monocytes (CMs) and nonclassical monocytes (NCMs) as a biomarker of SSc disease severity. METHODS SSc patients were recruited from the Prospective Registry for Early Systemic Sclerosis. Clinical data were collected, as well as peripheral blood for isolation of CMs and NCMs. Age-, sex-, and race-matched healthy volunteers were recruited as controls. Bulk macrophages were isolated from the skin in a separate cohort. All samples were assayed by RNA sequencing (RNA-seq). RESULTS We used an unbiased approach to cluster patients into 3 groups (groups A-C) based on the transcriptional signatures of CMs relative to controls. Each group maintained their characteristic transcriptional signature in NCMs. Genes up-regulated in group C demonstrated the highest expression compared to the other groups in SSc skin macrophages, relative to controls. Patients from groups B and C exhibited worse lung function than group A, although there was no difference in SSc skin disease at baseline, relative to controls. We validated our approach by applying our group classifications to published bulk monocyte RNA-seq data from SSc patients, and we found that patients without skin disease were most likely to be classified as group A. CONCLUSION We are the first to show that transcriptional signatures of CMs and NCMs can be used to unbiasedly stratify SSc patients and correlate with disease activity outcome measures.
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Affiliation(s)
- Hadijat-Kubura M. Makinde
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Julia L. M. Dunn
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
- Cincinnati Children’s Hospital Medical Center, Division of Allergy & Immunology. Cincinnati, OH 45229 (current affiliation)
| | - Gaurav Gadhvi
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Mary Carns
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Kathleen Aren
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Anh H. Chung
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Lutfiyya N. Muhammad
- Northwestern University, Feinberg School of Medicine Department of Preventive Medicine. Chicago, IL 60611
| | - Jing Song
- Northwestern University, Feinberg School of Medicine Department of Preventive Medicine. Chicago, IL 60611
| | - Carla M. Cuda
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Salina Dominguez
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - John E. Pandolfino
- Northwestern University, Feinberg School of Medicine, Department of Medicine, Division of Gastroenterology and Hepatology. Chicago, IL 60611
| | - Jane E. Dematte D’Amico
- Northwestern University, Feinberg School of Medicine, Department of Medicine, Division of Division of Pulmonary and Critical Care. Chicago, IL 60611
| | - G. Scott Budinger
- Northwestern University, Feinberg School of Medicine, Department of Medicine, Division of Division of Pulmonary and Critical Care. Chicago, IL 60611
| | - Shervin Assassi
- Prospective Registry of Early Systemic Sclerosis (PRESS) consortium. Shervin Assassi MD MS- University of Texas Health Sciences Center at Houston (TX), Elana Bernstein MD MS- Columbia University (NY), Robyn Domsic MD MS - University of Pittsburgh (PA), Tracy Frech MD MS - University of Utah (UT), Jessica Gordon - Hospital for Special Surgery (NY), Faye Hant - Medical University of South Carolina (SC), Monique Hinchcliff – Yale School of Medicine (CT), Dinesh Khanna MD MS - University of Michigan (MI), Ami Shah - Johns Hopkins University (MD), Victoria Shanmugam - George Washington University (DC)
- University of Texas Health Science Center at Houston, Division of Rheumatology, Houston, Texas 77030
| | - Tracy M. Frech
- Prospective Registry of Early Systemic Sclerosis (PRESS) consortium. Shervin Assassi MD MS- University of Texas Health Sciences Center at Houston (TX), Elana Bernstein MD MS- Columbia University (NY), Robyn Domsic MD MS - University of Pittsburgh (PA), Tracy Frech MD MS - University of Utah (UT), Jessica Gordon - Hospital for Special Surgery (NY), Faye Hant - Medical University of South Carolina (SC), Monique Hinchcliff – Yale School of Medicine (CT), Dinesh Khanna MD MS - University of Michigan (MI), Ami Shah - Johns Hopkins University (MD), Victoria Shanmugam - George Washington University (DC)
- Vanderbilt University, Department of Medicine, Division of Rheumatology and Immunology. Nashville, TN 37232
| | - Dinesh Khanna
- Prospective Registry of Early Systemic Sclerosis (PRESS) consortium. Shervin Assassi MD MS- University of Texas Health Sciences Center at Houston (TX), Elana Bernstein MD MS- Columbia University (NY), Robyn Domsic MD MS - University of Pittsburgh (PA), Tracy Frech MD MS - University of Utah (UT), Jessica Gordon - Hospital for Special Surgery (NY), Faye Hant - Medical University of South Carolina (SC), Monique Hinchcliff – Yale School of Medicine (CT), Dinesh Khanna MD MS - University of Michigan (MI), Ami Shah - Johns Hopkins University (MD), Victoria Shanmugam - George Washington University (DC)
- University of Michigan, Department of Medicine, Division of Rheumatology. Ann Arbor, MI 48109
| | - Alex Shaeffer
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Harris Perlman
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Monique Hinchcliff
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
- Prospective Registry of Early Systemic Sclerosis (PRESS) consortium. Shervin Assassi MD MS- University of Texas Health Sciences Center at Houston (TX), Elana Bernstein MD MS- Columbia University (NY), Robyn Domsic MD MS - University of Pittsburgh (PA), Tracy Frech MD MS - University of Utah (UT), Jessica Gordon - Hospital for Special Surgery (NY), Faye Hant - Medical University of South Carolina (SC), Monique Hinchcliff – Yale School of Medicine (CT), Dinesh Khanna MD MS - University of Michigan (MI), Ami Shah - Johns Hopkins University (MD), Victoria Shanmugam - George Washington University (DC)
- Yale University, School of Medicine, Section of Rheumatology, Allergy & Immunology. New Haven, CT 06520
| | - Deborah R. Winter
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
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Differentially expressed genes in systemic sclerosis: Towards predictive medicine with new molecular tools for clinicians. Autoimmun Rev 2023; 22:103314. [PMID: 36918090 DOI: 10.1016/j.autrev.2023.103314] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/09/2023] [Indexed: 03/13/2023]
Abstract
Systemic sclerosis (SSc) is a rare and chronic autoimmune disease characterized by a pathogenic triad of immune dysregulation, vasculopathy, and progressive fibrosis. Clinical tools commonly used to assess patients, such as the modified Rodnan skin score, difference between limited or diffuse forms of skin involvement, presence of lung, heart or kidney involvement, or of various autoantibodies, are important prognostic factors, but still fail to reflect the large heterogeneity of the disease. SSc treatment options are diverse, ranging from conventional drugs to autologous hematopoietic stem cell transplantation, and predicting response is challenging. Genome-wide technologies, such as high throughput microarray analyses and RNA sequencing, allow accurate, unbiased, and broad assessment of alterations in expression levels of multiple genes. In recent years, many studies have shown robust changes in the gene expression profiles of SSc patients compared to healthy controls, mainly in skin tissues and peripheral blood cells. The objective analysis of molecular patterns in SSc is a powerful tool that can further classify SSc patients with similar clinical phenotypes and help predict response to therapy. In this review, we describe the journey from the first discovery of differentially expressed genes to the identification of enriched pathways and intrinsic subsets identified in SSc, using machine learning algorithms. Finally, we discuss the use of these new tools to predict the efficacy of various treatments, including stem cell transplantation. We suggest that the use of RNA gene expression-based classifications according to molecular subsets may bring us one step closer to precision medicine in Systemic Sclerosis.
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15
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Keyes-Elstein L, Pinckney A, Goldmuntz E, Welch B, Franks JM, Martyanov V, Wood TA, Crofford L, Mayes M, McSweeney P, Nash R, Georges G, Csuka M, Simms R, Furst D, Khanna D, St Clair EW, Whitfield ML, Sullivan KM. Clinical and Molecular Findings After Autologous Stem Cell Transplantation or Cyclophosphamide for Scleroderma: Handling Missing Longitudinal Data. Arthritis Care Res (Hoboken) 2023; 75:307-316. [PMID: 34533286 PMCID: PMC8926930 DOI: 10.1002/acr.24785] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/23/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Among individuals with systemic sclerosis (SSc) randomized to cyclophosphamide (CYC) (n = 34) or hematopoietic stem cell transplantation (HSCT) (n = 33), we examined longitudinal trends of clinical, pulmonary function, and quality of life measures while accounting for the influence of early failures on treatment comparisons. METHODS Assuming that data were missing at random, mixed-effects regression models were used to estimate longitudinal trends for clinical measures when comparing treatment groups. Results were compared to observed means and to longitudinal trends estimated from shared parameter models, assuming that data were missing not at random. Longitudinal trends for SSc intrinsic molecular subsets defined by baseline gene expression signatures (normal-like, inflammatory, and fibroproliferative signatures) were also studied. RESULTS Available observed means for pulmonary function tests appeared to improve over time in both arms. However, after accounting for participant loss, forced vital capacity in HSCT recipients increased by 0.77 percentage points/year but worsened by -3.70/year for CYC (P = 0.004). Similar results were found for diffusing capacity for carbon monoxide and quality of life indicators. Results for both analytic models were consistent. HSCT recipients in the inflammatory (n = 20) and fibroproliferative (n = 20) subsets had superior long-term trends compared to CYC for pulmonary and quality of life measures. HSCT was also superior for modified Rodnan skin thickness scores in the fibroproliferative subset. For the normal-like subset (n = 22), superiority of HSCT was less apparent. CONCLUSION Longitudinal trends estimated from 2 statistical models affirm the efficacy of HSCT over CYC in severe SSc. Failure to account for early loss of participants may distort estimated clinical trends over the long term.
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Affiliation(s)
| | | | - Ellen Goldmuntz
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Beverly Welch
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | | | | | | | - Leslie Crofford
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Maureen Mayes
- University of Texas McGovern Medical School, Houston, TX
| | | | | | | | - M.E. Csuka
- Medical College of Wisconsin, Milwaukee, WI
| | - Robert Simms
- Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Daniel Furst
- University of California Los Angeles, Los Angeles, CA; University of Washington, Seattle, WA; University of Florence, Florence, Italy
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16
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Roberson ED, Carns M, Cao L, Aren K, Goldberg IA, Morales-Heil DJ, Korman BD, Atkinson JP, Varga J. Alterations of the Primary Cilia Gene SPAG17 and SOX9 Locus Noncoding RNAs Identified by RNA-Sequencing Analysis in Patients With Systemic Sclerosis. Arthritis Rheumatol 2023; 75:108-119. [PMID: 35762854 PMCID: PMC10445493 DOI: 10.1002/art.42281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/12/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Systemic sclerosis (SSc) is characterized by immune activation, vasculopathy, and unresolving fibrosis in the skin, lungs, and other organs. We performed RNA-sequencing analysis on skin biopsy samples and peripheral blood mononuclear cells (PBMCs) from SSc patients and unaffected controls to better understand the pathogenesis of SSc. METHODS We analyzed these data 1) to test for case/control differences and 2) to identify genes whose expression levels correlate with SSc severity as measured by local skin score, modified Rodnan skin thickness score (MRSS), forced vital capacity (FVC), or diffusing capacity for carbon monoxide (DLco). RESULTS We found that PBMCs from SSc patients showed a strong type I interferon signature. This signal was found to be replicated in the skin, with additional signals for increased extracellular matrix (ECM) genes, classical complement pathway activation, and the presence of B cells. Notably, we observed a marked decrease in the expression of SPAG17, a cilia component, in SSc skin. We identified genes that correlated with the MRSS, DLco, and FVC in SSc PBMCs and skin using weighted gene coexpression network analysis. These genes were largely distinct from the case/control differentially expressed genes. In PBMCs, type I interferon signatures negatively correlated with the DLco. In SSc skin, ECM gene expression positively correlated with the MRSS. Network analysis of SSc skin genes that correlated with clinical features identified the noncoding RNAs SOX9-AS1 and ROCR, both near the SOX9 locus, as highly connected, "hub-like" genes in the network. CONCLUSION These results identify noncoding RNAs and SPAG17 as novel factors potentially implicated in the pathogenesis of SSc.
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Affiliation(s)
- Elisha D.O. Roberson
- Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
| | - Mary Carns
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
| | - Li Cao
- Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA
| | - Kathleen Aren
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
| | - Isaac A. Goldberg
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
| | - David J. Morales-Heil
- Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA
| | - Benjamin D. Korman
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
| | - John P. Atkinson
- Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA
| | - John Varga
- Feinberg School of Medicine, Scleroderma Program, Northwestern University, Chicago, IL, USA
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI, USA
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17
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Jin J, Liu Y, Tang Q, Yan X, Jiang M, Zhao X, Chen J, Jin C, Ou Q, Zhao J. Bioinformatics-integrated screening of systemic sclerosis-specific expressed markers to identify therapeutic targets. Front Immunol 2023; 14:1125183. [PMID: 37063926 PMCID: PMC10098096 DOI: 10.3389/fimmu.2023.1125183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 04/18/2023] Open
Abstract
Background Systemic sclerosis (SSc) is a rare autoimmune disease characterized by extensive skin fibrosis. There are no effective treatments due to the severity, multiorgan presentation, and variable outcomes of the disease. Here, integrated bioinformatics was employed to discover tissue-specific expressed hub genes associated with SSc, determine potential competing endogenous RNAs (ceRNA) regulatory networks, and identify potential targeted drugs. Methods In this study, four datasets of SSc were acquired. To identify the genes specific to tissues or organs, the BioGPS web database was used. For differentially expressed genes (DEGs), functional and enrichment analyses were carried out, and hub genes were screened and shown in a network of protein-protein interactions (PPI). The potential lncRNA-miRNA-mRNA ceRNA network was constructed using the online databases. The specifically expressed hub genes and ceRNA network were validated in the SSc mouse and in normal mice. We also used the receiver operating characteristic (ROC) curve to determine the diagnostic values of effective biomarkers in SSc. Finally, the Drug-Gene Interaction Database (DGIdb) identified specific medicines linked to hub genes. Results The pooled datasets identified a total of 254 DEGs. The tissue/organ-specifically expressed genes involved in this analysis are commonly found in the hematologic/immune system and bone/muscle tissue. The enrichment analysis of DEGs revealed the significant terms such as regulation of actin cytoskeleton, immune-related processes, the VEGF signaling pathway, and metabolism. Cytoscape identified six gene cluster modules and 23 hub genes. And 4 hub genes were identified, including Serpine1, CCL2, IL6, and ISG15. Consistently, the expression of Serpine1, CCL2, IL6, and ISG15 was significantly higher in the SSc mouse model than in normal mice. Eventually, we found that MALAT1-miR-206-CCL2, let-7a-5p-IL6, and miR-196a-5p-SERPINE1 may be promising RNA regulatory pathways in SSc. Besides, ten potential therapeutic drugs associated with the hub gene were identified. Conclusions This study revealed tissue-specific expressed genes, SERPINE1, CCL2, IL6, and ISG15, as effective biomarkers and provided new insight into the mechanisms of SSc. Potential RNA regulatory pathways, including MALAT1-miR-206-CCL2, let-7a-5p-IL6, and miR-196a-5p-SERPINE1, contribute to our knowledge of SSc. Furthermore, the analysis of drug-hub gene interactions predicted TIPLASININ, CARLUMAB and BINDARIT as candidate drugs for SSc.
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Affiliation(s)
- Jiahui Jin
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yifan Liu
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qinyu Tang
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xin Yan
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Miao Jiang
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xu Zhao
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jie Chen
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Caixia Jin
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Caixia Jin, ; Qingjian Ou, ; Jingjun Zhao,
| | - Qingjian Ou
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Caixia Jin, ; Qingjian Ou, ; Jingjun Zhao,
| | - Jingjun Zhao
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Dermatology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- *Correspondence: Caixia Jin, ; Qingjian Ou, ; Jingjun Zhao,
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18
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Franks JM, Toledo DM, Martyanov V, Wang Y, Huang S, Wood TA, Spino C, Chung L, Denton CP, Derrett-Smith E, Gordon JK, Spiera R, Domsic R, Hinchcliff M, Khanna D, Whitfield ML. A genomic meta-analysis of clinical variables and their association with intrinsic molecular subsets in systemic sclerosis. Rheumatology (Oxford) 2022; 62:19-28. [PMID: 35751592 PMCID: PMC9788818 DOI: 10.1093/rheumatology/keac344] [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: 01/05/2022] [Revised: 05/19/2022] [Accepted: 06/06/2022] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES Four intrinsic molecular subsets (inflammatory, fibroproliferative, limited, normal-like) have previously been identified in SSc and are characterized by unique gene expression signatures and pathways. The intrinsic subsets have been linked to improvement with specific therapies. Here, we investigated associations between baseline demographics and intrinsic molecular subsets in a meta-analysis of published datasets. METHODS Publicly available gene expression data from skin biopsies of 311 SSc patients measured by DNA microarray were classified into the intrinsic molecular subsets. RNA-sequencing data from 84 participants from the ASSET trial were used as a validation cohort. Baseline clinical demographics and intrinsic molecular subsets were tested for statistically significant associations. RESULTS Males were more likely to be classified in the fibroproliferative subset (P = 0.0046). SSc patients who identified as African American/Black were 2.5 times more likely to be classified as fibroproliferative compared with White/Caucasian patients (P = 0.0378). ASSET participants sera positive for anti-RNA pol I and RNA pol III autoantibodies were enriched in the inflammatory subset (P = 5.8 × 10-5, P = 9.3 × 10-5, respectively), while anti-Scl-70 was enriched in the fibroproliferative subset. Mean modified Rodnan Skin Score (mRSS) was statistically higher in the inflammatory and fibroproliferative subsets compared with normal-like (P = 0.0027). The average disease duration for inflammatory subset was less than fibroproliferative and normal-like intrinsic subsets (P = 8.8 × 10-4). CONCLUSIONS We identified multiple statistically significant differences in baseline demographics between the intrinsic subsets that may represent underlying features of disease pathogenesis (e.g. chronological stages of fibrosis) and have implications for treatments that are more likely to work in certain SSc populations.
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Affiliation(s)
| | - Diana M Toledo
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | | | - Yue Wang
- Department of Biomedical Data Science
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Suiyuan Huang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Tammara A Wood
- Department of Biomedical Data Science
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Cathie Spino
- Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Lorinda Chung
- Palo Alto Health Care System, Palo Alto, Stanford, CA, USA
| | | | | | | | | | | | | | - Dinesh Khanna
- Correspondence to: Michael L. Whitfield, Department of Biomedical Data Science, Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, HB 7261, 1 Medical Center Drive, Lebanon, NH 03756, USA. E-mail: ; Dinesh Khanna, Division of Rheumatology, Department of Internal Medicine, University of Michigan Scleroderma Program, Suite 7C27, 300 North Ingalls Street, SP C 5422, Ann Arbor, MI 48109, USA. E-mail:
| | - Michael L Whitfield
- Correspondence to: Michael L. Whitfield, Department of Biomedical Data Science, Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, HB 7261, 1 Medical Center Drive, Lebanon, NH 03756, USA. E-mail: ; Dinesh Khanna, Division of Rheumatology, Department of Internal Medicine, University of Michigan Scleroderma Program, Suite 7C27, 300 North Ingalls Street, SP C 5422, Ann Arbor, MI 48109, USA. E-mail:
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19
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Mehta BK, Espinoza ME, Franks JM, Yuan Y, Wang Y, Wood T, Gudjonsson JE, Spino C, Fox DA, Khanna D, Whitfield ML. Machine-learning classification identifies patients with early systemic sclerosis as abatacept responders via CD28 pathway modulation. JCI Insight 2022; 7:155282. [PMID: 36355434 PMCID: PMC9869963 DOI: 10.1172/jci.insight.155282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Here, the efficacy of abatacept in patients with early diffuse systemic sclerosis (dcSSc) was analyzed to test the hypothesis that patients in the inflammatory intrinsic subset would show the most significant clinical improvement. Eighty-four participants with dcSSc were randomized to receive abatacept or placebo for 12 months. RNA-Seq was performed on 233 skin paired biopsies at baseline and at 3 and 6 months. Improvement was defined as a 5-point or more than 20% change in modified Rodnan skin score (mRSS) between baseline and 12 months. Samples were assigned to intrinsic gene expression subsets (inflammatory, fibroproliferative, or normal-like subsets). In the abatacept arm, change in mRSS was most pronounced for the inflammatory and normal-like subsets relative to the placebo subset. Gene expression for participants on placebo remained in the original molecular subset, whereas inflammatory participants treated with abatacept had gene expression that moved toward the normal-like subset. The Costimulation of the CD28 Family Reactome Pathway decreased in patients who improved on abatacept and was specific to the inflammatory subset. Patients in the inflammatory subset had elevation of the Costimulation of the CD28 Family pathway at baseline relative to that of participants in the fibroproliferative and normal-like subsets. There was a correlation between improved ΔmRSS and baseline expression of the Costimulation of the CD28 Family pathway. This study provides an example of precision medicine in systemic sclerosis clinical trials.
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Affiliation(s)
- Bhaven K. Mehta
- Department of Biomedical Data Science, Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Monica E. Espinoza
- Department of Biomedical Data Science, Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Jennifer M. Franks
- Department of Biomedical Data Science, Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Yiwei Yuan
- Department of Biomedical Data Science, Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Yue Wang
- Department of Biomedical Data Science, Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Tammara Wood
- Department of Biomedical Data Science, Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Johann E. Gudjonsson
- Department of Dermatology, Department of Medicine, Clinical Autoimmunity Center of Excellence and University of Michigan Scleroderma Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Cathie Spino
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - David A. Fox
- Division of Rheumatology, Department of Medicine, Clinical Autoimmunity Center of Excellence and University of Michigan Scleroderma Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Dinesh Khanna
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
- Division of Rheumatology, Department of Medicine, Clinical Autoimmunity Center of Excellence and University of Michigan Scleroderma Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael L. Whitfield
- Department of Biomedical Data Science, Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
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20
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Kim S, Park HJ, Lee SI. The Microbiome in Systemic Sclerosis: Pathophysiology and Therapeutic Potential. Int J Mol Sci 2022; 23:ijms232416154. [PMID: 36555792 PMCID: PMC9853331 DOI: 10.3390/ijms232416154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Systemic sclerosis (SSc), also known as scleroderma, is an autoimmune disease with unknown etiology characterized by multi-organ fibrosis. Despite substantial investigation on SSc-related cellular and molecular mechanisms, effective therapies are still lacking. The skin, lungs, and gut are the most affected organs in SSc, which act as physical barriers and constantly communicate with colonized microbiota. Recent reports have documented a unique microbiome signature, which may be the pathogenic trigger or driver of SSc. Since gut microbiota influences the efficacy and toxicity of oral drugs, evaluating drug-microbiota interactions has become an area of interest in disease treatment. The existing evidence highlights the potential of the microbial challenge as a novel therapeutic option in SSc. In this review, we have summarized the current knowledge about molecular mechanisms of SSc and highlighted the underlying role of the microbiome in SSc pathogenesis. We have also discussed the latest therapeutic interventions using microbiomes in SSc, including drug-microbiota interactions and animal disease models. This review aims to elucidate the pathophysiological connection and therapeutic potential of the microbiome in SSc. Insights into the microbiome will significantly improve our understanding of etiopathogenesis and developing therapeutics for SSc.
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21
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Wang W, Bale S, Yalavarthi B, Verma P, Tsou PS, Calderone KM, Bhattacharyya D, Fisher GJ, Varga J, Bhattacharyya S. Deficiency of inhibitory TLR4 homolog RP105 exacerbates fibrosis. JCI Insight 2022; 7:e160684. [PMID: 36136452 PMCID: PMC9675479 DOI: 10.1172/jci.insight.160684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022] Open
Abstract
Activation of TLR4 by its cognate damage-associated molecular patterns (DAMPs) elicits potent profibrotic effects and myofibroblast activation in systemic sclerosis (SSc), while genetic targeting of TLR4 or its DAMPs in mice accelerates fibrosis resolution. To prevent aberrant DAMP/TLR4 activity, a variety of negative regulators evolved to dampen the magnitude and duration of the signaling. These include radioprotective 105 kDa (RP105), a transmembrane TLR4 homolog that competitively inhibits DAMP recognition of TLR4, blocking TLR4 signaling in immune cells. The role of RP105 in TLR4-dependent fibrotic responses in SSc is unknown. Using unbiased transcriptome analysis of skin biopsies, we found that levels of both TLR4 and its adaptor protein MD2 were elevated in SSc skin and significantly correlated with each other. Expression of RP105 was negatively associated with myofibroblast differentiation in SSc. Importantly, RP105-TLR4 association was reduced, whereas TLR4-TLR4 showed strong association in fibroblasts from patients with SSc, as evidenced by PLA assays. Moreover, RP105 adaptor MD1 expression was significantly reduced in SSc skin biopsies and explanted SSc skin fibroblasts. Exogenous RP105-MD1 abrogated, while loss of RP105 exaggerated, fibrotic cellular responses. Importantly, ablation of RP105 in mice was associated with augmented TLR4 signaling and aggravated skin fibrosis in complementary disease models. Thus, we believe RP105-MD1 to be a novel cell-intrinsic negative regulator of TLR4-MD2-driven sustained fibroblast activation, representing a critical regulatory network governing the fibrotic process. Impaired RP105 function in SSc might contribute to persistence of progression of the disease.
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Affiliation(s)
- Wenxia Wang
- Northwestern Scleroderma Program, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Swarna Bale
- Northwestern Scleroderma Program, Feinberg School of Medicine, Chicago, Illinois, USA
- Michigan Scleroderma Program, Division of Rheumatology, Department of Internal Medicine, and
| | - Bharath Yalavarthi
- Michigan Scleroderma Program, Division of Rheumatology, Department of Internal Medicine, and
| | - Priyanka Verma
- Michigan Scleroderma Program, Division of Rheumatology, Department of Internal Medicine, and
| | - Pei-Suen Tsou
- Michigan Scleroderma Program, Division of Rheumatology, Department of Internal Medicine, and
| | - Ken M. Calderone
- Derpartment of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Dibyendu Bhattacharyya
- Michigan Scleroderma Program, Division of Rheumatology, Department of Internal Medicine, and
| | - Gary J. Fisher
- Derpartment of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - John Varga
- Northwestern Scleroderma Program, Feinberg School of Medicine, Chicago, Illinois, USA
- Michigan Scleroderma Program, Division of Rheumatology, Department of Internal Medicine, and
| | - Swati Bhattacharyya
- Northwestern Scleroderma Program, Feinberg School of Medicine, Chicago, Illinois, USA
- Michigan Scleroderma Program, Division of Rheumatology, Department of Internal Medicine, and
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22
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Bonomi F, Peretti S, Lepri G, Venerito V, Russo E, Bruni C, Iannone F, Tangaro S, Amedei A, Guiducci S, Matucci Cerinic M, Bellando Randone S. The Use and Utility of Machine Learning in Achieving Precision Medicine in Systemic Sclerosis: A Narrative Review. J Pers Med 2022; 12:1198. [PMID: 35893293 PMCID: PMC9331823 DOI: 10.3390/jpm12081198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a rare connective tissue disease that can affect different organs and has extremely heterogenous presentations. This complexity makes it difficult to perform an early diagnosis and a subsequent subclassification of the disease. This hinders a personalized approach in clinical practice. In this context, machine learning (ML), a branch of artificial intelligence (AI), is able to recognize relationships in data and predict outcomes. METHODS Here, we performed a narrative review concerning the application of ML in SSc to define the state of art and evaluate its role in a precision medicine context. RESULTS Currently, ML has been used to stratify SSc patients and identify those at high risk of severe complications. Additionally, ML may be useful in the early detection of organ involvement. Furthermore, ML might have a role in target therapy approach and in predicting drug response. CONCLUSION Available evidence about the utility of ML in SSc is sparse but promising. Future improvements in this field could result in a big step toward precision medicine. Further research is needed to define ML application in clinical practice.
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Affiliation(s)
- Francesco Bonomi
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Silvia Peretti
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Gemma Lepri
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Vincenzo Venerito
- Rheumatology Unit, Department of Emergency and Organ Transplantations, University of Bari Aldo Moro, 70121 Bari, Italy; (V.V.); (F.I.)
| | - Edda Russo
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Cosimo Bruni
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
- Department of Rheumatology, University Hospital of Zurich, University of Zurich, 8006 Zurich, Switzerland
| | - Florenzo Iannone
- Rheumatology Unit, Department of Emergency and Organ Transplantations, University of Bari Aldo Moro, 70121 Bari, Italy; (V.V.); (F.I.)
| | - Sabina Tangaro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70121 Bari, Italy;
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Serena Guiducci
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
| | - Marco Matucci Cerinic
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases (UnIRAR), IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Silvia Bellando Randone
- Department of Clinical and Experimental Medicine, University of Florence, 50134 Florence, Italy; (F.B.); (S.P.); (G.L.); (E.R.); (C.B.); (A.A.); (S.G.); (M.M.C.)
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23
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Assessment of disease outcome measures in systemic sclerosis. Nat Rev Rheumatol 2022; 18:527-541. [PMID: 35859133 DOI: 10.1038/s41584-022-00803-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2022] [Indexed: 01/08/2023]
Abstract
The assessment of disease activity in systemic sclerosis (SSc) is challenging owing to its heterogeneous manifestations across multiple organ systems, the variable rate of disease progression and regression, and the relative paucity of patients in early-phase therapeutic trials. Despite some recent successes, most clinical trials have failed to show efficacy, underscoring the need for improved outcome measures linked directly to disease pathogenesis, particularly applicable for biomarker studies focused on skin disease. Current outcome measures in SSc-associated interstitial lung disease and SSc skin disease are largely adequate, although advancing imaging technology and the incorporation of skin mRNA biomarkers might provide opportunities for earlier detection of the therapeutic effect. Biomarkers can further inform pathogenesis, enabling early phase trials to act as reverse translational studies through the incorporation of routine high-throughput sequencing.
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Guthridge JM, Wagner CA, James JA. The promise of precision medicine in rheumatology. Nat Med 2022; 28:1363-1371. [PMID: 35788174 PMCID: PMC9513842 DOI: 10.1038/s41591-022-01880-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/23/2022] [Indexed: 01/07/2023]
Abstract
Systemic autoimmune rheumatic diseases (SARDs) exhibit extensive heterogeneity in clinical presentation, disease course, and treatment response. Therefore, precision medicine - whereby treatment is tailored according to the underlying pathogenic mechanisms of an individual patient at a specific time - represents the 'holy grail' in SARD clinical care. Current strategies include treat-to-target therapies and autoantibody testing for patient stratification; however, these are far from optimal. Recent innovations in high-throughput 'omic' technologies are now enabling comprehensive profiling at multiple levels, helping to identify subgroups of patients who may taper off potentially toxic medications or better respond to current molecular targeted therapies. Such advances may help to optimize outcomes and identify new pathways for treatment, but there are many challenges along the path towards clinical translation. In this Review, we discuss recent efforts to dissect cellular and molecular heterogeneity across multiple SARDs and future directions for implementing stratification approaches for SARD treatment in the clinic.
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Affiliation(s)
- Joel M Guthridge
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Catriona A Wagner
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Judith A James
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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25
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Noviani M, Chellamuthu VR, Albani S, Low AHL. Toward Molecular Stratification and Precision Medicine in Systemic Sclerosis. Front Med (Lausanne) 2022; 9:911977. [PMID: 35847779 PMCID: PMC9279904 DOI: 10.3389/fmed.2022.911977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/06/2022] [Indexed: 01/01/2023] Open
Abstract
Systemic sclerosis (SSc), a complex multi-systemic disease characterized by immune dysregulation, vasculopathy and fibrosis, is associated with high mortality. Its pathogenesis is only partially understood. The heterogenous pathological processes that define SSc and its stages present a challenge to targeting appropriate treatment, with differing treatment outcomes of SSc patients despite similar initial clinical presentations. Timing of the appropriate treatments targeted at the underlying disease process is critical. For example, immunomodulatory treatments may be used for patients in a predominantly inflammatory phase, anti-fibrotic treatments for those in the fibrotic phase, or combination therapies for those in the fibro-inflammatory phase. In advancing personalized care through precision medicine, groups of patients with similar disease characteristics and shared pathological processes may be identified through molecular stratification. This would improve current clinical sub-setting systems and guide personalization of therapies. In this review, we will provide updates in SSc clinical and molecular stratification in relation to patient outcomes and treatment responses. Promises of molecular stratification through advances in high-dimensional tools, including omic-based stratification (transcriptomics, genomics, epigenomics, proteomics, cytomics, microbiomics) and machine learning will be discussed. Innovative and more granular stratification systems that integrate molecular characteristics to clinical phenotypes would potentially improve therapeutic approaches through personalized medicine and lead to better patient outcomes.
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Affiliation(s)
- Maria Noviani
- Department of Rheumatology and Immunology, Singapore General Hospital, Singapore, Singapore
- Duke–National University of Singapore Medical School, Singapore, Singapore
| | | | - Salvatore Albani
- Duke–National University of Singapore Medical School, Singapore, Singapore
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Andrea Hsiu Ling Low
- Department of Rheumatology and Immunology, Singapore General Hospital, Singapore, Singapore
- Duke–National University of Singapore Medical School, Singapore, Singapore
- *Correspondence: Andrea Hsiu Ling Low
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Xue D, Tabib T, Morse C, Yang Y, Domsic R, Khanna D, Lafyatis R. Expansion of Fcγ Receptor IIIa-Positive Macrophages, Ficolin 1-Positive Monocyte-Derived Dendritic Cells, and Plasmacytoid Dendritic Cells Associated With Severe Skin Disease in Systemic Sclerosis. Arthritis Rheumatol 2022; 74:329-341. [PMID: 34042322 PMCID: PMC8626521 DOI: 10.1002/art.41813] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 04/07/2021] [Accepted: 05/11/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE In this study, we sought a comprehensive understanding of myeloid cell types driving fibrosis in diffuse cutaneous systemic sclerosis (dcSSc) skin. METHODS We analyzed the transcriptomes of 2,465 myeloid cells from skin biopsy specimens from 12 dcSSc patients and 10 healthy control subjects using single-cell RNA sequencing. Monocyte-derived dendritic cells (mo-DCs) were assessed using immunohistochemical staining and immunofluorescence analyses targeting ficolin-1 (FCN-1). RESULTS A t-distributed stochastic neighbor embedding analysis of single-cell transcriptome data revealed 12 myeloid cell clusters, 9 of which paralleled previously described healthy control macrophage/DC clusters, and 3 of which were dcSSc-specific myeloid cell clusters. One SSc-associated macrophage cluster, highly expressing Fcγ receptor IIIA, was suggested on pseudotime analysis to be derived from normal CCR1+ and MARCO+ macrophages. A second SSc-associated myeloid population highly expressed monocyte markers FCN-1, epiregulin, S100A8, and S100A9, but was closely related to type 2 conventional DCs on pseudotime analysis and identified as mo-DCs. Mo-DCs were associated with more severe skin disease. Proliferating macrophages and plasmacytoid DCs were detected almost exclusively in dcSSc skin, the latter clustering with B cells and apparently derived from lymphoid progenitors. CONCLUSION Transcriptional signatures in these and other myeloid populations indicate innate immune system activation, possibly through Toll-like receptors and highly up-regulated chemokines. However, the appearance and activation of myeloid cells varies between patients, indicating potential differences in the underlying pathogenesis and/or temporal disease activity in dcSSc.
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Affiliation(s)
- Dan Xue
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan
| | - Tracy Tabib
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christina Morse
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yi Yang
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan
| | - Robyn Domsic
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dinesh Khanna
- Division of Rheumatology, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Barriga M, Benitez R, Robledo G, Caro M, O'Valle F, Campos-Salinas J, Delgado M. Neuropeptide Cortistatin Regulates Dermal and Pulmonary Fibrosis in an Experimental Model of Systemic Sclerosis. Neuroendocrinology 2022; 112:784-795. [PMID: 34649259 DOI: 10.1159/000520194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/13/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Scleroderma, or systemic sclerosis, is a complex connective tissue disorder characterized by autoimmunity, vasculopathy, and progressive fibrosis of the skin and internal organs. Because its aetiology is unknown, the identification of genes/factors involved in disease severity, differential clinical forms, and associated complications is critical for understanding its pathogenesis and designing novel treatments. Neuroendocrine mediators in the skin emerge as potential candidates. We investigated the role played by the neuropeptide cortistatin in a preclinical model of scleroderma. METHODS Dermal fibrosis was induced by repetitive intradermal injections of bleomycin in wild-type and cortistatin-deficient mice. The histopathological signs and expression of fibrotic markers were evaluated in the skin and lungs. RESULTS An inverse correlation between cortistatin levels and fibrogenic activation exists in the damaged skin and dermal fibroblasts. Bleomycin-challenged skin lesions of mice that are partially and totally deficient in cortistatin showed exacerbated histopathological signs of scleroderma, characterized by thicker and more fibrotic dermal layer, enlarged epidermis, and increased inflammatory infiltration in comparison to those of wild-type mice. Cortistatin deficiency enhanced dermal collagen deposits, connective tissue growth factor expression, loss of microvessels, and predisposition to suffer severe complications that co-occur with dermal exposition to bleomycin, including pulmonary fibrotic disease and increased mortality. Treatment with cortistatin mitigated these pathological processes. DISCUSSION/CONCLUSION We identify cortistatin as an endogenous break of skin inflammation and fibrosis. Deficiency in cortistatin could be a marker of poor prognosis of scleroderma and associated complications. Cortistatin-based therapies emerge as attractive candidates to treat severe forms of systemic sclerosis and to manage fibrosis-related side effects of bleomycin chemotherapy in oncologic patients.
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Affiliation(s)
- Margarita Barriga
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Raquel Benitez
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Gema Robledo
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Marta Caro
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Francisco O'Valle
- Pathology Department, School of Medicine, IBIMER, CIBM, University of Granada and Biosanitary Research Institute IBS-Granada, Granada, Spain
| | - Jenny Campos-Salinas
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Mario Delgado
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
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28
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Skaug B, Lyons MA, Swindell WR, Salazar GA, Wu M, Tran TM, Charles J, Vershel CP, Mayes MD, Assassi S. Large-scale analysis of longitudinal skin gene expression in systemic sclerosis reveals relationships of immune cell and fibroblast activity with skin thickness and a trend towards normalisation over time. Ann Rheum Dis 2021; 81:516-523. [PMID: 34937693 DOI: 10.1136/annrheumdis-2021-221352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/29/2021] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Determine relationships between skin gene expression and systemic sclerosis (SSc) clinical disease features, and changes in skin gene expression over time. METHODS A total of 339 forearm skin biopsies were obtained from 113 SSc patients and 44 matched healthy controls. 105 SSc patients had a second biopsy, and 76 had a third biopsy. Global gene expression profiling was performed, and differentially expressed genes and cell type-specific signatures in SSc were evaluated for relationships to modified Rodnan Skin Score (mRSS) and other clinical variables. Changes in skin gene expression over time were analysed by mixed effects models and principal component analysis. Immunohistochemical staining was performed to validate conclusions. RESULTS Gene expression dysregulation was greater in SSc patients with affected skin than in those with unaffected skin. Immune cell and fibroblast signatures positively correlated with mRSS. High baseline immune cell and fibroblast signatures predicted higher mRSS over time, but were not independently predictive of longitudinal mRSS after adjustment for baseline mRSS. In early diffuse cutaneous SSc, immune cell and fibroblast signatures declined over time, and overall skin gene expression trended towards normalisation. On immunohistochemical staining, most early diffuse cutaneous SSc patients with high baseline T cell and macrophage numbers had declines in these numbers at follow-up. CONCLUSIONS Skin thickness in SSc is related to dysregulated immune cell and fibroblast gene expression. Skin gene expression changes over time in early diffuse SSc, with a tendency towards normalisation. These observations are relevant for understanding SSc pathogenesis and could inform treatment strategies and clinical trial design.
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Affiliation(s)
- Brian Skaug
- Division of Rheumatology, University of Texas Health Science Center Houston, McGovern Medical School, Houston, Texas, USA
| | - Marka A Lyons
- Division of Rheumatology, University of Texas Health Science Center Houston, McGovern Medical School, Houston, Texas, USA
| | - William R Swindell
- Department of Internal Medicine, The Jewish Hospital, Cincinnati, Ohio, USA
| | - Gloria A Salazar
- Division of Rheumatology, University of Texas Health Science Center Houston, McGovern Medical School, Houston, Texas, USA
| | - Minghua Wu
- Division of Rheumatology, University of Texas Health Science Center Houston, McGovern Medical School, Houston, Texas, USA
| | - Tuan M Tran
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Julio Charles
- Division of Rheumatology, University of Texas Health Science Center Houston, McGovern Medical School, Houston, Texas, USA
| | - Connor P Vershel
- Division of Rheumatology, University of Texas Health Science Center Houston, McGovern Medical School, Houston, Texas, USA
| | - Maureen D Mayes
- Division of Rheumatology, University of Texas Health Science Center Houston, McGovern Medical School, Houston, Texas, USA
| | - Shervin Assassi
- Division of Rheumatology, University of Texas Health Science Center Houston, McGovern Medical School, Houston, Texas, USA
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Nevskaya T, Pope JE, Turk MA, Shu J, Marquardt A, van den Hoogen F, Khanna D, Fransen J, Matucci-Cerinic M, Baron M, Denton CP, Johnson SR. Systematic Analysis of the Literature in Search of Defining Systemic Sclerosis Subsets. J Rheumatol 2021; 48:1698-1717. [PMID: 33993109 PMCID: PMC10613330 DOI: 10.3899/jrheum.201594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Systemic sclerosis (SSc) is a multisystem disease with heterogeneity in presentation and prognosis.An international collaboration to develop new SSc subset criteria is underway. Our objectives were to identify systems of SSc subset classification and synthesize novel concepts to inform development of new criteria. METHODS Medline, Cochrane MEDLINE, the Cumulative Index to Nursing and Allied Health Literature, EMBASE, and Web of Science were searched from their inceptions to December 2019 for studies related to SSc subclassification, limited to humans and without language or sample size restrictions. RESULTS Of 5686 citations, 102 studies reported original data on SSc subsets. Subset classification systems relied on extent of skin involvement and/or SSc-specific autoantibodies (n = 61), nailfold capillary patterns (n = 29), and molecular, genomic, and cellular patterns (n = 12). While some systems of subset classification confer prognostic value for clinical phenotype, severity, and mortality, only subsetting by gene expression signatures in tissue samples has been associated with response to therapy. CONCLUSION Subsetting on extent of skin involvement remains important. Novel disease attributes including SSc-specific autoantibodies, nailfold capillary patterns, and tissue gene expression signatures have been proposed as innovative means of SSc subsetting.
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Affiliation(s)
- Tatiana Nevskaya
- T. Nevskaya, MD, PhD, J.E. Pope, MD, MPH, M.A. Turk, MSc, J. Shu, MD, HBSc, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Janet E Pope
- T. Nevskaya, MD, PhD, J.E. Pope, MD, MPH, M.A. Turk, MSc, J. Shu, MD, HBSc, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Matthew A Turk
- T. Nevskaya, MD, PhD, J.E. Pope, MD, MPH, M.A. Turk, MSc, J. Shu, MD, HBSc, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Jenny Shu
- T. Nevskaya, MD, PhD, J.E. Pope, MD, MPH, M.A. Turk, MSc, J. Shu, MD, HBSc, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - April Marquardt
- A. Marquardt, DO, D. Khanna, MD, MS, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank van den Hoogen
- F. van den Hoogen, MD, PhD, St. Maartenskliniek and Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Dinesh Khanna
- A. Marquardt, DO, D. Khanna, MD, MS, University of Michigan, Ann Arbor, Michigan, USA
| | - Jaap Fransen
- J. Fransen, MSc, PhD, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Marco Matucci-Cerinic
- M. Matucci-Cerinic, MD, PhD, Department of Experimental and Clinical Medicine & Division of Rheumatology AOUC, Florence Italy University of Florence, Florence, Italy
| | - Murray Baron
- M. Baron, MD, McGill University, Division Head Rheumatology, Jewish General Hospital, Montreal, Quebec, Canada
| | - Christopher P Denton
- C.P. Denton, FRCP, PhD, University College London, Division of Medicine, London, UK
| | - Sindhu R Johnson
- S.R. Johnson, MD, PhD, Toronto Scleroderma Program, Toronto Western and Mount Sinai Hospitals, Department of Medicine, and Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada.
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Abstract
From the clinical standpoint, systemic sclerosis (SSc) is characterized by skin and internal organ fibrosis, diffuse fibroproliferative vascular modifications, and autoimmunity. Clinical presentation and course are highly heterogenous and life expectancy variably affected mostly dependent on lung and heart involvement. SSc touches more women than men with differences in disease severity and environmental exposure. Pathogenetic events originate from altered homeostasis favored by genetic predisposition, environmental cues and a variety of endogenous and exogenous triggers. Epigenetic modifications modulate SSc pathogenesis which strikingly associate profound immune-inflammatory dysregulation, abnormal endothelial cell behavior, and cell trans-differentiation into myofibroblasts. SSc myofibroblasts show enhanced survival and enhanced extracellular matrix deposition presenting altered structure and altered physicochemical properties. Additional cell types of likely pathogenic importance are pericytes, platelets, and keratinocytes in conjunction with their relationship with vessel wall cells and fibroblasts. In SSc, the profibrotic milieu is favored by cell signaling initiated in the one hand by transforming growth factor-beta and related cytokines and in the other hand by innate and adaptive type 2 immune responses. Radical oxygen species and invariant receptors sensing danger participate to altered cell behavior. Conventional and SSc-specific T cell subsets modulate both fibroblasts as well as endothelial cell dysfunction. Beside autoantibodies directed against ubiquitous antigens important for enhanced clinical classification, antigen-specific agonistic autoantibodies may have a pathogenic role. Recent studies based on single-cell RNAseq and multi-omics approaches are revealing unforeseen heterogeneity in SSc cell differentiation and functional states. Advances in system biology applied to the wealth of data generated by unbiased screening are allowing to subgroup patients based on distinct pathogenic mechanisms. Deciphering heterogeneity in pathogenic mechanisms will pave the way to highly needed personalized therapeutic approaches.
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Rusek M, Krasowska D. Non-Coding RNA in Systemic Sclerosis: A Valuable Tool for Translational and Personalized Medicine. Genes (Basel) 2021; 12:1296. [PMID: 34573278 PMCID: PMC8471866 DOI: 10.3390/genes12091296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023] Open
Abstract
Epigenetic factors are heritable and ultimately play a role in modulating gene expression and, thus, in regulating cell functions. Non-coding RNAs have growing recognition as novel biomarkers and crucial regulators of pathological conditions in humans. Their characteristic feature is being transcribed in a tissue-specific pattern. Now, there is emerging evidence that lncRNAs have been identified to be involved in the differentiation of human skin, wound healing, fibrosis, inflammation, and immunological response. Systemic sclerosis (SSc) is a heterogeneous autoimmune disease characterized by fibrosis, vascular abnormalities, and immune system activation. The pathogenesis remains elusive, but clinical manifestations reveal autoimmunity with the presence of specific autoantibodies, activation of innate and adaptive immunity, vascular changes, and active deposition of extracellular matrix components leading to fibrosis. The use of multi-omics studies, including NGS, RNA-seq, or GWAS, has proposed that the non-coding genome may be a significant player in its pathogenesis. Moreover, it may unravel new therapeutic targets in the future. The aim of this review is to show the pathogenic role of long non-coding RNAs in systemic sclerosis. Investigation of these transcripts' functions has the potential to elucidate the molecular pathology of SSc and provide new opportunities for drug-targeted therapy for this disorder.
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Affiliation(s)
- Marta Rusek
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
- Department of Pathophysiology, Medical University of Lublin, 20-090 Lublin, Poland
| | - Dorota Krasowska
- Department of Dermatology, Venereology and Pediatric Dermatology, Laboratory for Immunology of Skin Diseases, Medical University of Lublin, 20-080 Lublin, Poland;
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Insights Into Systemic Sclerosis from Gene Expression Profiling. CURRENT TREATMENT OPTIONS IN RHEUMATOLOGY 2021. [DOI: 10.1007/s40674-021-00183-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Tabib T, Huang M, Morse N, Papazoglou A, Behera R, Jia M, Bulik M, Monier DE, Benos PV, Chen W, Domsic R, Lafyatis R. Myofibroblast transcriptome indicates SFRP2 hi fibroblast progenitors in systemic sclerosis skin. Nat Commun 2021; 12:4384. [PMID: 34282151 PMCID: PMC8289865 DOI: 10.1038/s41467-021-24607-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Skin and lung fibrosis in systemic sclerosis (SSc) is driven by myofibroblasts, alpha-smooth muscle actin expressing cells. The number of myofibroblasts in SSc skin correlates with the modified Rodnan skin score, the most widely used clinical measure of skin disease severity. Murine fibrosis models indicate that myofibroblasts can arise from a variety of different cell types, but their origin in SSc skin has remained uncertain. Utilizing single cell RNA-sequencing, we define different dermal fibroblast populations and transcriptome changes, comparing SSc to healthy dermal fibroblasts. Here, we show that SSc dermal myofibroblasts arise in two steps from an SFRP2hi/DPP4-expressing progenitor fibroblast population. In the first step, SSc fibroblasts show globally upregulated expression of transcriptome markers, such as PRSS23 and THBS1. A subset of these cells shows markers indicating that they are proliferating. Only a fraction of SFRP2hi SSc fibroblasts differentiate into myofibroblasts, as shown by expression of additional markers, SFRP4 and FNDC1. Bioinformatics analysis of the SSc fibroblast transcriptomes implicated upstream transcription factors, including FOSL2, RUNX1, STAT1, FOXP1, IRF7 and CREB3L1, as well as SMAD3, driving SSc myofibroblast differentiation. Myofibroblasts drive fibrosis in systemic sclerosis (SSc), but the cellular progenitors are unknown. Utilizing single cell RNA-sequencing, the authors show that SSc dermal myofibroblasts arise in a two-step process from SFRP2/DPP4-expressing progenitors and implicate upstream transcription factors.
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Affiliation(s)
- Tracy Tabib
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Mengqi Huang
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Nina Morse
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Anna Papazoglou
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Rithika Behera
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Minxue Jia
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Melissa Bulik
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Daisy E Monier
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - Wei Chen
- Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robyn Domsic
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, School of Medicine, University of Pittsburgh, Department of Medicine, Pittsburgh, PA, USA.
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Novel classifications for systemic sclerosis: challenging historical subsets to unlock new doors. Curr Opin Rheumatol 2021; 32:463-471. [PMID: 32941248 DOI: 10.1097/bor.0000000000000747] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW Systemic sclerosis (SSc) is a severe rheumatic disease characterized by a considerable heterogeneity in clinical presentations and pathophysiological mechanisms. This variability has a substantial impact on morbidity and mortality and limits the generalizability of clinical trial results. This review aims to highlight recent studies that have proposed new innovative approaches to decipher this heterogeneity, in particular, by attempting to optimize disease classification. RECENT FINDINGS The historical dichotomy limited/diffuse subsets based on cutaneous involvement has been challenged by studies highlighting an underestimated heterogeneity between these two subtypes and showing that presence of organ damage and autoantibody profiles markedly influenced survival beyond skin extension. Advanced computational methods using unsupervised machine learning analyses of clinical variables and/or high-throughput omics technologies, clinical variables trajectories modelling overtime or radiomics have provided significant insights on key pathogenic processes that could help defining new subgroups beyond the diffuse/limited subsets. SUMMARY We can anticipate that a future classification of SSc patients will integrate innovative approaches encompassing clinical phenotypes, variables trajectories, serological features and innovative omics molecular signatures. It nevertheless seems crucial to also pursue the implementation and standardization of readily available and easy to use tools that can be used in clinical practice.
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Inamo J. Association of differentially expressed genes and autoantibody type in patients with systemic sclerosis. Rheumatology (Oxford) 2021; 60:929-939. [PMID: 32911535 DOI: 10.1093/rheumatology/keaa447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/21/2020] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES The aims of this study were to investigate the relationship between the type of autoantibody and gene expression profile in skin lesions from patients with SSc, and to identify specific dysregulated pathways in SSc patients compared with healthy controls. METHODS Sixty-one patients with SSc from the Genetics vs Environment in Scleroderma Outcome Study cohort and 36 healthy controls were included in this study. Differentially expressed genes were extracted and functional enrichment and pathway analysis were conducted. RESULTS Compared with healthy controls, lists containing 2, 71, 10, 144 and 78 differentially expressed genes were created for patients without specific autoantibody, ACA, anti-U1 RNP antibody (RNP), anti-RNA polymerase III antibody (RNAP) and anti-topoisomerase I antibody (ATA), respectively. While part of the enriched pathways overlapped, distinct pathways were identified except in those patients lacking specific autoantibody. The distinct enriched pathways included 'keratinocyte differentiation' for ACA, 'nuclear factor κB signalling' and 'cellular response to TGF-β stimulus' for RNAP, 'interferon α/β signalling' for RNP, and 'cellular response to stress' for ATA. Cell type signature score analysis revealed that macrophages/monocytes, endothelial cells and fibroblasts were associated with ACA, RNAP, ATA and the severity of the SSc skin lesions. CONCLUSION Pathogenic pathways were identified according to the type of autoantibody by leveraging gene expression data of patients and controls from a multicentre cohort. The current study may promote the search for new therapeutic targets for SSc.
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Affiliation(s)
- Jun Inamo
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
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36
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Showalter K, Spiera R, Magro C, Agius P, Martyanov V, Franks JM, Sharma R, Geiger H, Wood TA, Zhang Y, Hale CR, Finik J, Whitfield ML, Orange DE, Gordon JK. Machine learning integration of scleroderma histology and gene expression identifies fibroblast polarisation as a hallmark of clinical severity and improvement. Ann Rheum Dis 2021; 80:228-237. [PMID: 33028580 PMCID: PMC8600653 DOI: 10.1136/annrheumdis-2020-217840] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/27/2020] [Accepted: 08/30/2020] [Indexed: 02/03/2023]
Abstract
OBJECTIVE We sought to determine histologic and gene expression features of clinical improvement in early diffuse cutaneous systemic sclerosis (dcSSc; scleroderma). METHODS Fifty-eight forearm biopsies were evaluated from 26 individuals with dcSSc in two clinical trials. Histologic/immunophenotypic assessments of global severity, alpha-smooth muscle actin (aSMA), CD34, collagen, inflammatory infiltrate, follicles and thickness were compared with gene expression and clinical data. Support vector machine learning was performed using scleroderma gene expression subset (normal-like, fibroproliferative, inflammatory) as classifiers and histology scores as inputs. Comparison of w-vector mean absolute weights was used to identify histologic features most predictive of gene expression subset. We then tested for differential gene expression according to histologic severity and compared those with clinical improvement (according to the Combined Response Index in Systemic Sclerosis). RESULTS aSMA was highest and CD34 lowest in samples with highest local Modified Rodnan Skin Score. CD34 and aSMA changed significantly from baseline to 52 weeks in clinical improvers. CD34 and aSMA were the strongest predictors of gene expression subset, with highest CD34 staining in the normal-like subset (p<0.001) and highest aSMA staining in the inflammatory subset (p=0.016). Analysis of gene expression according to CD34 and aSMA binarised scores identified a 47-gene fibroblast polarisation signature that decreases over time only in improvers (vs non-improvers). Pathway analysis of these genes identified gene expression signatures of inflammatory fibroblasts. CONCLUSION CD34 and aSMA stains describe distinct fibroblast polarisation states, are associated with gene expression subsets and clinical assessments, and may be useful biomarkers of clinical severity and improvement in dcSSc.
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Affiliation(s)
- Kimberly Showalter
- Department of Medicine, Division of Rheumatology, Hospital for Special Surgery, New York, New York, USA
| | - Robert Spiera
- Department of Medicine, Division of Rheumatology, Hospital for Special Surgery, New York, New York, USA
| | - Cynthia Magro
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | - Viktor Martyanov
- Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
- Biomedical Data Science, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Jennifer M Franks
- Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
- Biomedical Data Science, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | | | | | - Tammara A Wood
- Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
- Biomedical Data Science, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Yaxia Zhang
- Department of Pathology, Hospital for Special Surgery, New York, New York, USA
| | - Caryn R Hale
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York, USA
| | - Jackie Finik
- Department of Medicine, Hospital for Special Surgery, New York, New York, USA
| | - Michael L Whitfield
- Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
- Biomedical Data Science, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Dana E Orange
- Department of Medicine, Division of Rheumatology, Hospital for Special Surgery, New York, New York, USA
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York, USA
| | - Jessica K Gordon
- Department of Medicine, Division of Rheumatology, Hospital for Special Surgery, New York, New York, USA
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Baker Frost D, da Silveira W, Hazard ES, Atanelishvili I, Wilson RC, Flume J, Day KL, Oates JC, Bogatkevich GS, Feghali-Bostwick C, Hardiman G, Ramos PS. Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis. Genes (Basel) 2021; 12:129. [PMID: 33498390 PMCID: PMC7909410 DOI: 10.3390/genes12020129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/20/2023] Open
Abstract
The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc and yet are underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal fibroblasts from patients of African ancestry. Reduced representation bisulfite sequencing (RRBS) was performed on primary dermal fibroblasts from 15 SSc patients and 15 controls of African ancestry, and over 3.8 million CpG sites were tested for differential methylation patterns between cases and controls. The dermal fibroblasts from African American patients exhibited widespread reduced DNA methylation. Differentially methylated CpG sites were most enriched in introns and intergenic regions while depleted in 5' UTR, promoters, and CpG islands. Seventeen genes and eleven promoters showed significant differential methylation, mostly in non-coding RNA genes and pseudogenes. Gene set enrichment analysis (GSEA) and gene ontology (GO) analyses revealed an enrichment of pathways related to interferon signaling and mesenchymal differentiation. The hypomethylation of DLX5 and TMEM140 was accompanied by these genes' overexpression in patients but underexpression for lncRNA MGC12916. These data show that differential methylation occurs in dermal fibroblasts from African American patients with SSc and identifies novel coding and non-coding genes.
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Affiliation(s)
- DeAnna Baker Frost
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Willian da Silveira
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK; (W.d.S.); (G.H.)
| | - E. Starr Hazard
- Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Ilia Atanelishvili
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Robert C. Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Jonathan Flume
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | | | - James C. Oates
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
- Rheumatology Section, Ralph H. Johnson VA Medical Center, Charleston, SC 29425, USA
| | - Galina S. Bogatkevich
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Carol Feghali-Bostwick
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Gary Hardiman
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK; (W.d.S.); (G.H.)
| | - Paula S. Ramos
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
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Herrick AL, Shukla R, Watson REB. Frontiers in translational systemic sclerosis research: A focus on the unmet 'cutaneous' clinical needs (Viewpoint). Exp Dermatol 2020; 29:1144-1153. [DOI: 10.1111/exd.14179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 08/06/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Ariane L. Herrick
- Division of Musculoskeletal and Dermatological Sciences Salford Royal NHS Foundation Trust Manchester Academic Health Science Centre The University of Manchester Manchester UK
| | | | - Rachel E. B. Watson
- Division of Musculoskeletal and Dermatological Sciences Salford Royal NHS Foundation Trust Manchester Academic Health Science Centre The University of Manchester Manchester UK
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Xu X, Ramanujam M, Visvanathan S, Assassi S, Liu Z, Li L. Transcriptional insights into pathogenesis of cutaneous systemic sclerosis using pathway driven meta-analysis assisted by machine learning methods. PLoS One 2020; 15:e0242863. [PMID: 33253326 PMCID: PMC7703909 DOI: 10.1371/journal.pone.0242863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022] Open
Abstract
Pathophysiology of systemic sclerosis (SSc, Scleroderma), an autoimmune rheumatic disease, comprises of mechanisms that drive vasculopathy, inflammation and fibrosis. Understanding of the disease and associated clinical heterogeneity has advanced considerably in the past decade, highlighting the necessity of more specific targeted therapy. While many of the recent trials in SSc failed to meet the primary end points that predominantly relied on changes in modified Rodnan skin scores (MRSS), sub-group analysis, especially those focused on the basal skin transcriptomic data have provided insights into patient subsets that respond to therapies. These findings suggest that deeper understanding of the molecular changes in pathways is very important to define disease drivers in various patient subgroups. In view of these challenges, we performed meta-analysis on 9 public available SSc microarray studies using a novel pathway pivoted approach combining consensus clustering and machine learning assisted feature selection. Selected pathway modules were further explored through cluster specific topological network analysis in search of novel therapeutic concepts. In addition, we went beyond previously described SSc class divisions of 3 clusters (e.g. inflammation, fibro-proliferative, normal-like) and expanded into a much finer stratification in order to profile SSc patients more accurately. Our analysis unveiled an important 80 pathway signatures that differentiated SSc patients into 8 unique subtypes. The 5 pathway modules derived from such signature successfully defined the 8 SSc subsets and were validated by in-silico cellular deconvolution analysis. Myeloid cells and fibroblasts involvement in different clusters were confirmed and linked to corresponding pathway activities. Collectively, our findings revealed more complex disease subtypes in SSc; Key gene mediators such as IL6, FGFR1, TLR7, PLCG2, IRK2 identified by network analysis underscored the scientific rationale for exploring additional targets in treatment of SSc.
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Affiliation(s)
- Xiao Xu
- Computational Biology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
| | - Meera Ramanujam
- Immunology and Respiratory Diseases Research, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
| | - Sudha Visvanathan
- Translational Medicine and Clinical Pharmacology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
| | - Shervin Assassi
- Division of Rheumatology, University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Zheng Liu
- Computational Biology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
| | - Li Li
- Computational Biology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
- * E-mail:
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40
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Stone RC, Chen V, Burgess J, Pannu S, Tomic-Canic M. Genomics of Human Fibrotic Diseases: Disordered Wound Healing Response. Int J Mol Sci 2020; 21:ijms21228590. [PMID: 33202590 PMCID: PMC7698326 DOI: 10.3390/ijms21228590] [Citation(s) in RCA: 12] [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: 09/24/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
Fibrotic disease, which is implicated in almost half of all deaths worldwide, is the result of an uncontrolled wound healing response to injury in which tissue is replaced by deposition of excess extracellular matrix, leading to fibrosis and loss of organ function. A plethora of genome-wide association studies, microarrays, exome sequencing studies, DNA methylation arrays, next-generation sequencing, and profiling of noncoding RNAs have been performed in patient-derived fibrotic tissue, with the shared goal of utilizing genomics to identify the transcriptional networks and biological pathways underlying the development of fibrotic diseases. In this review, we discuss fibrosing disorders of the skin, liver, kidney, lung, and heart, systematically (1) characterizing the initial acute injury that drives unresolved inflammation, (2) identifying genomic studies that have defined the pathologic gene changes leading to excess matrix deposition and fibrogenesis, and (3) summarizing therapies targeting pro-fibrotic genes and networks identified in the genomic studies. Ultimately, successful bench-to-bedside translation of observations from genomic studies will result in the development of novel anti-fibrotic therapeutics that improve functional quality of life for patients and decrease mortality from fibrotic diseases.
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Affiliation(s)
- Rivka C. Stone
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
- Correspondence: (R.C.S.); (M.T.-C.)
| | - Vivien Chen
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
| | - Jamie Burgess
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
- Medical Scientist Training Program in Biomedical Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sukhmani Pannu
- Department of Dermatology, Tufts Medical Center, Boston, MA 02116, USA;
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
- John P. Hussman Institute for Human Genomics, University of Miami-Miller School of Medicine, Miami, FL 33136, USA
- Correspondence: (R.C.S.); (M.T.-C.)
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Mehta BK, Espinoza ME, Hinchcliff M, Whitfield ML. Molecular "omic" signatures in systemic sclerosis. Eur J Rheumatol 2020; 7:S173-S180. [PMID: 33164732 DOI: 10.5152/eurjrheum.2020.19192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/05/2020] [Indexed: 01/15/2023] Open
Abstract
Systemic sclerosis (SSc) is a connective tissue disorder characterized by immunologic, vascular, and extracellular matrix abnormalities. Variation in the proportion and/or timing of activation in the deregulated molecular pathways that underlie SSc may explain the observed clinical heterogeneity in terms of disease phenotype and treatment response. In recent years, SSc research has generated massive amounts of "omics" level data. In this review, we discuss the body of "omics" level work in SSc and how each layer provides unique insight to our understanding of SSc. We posit that effective integration of genomic, transcriptomic, metagenomic, and epigenomic data is an important step toward precision medicine and is vital to the identification of effective therapeutic options for patients with SSc.
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Affiliation(s)
- Bhaven K Mehta
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Monica E Espinoza
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Monique Hinchcliff
- Department of Rheumatology, Allergy & Immunology, Yale School of Medicine, New Haven, CT, USA
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Dartmouth College, Hanover, NH, USA
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42
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Franks JM, Martyanov V, Wang Y, Wood TA, Pinckney A, Crofford LJ, Keyes-Elstein L, Furst DE, Goldmuntz E, Mayes MD, McSweeney P, Nash RA, Sullivan KM, Whitfield ML. Machine learning predicts stem cell transplant response in severe scleroderma. Ann Rheum Dis 2020; 79:1608-1615. [PMID: 32933919 DOI: 10.1136/annrheumdis-2020-217033] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVE The Scleroderma: Cyclophosphamide or Transplantation (SCOT) trial demonstrated clinical benefit of haematopoietic stem cell transplant (HSCT) compared with cyclophosphamide (CYC). We mapped PBC (peripheral blood cell) samples from the SCOT clinical trial to scleroderma intrinsic subsets and tested the hypothesis that they predict long-term response to HSCT. METHODS We analysed gene expression from PBCs of SCOT participants to identify differential treatment response. PBC gene expression data were generated from 63 SCOT participants at baseline and follow-up timepoints. Participants who completed treatment protocol were stratified by intrinsic gene expression subsets at baseline, evaluated for event-free survival (EFS) and analysed for differentially expressed genes (DEGs). RESULTS Participants from the fibroproliferative subset on HSCT experienced significant improvement in EFS compared with fibroproliferative participants on CYC (p=0.0091). In contrast, EFS did not significantly differ between CYC and HSCT arms for the participants from the normal-like subset (p=0.77) or the inflammatory subset (p=0.1). At each timepoint, we observed considerably more DEGs in HSCT arm compared with CYC arm with HSCT arm showing significant changes in immune response pathways. CONCLUSIONS Participants from the fibroproliferative subset showed the most significant long-term benefit from HSCT compared with CYC. This study suggests that intrinsic subset stratification of patients may be used to identify patients with SSc who receive significant benefit from HSCT.
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Affiliation(s)
- Jennifer M Franks
- Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA.,Biomedical Data Science, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Viktor Martyanov
- Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA.,Biomedical Data Science, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Yue Wang
- Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA.,Biomedical Data Science, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Tammara A Wood
- Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA.,Biomedical Data Science, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Ashley Pinckney
- Rho Federal Systems Division, Chapel Hill, North Carolina, USA
| | - Leslie J Crofford
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | | | - Daniel E Furst
- Department of Medicine, Division of Rheumatology, University of California at Los Angeles, Los Angeles, California, USA
| | | | - Maureen D Mayes
- Rheumatology and Clinical Immunogenetics, The University of Texas Health Science Center Houston Medical School, Houston, Texas, USA
| | - Peter McSweeney
- Rocky Mountain Blood and Marrow Transplant Program, Colorado Blood Cancer Institute, Denver, Colorado, USA
| | - Richard A Nash
- Rocky Mountain Blood and Marrow Transplant Program, Colorado Blood Cancer Institute, Denver, Colorado, USA
| | - Keith M Sullivan
- Duke University Medical Center, Durham, North Carolina, United States
| | - Michael L Whitfield
- Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA .,Biomedical Data Science, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
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43
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Wang Y, Franks JM, Yang M, Toledo DM, Wood TA, Hinchcliff M, Whitfield ML. Regulator combinations identify systemic sclerosis patients with more severe disease. JCI Insight 2020; 5:137567. [PMID: 32721949 PMCID: PMC7526449 DOI: 10.1172/jci.insight.137567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/22/2020] [Indexed: 11/17/2022] Open
Abstract
Systemic sclerosis (SSc) is a heterogeneous autoimmune disorder that results in skin fibrosis, autoantibody production, and internal organ dysfunction. We previously identified 4 “intrinsic” subsets of SSc based upon skin gene expression that are found across organ systems. Gene expression regulators that underlie the SSc-intrinsic subsets, or are associated with clinical covariates, have not been systematically characterized. Here, we present a computational framework to calculate the activity scores of gene expression regulators and identify their associations with SSc clinical outcomes. We found that regulator activity scores can reproduce the intrinsic molecular subsets, with distinct sets of regulators identified for inflammatory, fibroproliferative, limited, and normal-like samples. Regulators most highly correlated with modified Rodnan skin score (MRSS) also varied by intrinsic subset. We identified subgroups of patients with fibroproliferative and inflammatory SSc with more severe pathophenotypes, such as higher MRSS and increased likelihood of interstitial lung disease (ILD). Using an independent cohort, we show that the group with more severe ILD was more likely to show forced vital capacity decline over a period of 36–54 months. Our results demonstrate an association among the activation of regulators, gene expression subsets, and clinical variables that can identify patients with SSc with more severe disease. An association between the activation of regulators, gene expression subsets, and clinical variables identifies systemic sclerosis patients with more severe disease.
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Affiliation(s)
- Yue Wang
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Jennifer M Franks
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Monica Yang
- Department of Internal Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Diana M Toledo
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Tammara A Wood
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Monique Hinchcliff
- Department of Internal Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Yale School of Medicine, Section of Allergy, Rheumatology and Immunology, New Haven, Connecticut, USA
| | - Michael L Whitfield
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
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44
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Khan AQ, Ahmad F, Raza SS, Zarif L, Siveen KS, Sher G, Agha MV, Rashid K, Kulinski M, Buddenkotte J, Uddin S, Steinhoff M. Role of non-coding RNAs in the progression and resistance of cutaneous malignancies and autoimmune diseases. Semin Cancer Biol 2020; 83:208-226. [PMID: 32717336 DOI: 10.1016/j.semcancer.2020.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/28/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
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Abstract
PURPOSE OF REVIEW Macrophages are key players in systemic sclerosis (SSc) and fibrosis. The mechanism by which macrophages regulate fibrogenesis is unclear and understanding the origin and function of macrophages is critical to developing effective therapeutics. Novel targets on macrophages are under investigation and recently, cadherins have emerged as a potential therapeutic target on macrophages. The current review will discuss the importance of macrophages in SSc and fibrosis and summarize recent studies on the role of cadherin-11 (Cdh11) on macrophages and fibrosis. RECENT FINDINGS Genome-wide expression studies demonstrate the importance of macrophages in SSc and fibrosis. Although M2 macrophages are associated with fibrosis, the presence of a mixed M1/M2 phenotype in fibrosis has recently been reported. Several studies aiming to identify macrophage subsets involved in fibrogenesis suggest that monocyte-derived alveolar macrophages are key players in the development of murine lung fibrosis. Recent functional studies show that Cdh11 regulates macrophages, fibroblast invasion, and adhesion of macrophages to myofibroblasts. SUMMARY Macrophages play an important role in SSc and fibrosis. New insights into the mechanisms by which macrophages regulate fibrogenesis have been discovered on the basis of Cdh11 studies and suggest that targeting Cdh11 may be an effective target to treat fibrosis.
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Pradines JR, Farutin V, Cilfone NA, Ghavami A, Kurtagic E, Guess J, Manning AM, Capila I. Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein. PLoS Comput Biol 2020; 16:e1007684. [PMID: 32058996 PMCID: PMC7046299 DOI: 10.1371/journal.pcbi.1007684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 02/27/2020] [Accepted: 01/27/2020] [Indexed: 12/27/2022] Open
Abstract
Identification of differentially expressed genes (DEGs) is well recognized to be variable across independent replications of genome-wide transcriptional studies. These are often employed to characterize disease state early in the process of discovery and prioritize novel targets aimed at addressing unmet medical need. Increasing reproducibility of biological findings from these studies could potentially positively impact the success rate of new clinical interventions. This work demonstrates that statistically sound combination of gene expression data with prior knowledge about biology in the form of large protein interaction networks can yield quantitatively more reproducible observations from studies characterizing human disease. The novel concept of Well-Associated Proteins (WAPs) introduced herein-gene products significantly associated on protein interaction networks with the differences in transcript levels between control and disease-does not require choosing a differential expression threshold and can be computed efficiently enough to enable false discovery rate estimation via permutation. Reproducibility of WAPs is shown to be on average superior to that of DEGs under easily-quantifiable conditions suggesting that they can yield a significantly more robust description of disease. Enhanced reproducibility of WAPs versus DEGs is first demonstrated with four independent data sets focused on systemic sclerosis. This finding is then validated over thousands of pairs of data sets obtained by random partitions of large studies in several other diseases. Conditions that individual data sets must satisfy to yield robust WAP scores are examined. Reproducible identification of WAPs can potentially benefit drug target selection and precision medicine studies.
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Affiliation(s)
- Joël R. Pradines
- Momenta Pharmaceuticals, 301 Binney Street, Cambridge, Massachusetts, United States of America
| | - Victor Farutin
- Momenta Pharmaceuticals, 301 Binney Street, Cambridge, Massachusetts, United States of America
- * E-mail: (VF); (IC)
| | - Nicholas A. Cilfone
- Momenta Pharmaceuticals, 301 Binney Street, Cambridge, Massachusetts, United States of America
| | - Abouzar Ghavami
- Momenta Pharmaceuticals, 301 Binney Street, Cambridge, Massachusetts, United States of America
| | - Elma Kurtagic
- Momenta Pharmaceuticals, 301 Binney Street, Cambridge, Massachusetts, United States of America
| | - Jamey Guess
- Momenta Pharmaceuticals, 301 Binney Street, Cambridge, Massachusetts, United States of America
| | - Anthony M. Manning
- Momenta Pharmaceuticals, 301 Binney Street, Cambridge, Massachusetts, United States of America
| | - Ishan Capila
- Momenta Pharmaceuticals, 301 Binney Street, Cambridge, Massachusetts, United States of America
- * E-mail: (VF); (IC)
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Galant C, Marchandise J, Stoenoiu MS, Ducreux J, De Groof A, Pirenne S, Van den Eynde B, Houssiau FA, Lauwerys BR. Overexpression of ubiquitin-specific peptidase 15 in systemic sclerosis fibroblasts increases response to transforming growth factor β. Rheumatology (Oxford) 2020; 58:708-718. [PMID: 30608617 PMCID: PMC6434377 DOI: 10.1093/rheumatology/key401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/03/2018] [Indexed: 12/18/2022] Open
Abstract
Objective Ubiquitination of proteins leads to their degradation by the proteasome, and is regulated by ubiquitin ligases and substrate-specific ubiquitin-specific peptidases (USPs). The ubiquitination process also plays important roles in the regulation of cell metabolism and cell cycle. Here, we found that the expression of several USPs is increased in SSc tenosynovial and skin biopsies, and we demonstrated that USP inhibition decreases TGF-β signalling in primary fibroblast cell lines. Methods High-density transcriptomic studies were performed using total RNA obtained from SSc tenosynovial samples. Confirmatory immunostaining experiments were performed on tenosynovial and skin samples. In vitro experiments were conducted in order to study the influence of USP modulation on responses to TGF-β stimulation. Results Tenosynovial biopsies from SSc patients overexpressed known disease-associated gene pathways: fibrosis, cytokines and chemokines, and Wnt/TGF-β signalling, but also several USPs. Immunohistochemistry experiments confirmed the detection of USPs in the same samples, and in SSc skin biopsies. Exposure of primary fibroblast cell lines to TGF-β induced USP gene expression. The use of a pan-USP inhibitor decreased SMAD3 phosphorylation, and expression of COL1A1, COL3A1 and fibronectin gene expression in TGF-β-stimulated fibroblasts. The effect of the USP inhibitor resulted in increased SMAD3 ubiquitination, and was blocked by a proteasome inhibitor, thereby confirming the specificity of its action. Conclusion Overexpression of several USPs, including USP15, amplifies fibrotic responses induced by TGF-β, and is a potential therapeutic target in SSc.
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Affiliation(s)
- Christine Galant
- Pôle de Pathologies Rhumatismales Inflammatoires et Systémiques, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Belgium.,Department of Pathology, Cliniques Universitaires Saint-Luc, Belgium
| | - Joel Marchandise
- Pôle de Pathologies Rhumatismales Inflammatoires et Systémiques, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Belgium.,Department of Pathology, Cliniques Universitaires Saint-Luc, Belgium
| | - Maria S Stoenoiu
- Pôle de Pathologies Rhumatismales Inflammatoires et Systémiques, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Belgium.,Department of Rheumatology, Cliniques Universitaires Saint-Luc, Belgium
| | - Julie Ducreux
- Pôle de Pathologies Rhumatismales Inflammatoires et Systémiques, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Belgium
| | - Aurélie De Groof
- Pôle de Pathologies Rhumatismales Inflammatoires et Systémiques, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Belgium
| | - Sophie Pirenne
- Department of Pathology, Cliniques Universitaires Saint-Luc, Belgium
| | - Benoit Van den Eynde
- Institut de Duve, Department of Cancer Immunology and Immunotherapy, Université catholique de Louvain, Brussels, Belgium
| | - Frédéric A Houssiau
- Pôle de Pathologies Rhumatismales Inflammatoires et Systémiques, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Belgium.,Department of Rheumatology, Cliniques Universitaires Saint-Luc, Belgium
| | - Bernard R Lauwerys
- Pôle de Pathologies Rhumatismales Inflammatoires et Systémiques, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Belgium.,Department of Rheumatology, Cliniques Universitaires Saint-Luc, Belgium
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Karimizadeh E, Sharifi-Zarchi A, Nikaein H, Salehi S, Salamatian B, Elmi N, Gharibdoost F, Mahmoudi M. Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis. BMC Med Genomics 2019; 12:199. [PMID: 31881890 PMCID: PMC6935135 DOI: 10.1186/s12920-019-0632-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background Systemic sclerosis (SSc), a multi-organ disorder, is characterized by vascular abnormalities, dysregulation of the immune system, and fibrosis. The mechanisms underlying tissue pathology in SSc have not been entirely understood. This study intended to investigate the common and tissue-specific pathways involved in different tissues of SSc patients. Methods An integrative gene expression analysis of ten independent microarray datasets of three tissues was conducted to identify differentially expressed genes (DEGs). DEGs were mapped to the search tool for retrieval of interacting genes (STRING) to acquire protein–protein interaction (PPI) networks. Then, functional clusters in PPI networks were determined. Enrichr, a gene list enrichment analysis tool, was utilized for the functional enrichment of clusters. Results A total of 12, 2, and 4 functional clusters from 619, 52, and 119 DEGs were determined in the lung, peripheral blood mononuclear cell (PBMC), and skin tissues, respectively. Analysis revealed that the tumor necrosis factor (TNF) signaling pathway was enriched significantly in the three investigated tissues as a common pathway. In addition, clusters associated with inflammation and immunity were common in the three investigated tissues. However, clusters related to the fibrosis process were common in lung and skin tissues. Conclusions Analysis indicated that there were common pathological clusters that contributed to the pathogenesis of SSc in different tissues. Moreover, it seems that the common pathways in distinct tissues stem from a diverse set of genes.
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Affiliation(s)
- Elham Karimizadeh
- Rheumatology Research Center, Tehran University of Medical Sciences Shariati Hospital, Kargar Ave, P.O. BOX 1411713137, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Azadi Ave, P.O. BOX 11365-11155, Tehran, Iran.
| | - Hassan Nikaein
- Department of Computer Engineering, Sharif University of Technology, Azadi Ave, P.O. BOX 11365-11155, Tehran, Iran
| | - Seyedehsaba Salehi
- Department of Mathematical Sciences, Sharif University of Technology, Tehran, Iran
| | - Bahar Salamatian
- Department of Mathematical Sciences, Sharif University of Technology, Tehran, Iran
| | - Naser Elmi
- Rheumatology Research Center, Tehran University of Medical Sciences Shariati Hospital, Kargar Ave, P.O. BOX 1411713137, Tehran, Iran
| | - Farhad Gharibdoost
- Rheumatology Research Center, Tehran University of Medical Sciences Shariati Hospital, Kargar Ave, P.O. BOX 1411713137, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences Shariati Hospital, Kargar Ave, P.O. BOX 1411713137, Tehran, Iran. .,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Skaug B, Khanna D, Swindell WR, Hinchcliff ME, Frech TM, Steen VD, Hant FN, Gordon JK, Shah AA, Zhu L, Zheng WJ, Browning JL, Barron AMS, Wu M, Visvanathan S, Baum P, Franks JM, Whitfield ML, Shanmugam VK, Domsic RT, Castelino FV, Bernstein EJ, Wareing N, Lyons MA, Ying J, Charles J, Mayes MD, Assassi S. Global skin gene expression analysis of early diffuse cutaneous systemic sclerosis shows a prominent innate and adaptive inflammatory profile. Ann Rheum Dis 2019; 79:379-386. [PMID: 31767698 DOI: 10.1136/annrheumdis-2019-215894] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 01/01/2023]
Abstract
OBJECTIVES Determine global skin transcriptome patterns of early diffuse systemic sclerosis (SSc) and how they differ from later disease. METHODS Skin biopsy RNA from 48 patients in the Prospective Registry for Early Systemic Sclerosis (PRESS) cohort (mean disease duration 1.3 years) and 33 matched healthy controls was examined by next-generation RNA sequencing. Data were analysed for cell type-specific signatures and compared with similarly obtained data from 55 previously biopsied patients in Genetics versus Environment in Scleroderma Outcomes Study cohort with longer disease duration (mean 7.4 years) and their matched controls. Correlations with histological features and clinical course were also evaluated. RESULTS SSc patients in PRESS had a high prevalence of M2 (96%) and M1 (94%) macrophage and CD8 T cell (65%), CD4 T cell (60%) and B cell (69%) signatures. Immunohistochemical staining of immune cell markers correlated with the gene expression-based immune cell signatures. The prevalence of immune cell signatures in early diffuse SSc patients was higher than in patients with longer disease duration. In the multivariable model, adaptive immune cell signatures were significantly associated with shorter disease duration, while fibroblast and macrophage cell type signatures were associated with higher modified Rodnan Skin Score (mRSS). Immune cell signatures also correlated with skin thickness progression rate prior to biopsy, but did not predict subsequent mRSS progression. CONCLUSIONS Skin in early diffuse SSc has prominent innate and adaptive immune cell signatures. As a prominently affected end organ, these signatures reflect the preceding rate of disease progression. These findings could have implications in understanding SSc pathogenesis and clinical trial design.
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Affiliation(s)
- Brian Skaug
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Dinesh Khanna
- Scleroderma Program, Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, Michigan, USA
| | - William R Swindell
- Ohio University Heritage College of Osteopathic Medicine, Athens, Ohio, USA.,Department of Internal Medicine, The Jewish Hospital, Cincinnati, Ohio, USA
| | - Monique E Hinchcliff
- Department of Medicine, Section of Allergy, Rheumatology, and Immunology, Yale University, New Haven, Connecticut, USA
| | - Tracy M Frech
- Division of Rheumatology, Department of Internal Medicine, University of Utah and Salt Lake Regional Veterans Affairs Medical Center, Salt Lake City, Utah, USA
| | - Virginia D Steen
- Division of Rheumatology, Department of Medicine, MedStar Georgetown University Hospital, Washington, DC, USA
| | - Faye N Hant
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Jessica K Gordon
- Department of Rheumatology, Hospital for Special Surgery, New York City, New York, USA
| | - Ami A Shah
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lisha Zhu
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - W Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jeffrey L Browning
- Department of Microbiology, Section of Rheumatology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Alexander M S Barron
- Department of Microbiology, Section of Rheumatology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Minghua Wu
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Sudha Visvanathan
- Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, Connecticut, USA
| | - Patrick Baum
- Boehringer Ingelheim International GmbH, Biberach, Germany
| | - Jennifer M Franks
- Department of Biomedical Data Science, Dartmouth College Geisel School of Medicine, Lebanon, New Hampshire, USA.,Department of Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Michael L Whitfield
- Department of Biomedical Data Science, Dartmouth College Geisel School of Medicine, Lebanon, New Hampshire, USA.,Department of Molecular and Systems Biology, Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Victoria K Shanmugam
- Division of Rheumatology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Robyn T Domsic
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Flavia V Castelino
- Division of Rheumatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Elana J Bernstein
- Division of Rheumatology, Vagelos College of Physicians and Surgeons, New York City, New York, USA
| | - Nancy Wareing
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Marka A Lyons
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jun Ying
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Julio Charles
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Maureen D Mayes
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Shervin Assassi
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
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50
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Recent advances steer the future of systemic sclerosis toward precision medicine. Clin Rheumatol 2019; 39:1-4. [PMID: 31760537 DOI: 10.1007/s10067-019-04834-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
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