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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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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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Johnson SR, Foeldvari I. Approach to Systemic Sclerosis Patient Assessment. Rheum Dis Clin North Am 2023; 49:193-210. [PMID: 37028831 DOI: 10.1016/j.rdc.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Systemic sclerosis (SSc) is a heterogeneous disease comprising of a wide spectrum of ages of onset, sex-based differences, ethnic variations, disease manifestations, differential serologic profiles, and variable response to therapy resulting in reduced health-related quality of life, disability, and survival. The ability to subset groups of patients with SSc can assist with refining the diagnosis, guide appropriate monitoring, inform aggressiveness of immunosuppression, and predict prognosis. The ability to subset patients with SSc has several important practical implications for patient care.
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Mlakar L, Garrett SM, Watanabe T, Sanderson M, Nishimoto T, Heywood J, Helke KL, Pilewski JM, Herzog EL, Feghali-Bostwick C. Ameliorating Fibrosis in Murine and Human Tissues with END55, an Endostatin-Derived Fusion Protein Made in Plants. Biomedicines 2022; 10:2861. [PMID: 36359382 PMCID: PMC9687961 DOI: 10.3390/biomedicines10112861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Organ fibrosis, particularly of the lungs, causes significant morbidity and mortality. Effective treatments are needed to reduce the health burden. A fragment of the carboxyl-terminal end of collagen XVIII/endostatin reduces skin and lung fibrosis. This fragment was modified to facilitate its production in plants, which resulted in the recombinant fusion protein, END55. We found that expression of END55 had significant anti-fibrotic effects on the treatment and prevention of skin and lung fibrosis in a bleomycin mouse model. We validated these effects in a second mouse model of pulmonary fibrosis involving inducible, lung-targeted expression of transforming growth factor β1. END55 also exerted anti-fibrotic effects in human lung and skin tissues maintained in organ culture in which fibrosis was experimentally induced. The anti-fibrotic effect of END55 was mediated by a decrease in the expression of extracellular matrix genes and an increase in the levels of matrix-degrading enzymes. Finally, END55 reduced fibrosis in the lungs of patients with systemic sclerosis (SSc) and idiopathic pulmonary fibrosis (IPF) who underwent lung transplantation due to the severity of their lung disease, displaying efficacy in human tissues directly relevant to human disease. These findings demonstrate that END55 is an effective anti-fibrotic therapy in different organs.
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Affiliation(s)
- Logan Mlakar
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sara M. Garrett
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Tomoya Watanabe
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Matthew Sanderson
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Tetsuya Nishimoto
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Jonathan Heywood
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Kristi L. Helke
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Joseph M. Pilewski
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Erica L. Herzog
- Yale ILD Center of Excellence, Department of Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Carol Feghali-Bostwick
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
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5
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Hinchcliff M, Garcia-Milian R, Di Donato S, Dill K, Bundschuh E, Galdo FD. Cellular and Molecular Diversity in Scleroderma. Semin Immunol 2021; 58:101648. [PMID: 35940960 DOI: 10.1016/j.smim.2022.101648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the increasing armamentarium of high-throughput tools available at manageable cost, it is attractive and informative to determine the molecular underpinnings of patient heterogeneity in systemic sclerosis (SSc). Given the highly variable clinical outcomes of patients labelled with the same diagnosis, unravelling the cellular and molecular basis of disease heterogeneity will be crucial to predicting disease risk, stratifying management and ultimately informing a patient-centered precision medicine approach. Herein, we summarise the findings of the past several years in the fields of genomics, transcriptomics, and proteomics that contribute to unraveling the cellular and molecular heterogeneity of SSc. Expansion of these findings and their routine integration with quantitative analysis of histopathology and imaging studies into clinical care promise to inform a scientifically driven patient-centred personalized medicine approach to SSc in the near future.
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Affiliation(s)
- Monique Hinchcliff
- Yale School of Medicine, Department of Internal Medicine, Section of Rheumatology, Allergy & Immunology, USA.
| | | | - Stefano Di Donato
- Raynaud's and Scleroderma Programme, Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Biomedical Research Centre, University of Leeds, UK
| | | | - Elizabeth Bundschuh
- Yale School of Medicine, Department of Internal Medicine, Section of Rheumatology, Allergy & Immunology, USA
| | - Francesco Del Galdo
- Raynaud's and Scleroderma Programme, Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Biomedical Research Centre, University of Leeds, UK.
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6
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Leong E, Bezuhly M, Marshall JS. Distinct Metalloproteinase Expression and Functions in Systemic Sclerosis and Fibrosis: What We Know and the Potential for Intervention. Front Physiol 2021; 12:727451. [PMID: 34512395 PMCID: PMC8432940 DOI: 10.3389/fphys.2021.727451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic sclerosis (SSc) is a chronic debilitating idiopathic disorder, characterized by deposition of excessive extracellular matrix (ECM) proteins such as collagen which leads to fibrosis of the skin and other internal organs. During normal tissue repair and remodeling, the accumulation and turnover of ECM proteins are tightly regulated by the interaction of matrix metalloproteinases (MMPs) and endogenous tissue inhibitors of metalloproteinases (TIMPs). SSc is associated with dysregulation of the activity of these proteolytic and inhibitory proteins within the tissue microenvironment, tipping the balance toward fibrosis. The resultant ECM accumulation further perpetuates tissue stiffness and decreased function, contributing to poor clinical outcomes. Understanding the expression and function of these endogenous enzymes and inhibitors within specific tissues is therefore critical to the development of therapies for SSc. This brief review describes recent advances in our understanding of the functions and mechanisms of ECM remodeling by metalloproteinases and their inhibitors in the skin and lungs affected in SSc. It highlights recent progress on potential candidates for intervention and therapeutic approaches for treating SSc fibrosis.
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Affiliation(s)
- Edwin Leong
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Michael Bezuhly
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.,Department of Surgery, Dalhousie University, Halifax, NS, Canada
| | - Jean S Marshall
- Department of Pathology, Dalhousie University, Halifax, NS, Canada.,Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
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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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8
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Lansiaux P, Loisel S, Castilla-Llorente C, Fontenille C, Kabdani S, Marjanovic Z, Pugnet G, Puyade M, Robert E, Terriou L, Ait Abdallah N, Maria ATJ, Michel L, Tréton X, Yakoub-Agha I, Farge D. [Autologous hematopoietic cells for severe autoimmune diseases: Guidelines of the Francophone Society of Bone Marrow Transplantation and Cellular Therapy (SFGM-TC) for immune monitoring and biobanking]. Bull Cancer 2021; 108:S72-S81. [PMID: 34272057 DOI: 10.1016/j.bulcan.2021.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/29/2022]
Abstract
Autologous hematopoietic cell transplantation (AHCT) is a new treatment option for patients with severe autoimmune diseases (AD), based on the use of intensive or myeloablative chemotherapy to eradicate the pathogenic autoreactive immune cells and to allow the installation of a new and tolerant immune system during immune reconstitution process. Immune reconstitution analysis after AHCT is required for patients clinical follow-up and to further identify biological and immunological markers of the clinical response to develop individualized AHCT protocols. These MATHEC-SFGM-TC good clinical practice guidelines were developed by a multidisciplinary group of experts including members of the french reference center for stem Cell Therapy in Auto-immune Diseases (MATHEC), hematologists from the French speaking Society of Bone Marrow Transplantation and Cellular Therapy (SFGM-TC) and experts in immune monitoring and biobanking. The objectives are to provide practical recommandations for immune monitoring and biobanking of samples in patients with AD undergoing AHCT, for routine care purposes and investigational studies.
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Affiliation(s)
- Pauline Lansiaux
- AP-HP, hôpital Saint-Louis, unité de médecine interne (UF 04): CRMR MATHEC, Maladies auto-immunes et thérapie cellulaire, Centre de Référence des Maladies auto-immunes systémiques Rares d'Ile-de-France MATHEC (FAI2R), 75010 Paris, France; Université de Paris, Institut de recherche Saint-Louis, recherche clinique appliquée à l'hématologie, EA3518, 75010 Paris, France
| | - Séverine Loisel
- CHU de Rennes, établissement français du sang Bretagne, SITI, 35000 Rennes, France
| | - Cristina Castilla-Llorente
- Gustave-Roussy Cancer Center, département d'hématologie, 114, rue Edouard-Vaillant, 94800 Villejuif, France
| | - Claire Fontenille
- Institut Paoli-Calmettes, Association CRYOSTEM, 13009 Marseille, France
| | - Sarah Kabdani
- EFS HFNO site de Lille, unité de thérapie cellulaire, parc Eurasanté, 20, avenue Pierre-Mauroy, 59373 Loos, France
| | - Zora Marjanovic
- AP-HP, hôpital Saint-Antoine, service d'hématologie, 184, rue du Faubourg Saint-Antoine, 75012 Paris, France
| | - Grégory Pugnet
- CHU de Rangueil, service de médecine interne et immunologie clinique, 1, avenue du Professeur Jean-Poulhès, 31059 Toulouse cedex 9, France
| | - Mathieu Puyade
- CHU de Poitiers, service de médecine interne, 2, rue de la Miletrie, 86021 Poitiers, France; CHU de Poitiers, CIC-1402, 2, rue de la Miletrie, 86021 Poitiers, France
| | - Emilie Robert
- Institut Paoli-Calmettes, Association CRYOSTEM, 13009 Marseille, France
| | - Louis Terriou
- Hôpital Claude-Huriez, CHRU Lille, service de médecine interne et immunologie clinique, rue Michel-Polonovski, 59000 Lille, France
| | - Nassim Ait Abdallah
- AP-HP, hôpital Saint-Louis, unité de médecine interne (UF 04): CRMR MATHEC, Maladies auto-immunes et thérapie cellulaire, Centre de Référence des Maladies auto-immunes systémiques Rares d'Ile-de-France MATHEC (FAI2R), 75010 Paris, France; Université de Paris, Institut de recherche Saint-Louis, recherche clinique appliquée à l'hématologie, EA3518, 75010 Paris, France
| | - Alexandre Thibault Jacques Maria
- CHRU de Montpellier, hôpital Saint-Éloi, médecine interne : maladies multi-organiques de l'adulte, Inserm U1183 IRMB, 34295 Montpellier cedex 5, France
| | - Laure Michel
- CHU de Rennes, seervice de neurologie, Rennes, France
| | - Xavier Tréton
- Hôpital Beaujon, université de Paris, service de gastro-entérologie, MICI et Assistance Nutritive, DMU DIGEST, 100, boulevard Leclerc, 92110 Clichy, France
| | | | - Dominique Farge
- AP-HP, hôpital Saint-Louis, unité de médecine interne (UF 04): CRMR MATHEC, Maladies auto-immunes et thérapie cellulaire, Centre de Référence des Maladies auto-immunes systémiques Rares d'Ile-de-France MATHEC (FAI2R), 75010 Paris, France; Université de Paris, Institut de recherche Saint-Louis, recherche clinique appliquée à l'hématologie, EA3518, 75010 Paris, France; McGill University, Department of Medicine, H3A 1A1, Montreal, Canada.
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Zhang Y, Michelakis ED. A Phase-2 NIH-sponsored Randomized Clinical Trial of Rituximab in Scleroderma-associated Pulmonary Arterial Hypertension Did Not Reach Significance for Its Endpoints: End of Story? Not So Fast! Am J Respir Crit Care Med 2021; 204:123-125. [PMID: 33856964 PMCID: PMC8650784 DOI: 10.1164/rccm.202103-0612ed] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Yongneng Zhang
- Department of Medicine University of Alberta Edmonton, Alberta, Canada
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Genetic Interactions Affect Lung Function in Patients with Systemic Sclerosis. G3-GENES GENOMES GENETICS 2020; 10:151-163. [PMID: 31694854 PMCID: PMC6945038 DOI: 10.1534/g3.119.400775] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Scleroderma, or systemic sclerosis (SSc), is an autoimmune disease characterized by progressive fibrosis of the skin and internal organs. The most common cause of death in people with SSc is lung disease, but the pathogenesis of lung disease in SSc is insufficiently understood to devise specific treatment strategies. Developing targeted treatments requires not only the identification of molecular processes involved in SSc-associated lung disease, but also understanding of how these processes interact to drive pathology. One potentially powerful approach is to identify alleles that interact genetically to influence lung outcomes in patients with SSc. Analysis of interactions, rather than individual allele effects, has the potential to delineate molecular interactions that are important in SSc-related lung pathology. However, detecting genetic interactions, or epistasis, in human cohorts is challenging. Large numbers of variants with low minor allele frequencies, paired with heterogeneous disease presentation, reduce power to detect epistasis. Here we present an analysis that increases power to detect epistasis in human genome-wide association studies (GWAS). We tested for genetic interactions influencing lung function and autoantibody status in a cohort of 416 SSc patients. Using Matrix Epistasis to filter SNPs followed by the Combined Analysis of Pleiotropy and Epistasis (CAPE), we identified a network of interacting alleles influencing lung function in patients with SSc. In particular, we identified a three-gene network comprising WNT5A, RBMS3, and MSI2, which in combination influenced multiple pulmonary pathology measures. The associations of these genes with lung outcomes in SSc are novel and high-confidence. Furthermore, gene coexpression analysis suggested that the interactions we identified are tissue-specific, thus differentiating SSc-related pathogenic processes in lung from those in skin.
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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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12
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Winthrop KL, Weinblatt ME, Bathon J, Burmester GR, Mease PJ, Crofford L, Bykerk V, Dougados M, Rosenbaum JT, Mariette X, Sieper J, Melchers F, Cronstein BN, Breedveld FC, Kalden J, Smolen JS, Furst D. Unmet need in rheumatology: reports from the Targeted Therapies meeting 2019. Ann Rheum Dis 2019; 79:88-93. [PMID: 31662322 PMCID: PMC6937409 DOI: 10.1136/annrheumdis-2019-216151] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/04/2019] [Indexed: 12/30/2022]
Abstract
Objectives To detail the greatest areas of unmet scientific and clinical needs in rheumatology. Methods The 21st annual international Advances in Targeted Therapies meeting brought together more than 100 leading basic scientists and clinical researchers in rheumatology, immunology, epidemiology, molecular biology and other specialties. During the meeting, breakout sessions were convened, consisting of 5 disease-specific groups with 20–30 experts assigned to each group based on expertise. Specific groups included: rheumatoid arthritis, psoriatic arthritis, axial spondyloarthritis, systemic lupus erythematosus and other systemic autoimmune rheumatic diseases. In each group, experts were asked to identify unmet clinical and translational research needs in general and then to prioritise and detail the most important specific needs within each disease area. Results Overarching themes across all disease states included the need to innovate clinical trial design with emphasis on studying patients with refractory disease, the development of trials that take into account disease endotypes and patients with overlapping inflammatory diseases, the need to better understand the prevalence and incidence of inflammatory diseases in developing regions of the world and ultimately to develop therapies that can cure inflammatory autoimmune diseases. Conclusions Unmet needs for new therapies and trial designs, particularly for those with treatment refractory disease, remain a top priority in rheumatology.
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Affiliation(s)
| | | | - Joan Bathon
- Columbia University, College of Physicians & Surgeons, New York City, New York, USA
| | | | - Philip J Mease
- Swedish Medical Center, University of Washington, Seattle, Washington, USA
| | | | - Vivian Bykerk
- Hospital for Special Surgery, New York City, New York, USA
| | | | - James Todd Rosenbaum
- Oregon Health Sciences University, Portland, Oregon, USA.,Legacy Devers Eye Institute, Portland, Oregon, USA
| | - Xavier Mariette
- Paris-Sud University, APHP Université Paris-Saclay, Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Joachim Sieper
- Department of Gastroenterology, Infectious Diseases and Rheumatology, Campus Benjamin Franklin, Charité, Berlin, Germany
| | - Fritz Melchers
- Max Planck Institute for Infection Biology, Berlin, Germany
| | | | | | | | - Josef S Smolen
- Division of Rheumatology, Department of Medicine 3, Medical University of, Vienna, Vienna, Austria
| | - Daniel Furst
- Swedish Medical Center, University of Washington, Seattle, Washington, USA.,University of California, Los Angeles Medical Center, Los Angeles, CA, USA.,University of Florence, Florence, Italy
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13
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Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis. BMC Med Genomics 2019; 12:144. [PMID: 31651337 PMCID: PMC6813992 DOI: 10.1186/s12920-019-0602-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/11/2019] [Indexed: 12/24/2022] Open
Abstract
Background Systemic sclerosis (SSc) is a rare autoimmune connective tissue disease whose pathogenesis remains incompletely understood. Increasing evidence suggests that both genetic susceptibilities and changes in DNA methylation influence pivotal biological pathways and thereby contribute to the disease. The role of DNA methylation in SSc has not been fully elucidated, because existing investigations of DNA methylation predominantly focused on nucleotide CpGs within restricted genic regions, and were performed on samples containing mixed cell types. Methods We performed whole-genome bisulfite sequencing on purified CD4+ T lymphocytes from nine SSc patients and nine controls in a pilot study, and then profiled genome-wide cytosine methylation as well as genetic variations. We adopted robust statistical methods to identify differentially methylated genomic regions (DMRs). We then examined pathway enrichment associated with genes located in these DMRs. We also tested whether changes in CpG methylation were associated with adjacent genetic variation. Results We profiled DNA methylation at more than three million CpG dinucleotides genome-wide. We identified 599 DMRs associated with 340 genes, among which 54 genes exhibited further associations with adjacent genetic variation. We also found these genes were associated with pathways and functions that are known to be abnormal in SSc, including Wnt/β-catenin signaling pathway, skin lesion formation and progression, and angiogenesis. Conclusion The CD4+ T cell DNA cytosine methylation landscape in SSc involves crucial genes in disease pathogenesis. Some of the methylation patterns are also associated with genetic variation. These findings provide essential foundations for future studies of epigenetic regulation and genome-epigenome interaction in SSc.
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14
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Moon SJ, Bae JM, Park KS, Tagkopoulos I, Kim KJ. Compendium of skin molecular signatures identifies key pathological features associated with fibrosis in systemic sclerosis. Ann Rheum Dis 2019; 78:817-825. [DOI: 10.1136/annrheumdis-2018-214778] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/26/2019] [Accepted: 03/23/2019] [Indexed: 01/02/2023]
Abstract
ObjectivesTreatment of patients with systemic sclerosis (SSc) can be challenging because of clinical heterogeneity. Integration of genome-scale transcriptomic profiling for patients with SSc can provide insights on patient categorisation and novel drug targets.MethodsA normalised compendium was created from 344 skin samples of 173 patients with SSc, covering an intersection of 17 424 genes from eight data sets. Differentially expressed genes (DEGs) identified by three independent methods were subjected to functional network analysis, where samples were grouped using non-negative matrix factorisation. Finally, we investigated the pathways and biomarkers associated with skin fibrosis using gene-set enrichment analysis.ResultsWe identified 1089 upregulated DEGs, including 14 known genetic risk factors and five potential drug targets. Pathway-based subgrouping revealed four distinct clusters of patients with SSc with distinct activity signatures for SSc-relevant pathways. The inflammatory subtype was related to significant improvement in skin fibrosis at follow-up. The phosphoinositide-3-kinase-protein kinase B (PI3K-Akt) signalling pathway showed both the closest correlation and temporal pattern to skin fibrosis score. COMP, THBS1, THBS4, FN1, and TNC were leading-edge genes of the PI3K-Akt pathway in skin fibrogenesis.ConclusionsConstruction and analysis of normalised skin transcriptomic compendia can provide useful insights on pathway involvement by SSc subsets and discovering viable biomarkers for a skin fibrosis index. Particularly, the PI3K-Akt pathway and its leading players are promising therapeutic targets.
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15
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Rezaei R, Aslani S, Dashti N, Jamshidi A, Gharibdoost F, Mahmoudi M. Genetic implications in the pathogenesis of systemic sclerosis. Int J Rheum Dis 2018; 21:1478-1486. [DOI: 10.1111/1756-185x.13344] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ramazan Rezaei
- Rheumatology Research Center Tehran University of Medical Sciences Tehran Iran
- Department of Immunology School of Medicine Shahid Beheshti University of Medical Sciences Tehran Iran
| | - Saeed Aslani
- Rheumatology Research Center Tehran University of Medical Sciences Tehran Iran
| | - Navid Dashti
- Rheumatology Research Center Tehran University of Medical Sciences Tehran Iran
- Department of Immunology School of Medicine Tehran University of Medical Sciences Tehran Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center Tehran University of Medical Sciences Tehran Iran
| | - Farhad Gharibdoost
- Rheumatology Research Center Tehran University of Medical Sciences Tehran Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center Tehran University of Medical Sciences Tehran Iran
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16
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Çildağ S, Kara Y, Şentürk T. ABO blood groups and rheumatic diseases. Eur J Rheumatol 2017; 4:250-253. [PMID: 29308278 DOI: 10.5152/eurjrheum.2017.17044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/06/2017] [Indexed: 01/09/2023] Open
Abstract
Objective Various genetic and environmental risk factors have been shown to be associated with the incidence of rheumatic diseases. However, the pathogenesis of rheumatic diseases poorly understood. Several studies have shown associations of ABO blood groups with various diseases. Our study aimed to determine whether there is an association between the types of rheumatic diseases and ABO and Rh blood groups. Material and Methods The study included the patients, followed up at the Immunology-Rheumatology clinic between January 2016 and December 2016 for diagnosis of rheumatic disease, who had an ABO Rh blood data. Age, gender, type of rheumatic disease, ABO Rh blood groups were recorded. Results When 823 patients were assessed for blood types, 42.5% patients had A type, 33.2% had O type, 15.4% had B type, and 8.9% had AB type. There was significant difference in the distribution of blood types in rheumatic diseases. While SpA, vasculitis, UCTD, Behçet's and RA were more common in the patients with A blood type; FMF, SLE, SSc and SjS were more common in the patients with O blood type. In addition, the blood type where all the diseases are observed the least commonly was AB. There was significant difference in the distribution of Rh factor in rheumatic diseases. 92.2% patients were Rh positive and 7.8% patients were Rh negative. Conclusion In our study, we thought that the higher incidence of different rheumatic diseases in different blood types was associated with different genetic predisposition.
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Affiliation(s)
- Songül Çildağ
- Department of Immunology-Rheumatology, Adnan Menderes University School of Medicine, Aydın, Turkey
| | - Yasemin Kara
- Department of Immunology-Rheumatology, Adnan Menderes University School of Medicine, Aydın, Turkey
| | - Taşkın Şentürk
- Department of Immunology-Rheumatology, Adnan Menderes University School of Medicine, Aydın, Turkey
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17
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Abstract
Systemic sclerosis, also called scleroderma, is an immune-mediated rheumatic disease that is characterised by fibrosis of the skin and internal organs and vasculopathy. Although systemic sclerosis is uncommon, it has a high morbidity and mortality. Improved understanding of systemic sclerosis has allowed better management of the disease, including improved classification and more systematic assessment and follow-up. Additionally, treatments for specific complications have emerged and a growing evidence base supports the use of immune suppression for the treatment of skin and lung fibrosis. Some manifestations of the disease, such as scleroderma renal crisis, pulmonary arterial hypertension, digital ulceration, and gastro-oesophageal reflux, are now treatable. However, the burden of non-lethal complications associated with systemic sclerosis is substantial and is likely to become more of a challenge. Here, we review the clinical features of systemic sclerosis and describe the best practice approaches for its management. Furthermore, we identify future areas for development.
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Affiliation(s)
- Christopher P Denton
- UCL Division of Medicine, University College London, London, UK; UCL Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital, London, UK.
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18
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Taroni JN, Mahoney JM, Whitfield ML. The mechanistic implications of gene expression studies in SSc: Insights from Systems Biology. CURRENT TREATMENT OPTIONS IN RHEUMATOLOGY 2017. [PMID: 29520335 DOI: 10.1007/s40674-017-0072-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jaclyn N Taroni
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755
| | - J Matthew Mahoney
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington VT
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755.,Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover NH 03755
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19
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The Influence of Different Solvents on Systemic Sclerosis: An Updated Meta-analysis of 14 Case-Control Studies. J Clin Rheumatol 2017; 22:253-9. [PMID: 27464769 DOI: 10.1097/rhu.0000000000000354] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Several studies have collected detailed data to examine which specific solvents account for the association between solvents and risk of systemic sclerosis (SSc). These studies generally reported elevated risks associated with many of the specific solvents examined, such as toluene, xylene, and trichloroethylene. The previous meta-analysis was not able to conduct separate analyses for specific solvent subtypes. OBJECTIVE The aims of the new meta-analysis were to investigate a more comprehensive estimate and to consider the effect of different solvents on SSc. METHODS We searched PubMed, Biosis Previews, China National Knowledge Infrastructure, and Wanfang for all articles published before July 2015. Fourteen case-control studies (1657 patients and 3838 controls) were included. The quality of studies was scored according to the Newcastle-Ottawa scale. The final odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by a fixed- or random-effects model according to heterogeneity test. Publication bias was assessed using Begg test. RESULTS The risk of SSc was significantly different among sex, age, and exposure assessment methods. Separate analyses for specific solvent subtypes indicated that SSc was associated with aromatic solvents (OR, 2.72; 95% CI, 1.21-6.09), trichloroethylene (OR, 2.07; 95% CI, 1.34-3.17), halogenated solvents (OR, 1.49; 95% CI, 1.12-1.99), and ketones (OR, 4.20; 95% CI, 2.19-8.06). CONCLUSIONS Exposure to identified types solvents does seem to be a risk factor for developing SSc. Needed efforts to decrease such exposures are discussed.
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20
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Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann RB, Farber HW, Lafyatis RA, Denton CP, Hinchcliff ME, Pioli PA, Mahoney JM, Whitfield ML. A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis. Genome Med 2017; 9:27. [PMID: 28330499 PMCID: PMC5363043 DOI: 10.1186/s13073-017-0417-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/23/2017] [Indexed: 12/22/2022] Open
Abstract
Background Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved affected tissues or if each manifestation has a distinct underlying pathology. Methods We used consensus clustering to compare gene expression profiles of biopsies from four SSc-affected tissues (skin, lung, esophagus, and peripheral blood) from patients with SSc, and the related conditions pulmonary fibrosis (PF) and pulmonary arterial hypertension, and derived a consensus disease-associate signature across all tissues. We used this signature to query tissue-specific functional genomic networks. We performed novel network analyses to contrast the skin and lung microenvironments and to assess the functional role of the inflammatory and fibrotic genes in each organ. Lastly, we tested the expression of macrophage activation state-associated gene sets for enrichment in skin and lung using a Wilcoxon rank sum test. Results We identified a common pathogenic gene expression signature—an immune–fibrotic axis—indicative of pro-fibrotic macrophages (MØs) in multiple tissues (skin, lung, esophagus, and peripheral blood mononuclear cells) affected by SSc. While the co-expression of these genes is common to all tissues, the functional consequences of this upregulation differ by organ. We used this disease-associated signature to query tissue-specific functional genomic networks to identify common and tissue-specific pathologies of SSc and related conditions. In contrast to skin, in the lung-specific functional network we identify a distinct lung-resident MØ signature associated with lipid stimulation and alternative activation. In keeping with our network results, we find distinct MØ alternative activation transcriptional programs in SSc-associated PF lung and in the skin of patients with an “inflammatory” SSc gene expression signature. Conclusions Our results suggest that the innate immune system is central to SSc disease processes but that subtle distinctions exist between tissues. Our approach provides a framework for examining molecular signatures of disease in fibrosis and autoimmune diseases and for leveraging publicly available data to understand common and tissue-specific disease processes in complex human diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0417-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaclyn N Taroni
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, 7400 Remsen, Hanover, NH, 03755, USA
| | - Casey S Greene
- Department of Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Viktor Martyanov
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, 7400 Remsen, Hanover, NH, 03755, USA
| | - Tammara A Wood
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, 7400 Remsen, Hanover, NH, 03755, USA
| | - Romy B Christmann
- Division of Rheumatology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Harrison W Farber
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Robert A Lafyatis
- Division of Rheumatology, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.,Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, 15261, USA
| | | | - Monique E Hinchcliff
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Patricia A Pioli
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA
| | - J Matthew Mahoney
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, HSRF 426, 149 Beaumont Avenue, Burlington, VT, 05405, USA.
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, 7400 Remsen, Hanover, NH, 03755, USA.
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21
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The role of common protective alleles HLA-DRB1*13 among systemic autoimmune diseases. Genes Immun 2016; 18:1-7. [PMID: 27829665 DOI: 10.1038/gene.2016.40] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/26/2016] [Accepted: 09/30/2016] [Indexed: 12/25/2022]
Abstract
Associations between human leukocyte antigen (HLA) and susceptibility to systemic autoimmune diseases have been reported. The predisposing alleles are variable among ethnic groups and/or diseases. On the other hand, some HLA alleles are associated with resistance to systemic autoimmune diseases, including systemic sclerosis, systemic lupus erythematosus and rheumatoid arthritis. Interestingly, DRB1*13 alleles are the protective alleles shared by multiple autoimmune diseases. DRB1*13:01 allele is protective in European populations and DRB1*13:02 in Japanese. Because alleles in multiple HLA loci are in strong linkage disequilibrium, it is difficult to determine which of the protective alleles is functionally responsible for the protective effects. Thus far, association studies suggested that DRB1*13:02 represents at least one of the causally associated protective factors against multiple systemic autoimmune diseases in the Japanese population. The protective effect of DRB1*13 alleles appears to overcome the predisposing effect of the susceptible alleles in heterozygous individuals of DRB1*13 and the susceptible allele. A gene dosage effect was observed in the associations of DRB1*13:02 with the protection from systemic autoimmune diseases; thus homozygous individuals are more effectively protected from the systemic autoimmune diseases than heterozygotes. DRB1*13:02 also confers protection against organ-specific autoimmune diseases and some infectious diseases. Several hypotheses can be proposed for the molecular mechanisms of the protection conferred by DRB1*13, some of which can explain the dominant effect of DRB1*13 molecules over the susceptible alleles, but the actual protective function of DRB1*13 requires further study. Understanding of the protective mechanisms of DRB1*13 may lead to the identification of targets for the curative treatment of systemic autoimmune diseases.
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22
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Abstract
Purpose of review Large-scale and follow-up genetic association studies in systemic sclerosis (SSc) have implicated over 40 regions in disease risk, 15 of which with robust associations. Nevertheless, the causal variants and the functional mechanisms underlying the genetic associations remain elusive, and the reasons for the higher disease burden in African Americans unknown. Incorporating tools from diverse fields is beginning to unveil the role of genetic diversity and regulatory variation in SSc susceptibility. This review will summarize recent advances in SSc genetics, including autoimmune disease overlap, evidence of natural selection, and current progress towards the dissection of the functional role of associated risk variants. Recent findings In the past year, multiple large-scale studies reported novel strong and suggestive SSc associations. These results, coupled with the regions shared with other autoimmune diseases, emphasize the role of dysregulation of immune pathways as a key causative factor in SSc pathogenesis. Strong evidence implicates natural selection as a mechanism contributing to the maintenance of some of these SSc alleles in the population. Studies integrating genomic, transcriptomic, and epigenomic datasets in specific cell types to identify causal autoimmune disease variants are emerging. Summary The identification and comprehensive understanding of the factors and mechanisms contributing to SSc will contribute to improved diagnosis and disease management.
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23
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Furukawa H, Oka S, Kawasaki A, Shimada K, Sugii S, Matsushita T, Hashimoto A, Komiya A, Fukui N, Kobayashi K, Osada A, Ihata A, Kondo Y, Nagai T, Setoguchi K, Okamoto A, Okamoto A, Chiba N, Suematsu E, Kono H, Katayama M, Hirohata S, Sumida T, Migita K, Hasegawa M, Fujimoto M, Sato S, Nagaoka S, Takehara K, Tohma S, Tsuchiya N. Human Leukocyte Antigen and Systemic Sclerosis in Japanese: The Sign of the Four Independent Protective Alleles, DRB1*13:02, DRB1*14:06, DQB1*03:01, and DPB1*02:01. PLoS One 2016; 11:e0154255. [PMID: 27116456 PMCID: PMC4846066 DOI: 10.1371/journal.pone.0154255] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/11/2016] [Indexed: 12/15/2022] Open
Abstract
Objective Several studies on associations between human leukocyte antigen (HLA) allele frequencies and susceptibility to systemic sclerosis (SSc) have been reported. Anti-centromere antibodies (ACA) and anti-topoisomerase I antibodies (ATA) are found in SSc patients. Here, we sought to identify HLA alleles associated with SSc in Japanese, and explored their associations with SSc phenotypes including the presence of autoantibodies. Methods Associations of HLA-DRB1, DQB1, and DPB1 were analyzed in 463 Japanese SSc patients and 413 controls. Results We found that DRB1*13:02 (P = 0.0011, Pc = 0.0319, odds ratio [OR] 0.46, 95% confidence interval [CI] 0.29–0.73), DRB1*14:06 (P = 6.60X10-5, Pc = 0.0020, OR 0.05, 95%CI 0.01–0.41), DQB1*03:01 (P = 0.0009, Pc = 0.0150, OR 0.56, 95%CI 0.40–0.79), and DPB1*02:01 (P = 5.16X10-6, Pc = 8.77X10-5, OR 0.52, 95%CI 0.39–0.69) were protectively associated with SSc. In addition, these four alleles seemed to be independently associated with the protection against the susceptibility of SSc. On the other hand, we could not find predisposing alleles for overall SSc. With respect to SSc subsets, a tendency for these four alleles to be protectively associated was observed. However, there was a significant association between DRB1*01:01, DRB1*10:01, DQB1*05:01, and DPB1*04:02 and the susceptibility to SSc with ACA. On the other hand, the presence of DRB1*15:02, DQB1*06:01, DPB1*03:01, and DPB1*09:01 was associated with SSc with ATA. Conclusion Thus, the present study has identified protective associations of the four HLA class II alleles with overall Japanese SSc and predisposing associations of HLA class II alleles with Japanese SSc subsets.
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Affiliation(s)
- Hiroshi Furukawa
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Japan
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, 18-1 Sakuradai, Minami-ku, Sagamihara, Japan
- * E-mail:
| | - Shomi Oka
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Japan
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, 18-1 Sakuradai, Minami-ku, Sagamihara, Japan
| | - Aya Kawasaki
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Japan
| | - Kota Shimada
- Department of Rheumatology, Sagamihara Hospital, National Hospital Organization, 18-1 Sakuradai, Minami-ku, Sagamihara, Japan
- Department of Rheumatic Diseases, Tokyo Metropolitan Tama Medical Center, 2-8-29 Musashi-dai, Fuchu, Japan
| | - Shoji Sugii
- Department of Rheumatic Diseases, Tokyo Metropolitan Tama Medical Center, 2-8-29 Musashi-dai, Fuchu, Japan
| | - Takashi Matsushita
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa, Japan
| | - Atsushi Hashimoto
- Department of Rheumatology, Sagamihara Hospital, National Hospital Organization, 18-1 Sakuradai, Minami-ku, Sagamihara, Japan
| | - Akiko Komiya
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, 18-1 Sakuradai, Minami-ku, Sagamihara, Japan
| | - Naoshi Fukui
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, 18-1 Sakuradai, Minami-ku, Sagamihara, Japan
| | - Kouji Kobayashi
- Department of Rheumatology, Yokohama Minami Kyosai Hospital, 1-21-1 Rokuura-higashi, Kanazawa-ku, Yokohama, Japan
| | - Atsumu Osada
- Department of Rheumatology, Yokohama Minami Kyosai Hospital, 1-21-1 Rokuura-higashi, Kanazawa-ku, Yokohama, Japan
| | - Atsushi Ihata
- Department of Rheumatology, Yokohama Minami Kyosai Hospital, 1-21-1 Rokuura-higashi, Kanazawa-ku, Yokohama, Japan
| | - Yuya Kondo
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Japan
| | - Tatsuo Nagai
- Department of Rheumatology and Infectious Diseases, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Japan
| | - Keigo Setoguchi
- Department of Allergy and Immunological Diseases, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, 3-18-22 Hon-komagome, Bunkyo-ku, Tokyo, Japan
| | - Akiko Okamoto
- Department of Internal Medicine, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Akira Okamoto
- Department of Rheumatology, Himeji Medical Center, National Hospital Organization, 68 Hon-machi, Himeji, Japan
| | - Noriyuki Chiba
- Department of Rheumatology, Morioka Hospital, National Hospital Organization, 1-25-1 Aoyama, Morioka, Japan
| | - Eiichi Suematsu
- Department of Internal Medicine and Rheumatology, Clinical Research Institute, Kyushu Medical Center, National Hospital Organization, 1-8-1 Jigyohama, Chuo-ku, Fukuoka, Japan
| | - Hajime Kono
- Department of Internal Medicine, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Masao Katayama
- Department of Internal Medicine, Nagoya Medical Center, National Hospital Organization, 4-1-1 Sannomaru, Naka-ku, Nagoya, Japan
| | - Shunsei Hirohata
- Department of Rheumatology and Infectious Diseases, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Japan
| | - Takayuki Sumida
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Japan
| | - Kiyoshi Migita
- Clinical Research Center, Nagasaki Medical Center, National Hospital Organization, 2-1001-1 Kubara, Omura, Japan
| | - Minoru Hasegawa
- Department of Dermatology, School of Medicine, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji, Japan
| | - Manabu Fujimoto
- Department of Dermatology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Japan
| | - Shinichi Sato
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Shouhei Nagaoka
- Department of Rheumatology, Yokohama Minami Kyosai Hospital, 1-21-1 Rokuura-higashi, Kanazawa-ku, Yokohama, Japan
| | - Kazuhiko Takehara
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa, Japan
| | - Shigeto Tohma
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, 18-1 Sakuradai, Minami-ku, Sagamihara, Japan
| | - Naoyuki Tsuchiya
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Japan
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Fuschiotti P. Current perspectives on the immunopathogenesis of systemic sclerosis. Immunotargets Ther 2016; 5:21-35. [PMID: 27529059 PMCID: PMC4970639 DOI: 10.2147/itt.s82037] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Systemic sclerosis (SSc or scleroderma) is a progressive and highly debilitating autoimmune disorder characterized by inflammation, vasculopathy, and extensive fibrosis. SSc is highly heterogeneous in its clinical presentation, extent and severity of skin and internal organ involvement, and clinical course and has the highest fatality rate among connective tissue diseases. While clinical outcomes have improved in recent years, no current therapy is able to reverse or slow the natural progression of SSc, a reflection of its complex pathogenesis. Although activation of the immune system has long been recognized, the mechanisms responsible for the initiation of autoimmunity and the role of immune effector pathways in the pathogenesis of SSc remain incompletely understood. This review summarizes recent progress in disease pathogenesis with particular focus on the immunopathogenetic mechanisms of SSc.
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Affiliation(s)
- Patrizia Fuschiotti
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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25
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Abstract
Significant advances have been made in understanding the genetic basis of systemic sclerosis (SSc) in recent years. Genomewide association and other large-scale genetic studies have identified 30 largely immunity-related genes which are significantly associated with SSc. We review these studies, along with genomewide expression studies, proteomic studies, genetic mouse models, and insights from rare sclerodermatous diseases. Collectively, these studies have begun to identify pathways that are relevant to SSc pathogenesis. The findings presented in this review illustrate how both genetic and genomic aberrations play important roles in the development of SSc. However, despite these recent discoveries, there remain major gaps between current knowledge of SSc, a unified understanding of pathogenesis, and effective treatment. To this aim, we address the important issue of SSc heterogeneity and discuss how future research needs to address this in order to develop a clearer understanding of this devastating and complex disease.
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López-Isac E, Campillo-Davo D, Bossini-Castillo L, Guerra SG, Assassi S, Simeón CP, Carreira P, Ortego-Centeno N, García de la Peña P, Beretta L, Santaniello A, Bellocchi C, Lunardi C, Moroncini G, Gabrielli A, Riemekasten G, Witte T, Hunzelmann N, Kreuter A, Distler JH, Voskuyl AE, de Vries-Bouwstra J, Herrick A, Worthington J, Denton CP, Fonseca C, Radstake TR, Mayes MD, Martín J. Influence of TYK2 in systemic sclerosis susceptibility: a new locus in the IL-12 pathway. Ann Rheum Dis 2015; 75:1521-6. [PMID: 26338038 DOI: 10.1136/annrheumdis-2015-208154] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/13/2015] [Indexed: 12/14/2022]
Abstract
OBJECTIVES TYK2 is a common genetic risk factor for several autoimmune diseases. This gene encodes a protein kinase involved in interleukin 12 (IL-12) pathway, which is a well-known player in the pathogenesis of systemic sclerosis (SSc). Therefore, we aimed to assess the possible role of this locus in SSc. METHODS This study comprised a total of 7103 patients with SSc and 12 220 healthy controls of European ancestry from Spain, USA, Germany, the Netherlands, Italy and the UK. Four TYK2 single-nucleotide polymorphisms (V362F (rs2304256), P1104A (rs34536443), I684S (rs12720356) and A928V (rs35018800)) were selected for follow-up based on the results of an Immunochip screening phase of the locus. Association and dependence analyses were performed by the means of logistic regression and conditional logistic regression. Meta-analyses were performed using the inverse variance method. RESULTS Genome-wide significance level was reached for TYK2 V362F common variant in our pooled analysis (p=3.08×10(-13), OR=0.83), while the association of P1104A, A928V and I684S rare and low-frequency missense variants remained significant with nominal signals (p=2.28×10(-3), OR=0.80; p=1.27×10(-3), OR=0.59; p=2.63×10(-5), OR=0.83, respectively). Interestingly, dependence and allelic combination analyses showed that the strong association observed for V362F with SSc, corresponded to a synthetic association dependent on the effect of the three previously mentioned TYK2 missense variants. CONCLUSIONS We report for the first time the association of TYK2 with SSc and reinforce the relevance of the IL-12 pathway in SSc pathophysiology.
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Affiliation(s)
- Elena López-Isac
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, PTS Granada, Granada, Spain
| | - Diana Campillo-Davo
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, PTS Granada, Granada, Spain
| | - Lara Bossini-Castillo
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, PTS Granada, Granada, Spain
| | - Sandra G Guerra
- Centre for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Shervin Assassi
- Division of Rheumatology and Clinical Immunogenetics, The University of Texas Health Science Center-Houston, Houston, USA
| | | | - Patricia Carreira
- Department of Rheumatology, 12 de Octubre University Hospital, Madrid, Spain
| | | | | | | | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Alessandro Santaniello
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Chiara Bellocchi
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Claudio Lunardi
- Department of Medicine, Università degli Studi di Verona, Verona, Italy
| | - Gianluca Moroncini
- Clinica Medica, Dipartimento di Scienze Cliniche e Molecolari, Università Politecnica delle Marche and Ospedali Riuniti, Ancona, Italy
| | - Armando Gabrielli
- Clinica Medica, Dipartimento di Scienze Cliniche e Molecolari, Università Politecnica delle Marche and Ospedali Riuniti, Ancona, Italy
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, Charité University Hospital, Berlin, Germany German Rheumatism Research Center (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Torsten Witte
- Department of Clinical Immunology, Hannover Medical School, Hannover, Germany
| | | | - Alexander Kreuter
- Department of Dermatology, Venereology, and Allergology, HELIOS St Elisabeth Hospital Oberhausen, Germany
| | - Jörg Hw Distler
- Department of Internal Medicine, Institute for Clinical Immunology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Alexandre E Voskuyl
- Department of Rheumatology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Ariane Herrick
- Centre for Musculoskeletal Research and NIHR Manchester Musculoskeletal Biomedical Research Unit, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Jane Worthington
- Centre for Musculoskeletal Research and NIHR Manchester Musculoskeletal Biomedical Research Unit, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Christopher P Denton
- Centre for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Carmen Fonseca
- Centre for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Timothy Rdj Radstake
- Department of Rheumatology & Clinical Immunology, Laboratory of Translational Immunology, department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maureen D Mayes
- Division of Rheumatology and Clinical Immunogenetics, The University of Texas Health Science Center-Houston, Houston, USA
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, PTS Granada, Granada, Spain
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Johnson ME, Pioli PA, Whitfield ML. Gene expression profiling offers insights into the role of innate immune signaling in SSc. Semin Immunopathol 2015; 37:501-9. [PMID: 26223504 PMCID: PMC4722533 DOI: 10.1007/s00281-015-0512-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/02/2015] [Indexed: 12/22/2022]
Abstract
Systemic sclerosis (SSc) is characterized by inflammation, vascular dysfunction, and ultimately fibrosis. Progress in understanding disease pathogenesis and developing effective disease treatments has been hampered by an incomplete understanding of SSc heterogeneity. To clarify this, we have used genomic approaches to identify distinct patient subsets based on gene expression patterns in SSc skin and other end-target organs. Here, we review what is known about the gene expression-based subsets in SSc, currently defined as the inflammatory, fibroproliferative, limited, and normal-like subsets. The inflammatory subset of patients is characterized by infiltrating immune cells that include T cells, macrophages, and possibly dendritic cells, although little is known about the mediators these cells secrete and the pathways that govern cell activation. Prior studies have suggested a role for pathogens as a trigger of immune responses in SSc, and recent data have identified viral and mycobiome components as potential environmental triggers. We present a model based on analyses of gene expression data and a review of the literature, which suggests that the gene expression subsets observed in patients possibly represent distinct, interconnected molecular states of disease, to which an innate immune response is central that results in the generation of clinical disease.
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Affiliation(s)
- Michael E. Johnson
- Department of Genetics, Geisel School of Medicine at Dartmouth, 7400 Remsen, Hanover, NH 03755, USA
| | - Patricia A. Pioli
- Department of Obstetrics and Gynecology, Geisel School of Medicine at Dartmouth, One Medical Center Drive, Lebanon, NH 03756, USA
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, One Medical Center Drive, Lebanon, NH 03756, USA
| | - Michael L. Whitfield
- Department of Genetics, Geisel School of Medicine at Dartmouth, 7400 Remsen, Hanover, NH 03755, USA
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Bhattacharyya S, Varga J. Emerging roles of innate immune signaling and toll-like receptors in fibrosis and systemic sclerosis. Curr Rheumatol Rep 2015; 17:474. [PMID: 25604573 DOI: 10.1007/s11926-014-0474-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Pathological fibrosis is a distinguishing hallmark of systemic sclerosis (SSc) as well as a number of more common conditions. Fibrosis is a complex and dynamic process associated with immune dysregulation, vasculopathy, and uncontrolled extracellular matrix production leading to intractable scar formation in the skin and internal organs. Persistent or recurrent chemical, infectious, mechanical, or autoimmune injury in genetically predisposed individuals causes sustained fibroblasts activation. Innate immune signaling via toll-like receptors (TLRs) is increasingly recognized as a key player driving the persistent fibrotic response in SSc. In particular, expression of TLR4 as well as its endogenous ligands are elevated in lesional tissue from patients with SSc. Ligand-induced TLR4 activation elicits potent stimulatory effects on fibrotic gene expression and myofibroblast differentiation. Furthermore, TLR4 appears to sensitize fibroblasts to the profibrotic stimulatory effect of transforming growth factor-β. This review highlights recent advances and emerging paradigms for understanding the regulation, complex functional roles, and therapeutic potential of TLRs in SSc pathogenesis.
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Affiliation(s)
- Swati Bhattacharyya
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, 240 E. Huron St., Chicago, IL, 60611, USA,
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29
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Abstract
Although scleroderma-associated interstitial lung disease (SSc-ILD) is a significant contributor to both morbidity and mortality, its pathogenesis is largely unclear. Pulmonary function tests and high-resolution computed tomographic scanning continue to be the most effective tools to screen for lung involvement and to monitor for disease progression. More research and better biomarkers are needed to identify patients most at risk for developing SSc-ILD as well as to recognize which of these patients will progress to more severe disease. Although immunosuppression remains the mainstay of treatment, antifibrotic agents may offer new avenues of treatment for patients with SSc-ILD in the future.
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Affiliation(s)
- Katherine Culp Silver
- Fellow, Adult & Pediatric Rheumatology, Medical University of South Carolina, Suite 816, Clinical Sciences Building, 96 Jonathan Lucas Street, Charleston, SC 29425, 843-792-3484
| | - Richard M. Silver
- Distinguished University Professor, Director, Division of Rheumatology & Immunology, Medical University of South Carolina, Suite 816, Clinical Sciences Building, 96 Jonathan Lucas Street, Charleston, SC 29425, 843-792-3484
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Pattanaik D, Brown M, Postlethwaite BC, Postlethwaite AE. Pathogenesis of Systemic Sclerosis. Front Immunol 2015; 6:272. [PMID: 26106387 PMCID: PMC4459100 DOI: 10.3389/fimmu.2015.00272] [Citation(s) in RCA: 253] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 05/16/2015] [Indexed: 01/04/2023] Open
Abstract
Systemic scleroderma (SSc) is one of the most complex systemic autoimmune diseases. It targets the vasculature, connective tissue-producing cells (namely fibroblasts/myofibroblasts), and components of the innate and adaptive immune systems. Clinical and pathologic manifestations of SSc are the result of: (1) innate/adaptive immune system abnormalities leading to production of autoantibodies and cell-mediated autoimmunity, (2) microvascular endothelial cell/small vessel fibroproliferative vasculopathy, and (3) fibroblast dysfunction generating excessive accumulation of collagen and other matrix components in skin and internal organs. All three of these processes interact and affect each other. The disease is heterogeneous in its clinical presentation that likely reflects different genetic or triggering factor (i.e., infection or environmental toxin) influences on the immune system, vasculature, and connective tissue cells. The roles played by other ubiquitous molecular entities (such as lysophospholipids, endocannabinoids, and their diverse receptors and vitamin D) in influencing the immune system, vasculature, and connective tissue cells are just beginning to be realized and studied and may provide insights into new therapeutic approaches to treat SSc.
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Affiliation(s)
- Debendra Pattanaik
- Department of Medicine, Division of Connective Tissue Diseases, The University of Tennessee Health Science Center , Memphis, TN , USA ; Department of Veterans Affairs Medical Center , Memphis, TN , USA
| | - Monica Brown
- Section of Pediatric Rheumatology, Department of Pediatrics, The University of Tennessee Health Science Center , Memphis, TN , USA
| | - Bradley C Postlethwaite
- Department of Medicine, Division of Connective Tissue Diseases, The University of Tennessee Health Science Center , Memphis, TN , USA
| | - Arnold E Postlethwaite
- Department of Medicine, Division of Connective Tissue Diseases, The University of Tennessee Health Science Center , Memphis, TN , USA ; Department of Veterans Affairs Medical Center , Memphis, TN , USA
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Abstract
Systemic sclerosis (SSc) is a complex autoimmune disease that occurs in a genetically susceptible host. Genetic studies performed so far reveal that multiple genetic loci contribute to disease susceptibility in SSc. The purpose of this review is to discuss the current knowledge of genetics in SSc by exploring the observational evidence, the different genetic studies, and their modalities as well as the most relevant genes discovered by these. The importance of gene expression variation and the different mechanisms that govern it, including the recently discovered field of epigenetics, are also explored, with an emphasis on microRNA.
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Affiliation(s)
- Gloria Salazar
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 5.270, Houston, TX 77030, USA
| | - Maureen D Mayes
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 5.270, Houston, TX 77030, USA.
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Furukawa H, Oka S, Shimada K, Tsuchiya N, Tohma S. Genetics of Interstitial Lung Disease: Vol de Nuit (Night Flight). CLINICAL MEDICINE INSIGHTS-CIRCULATORY RESPIRATORY AND PULMONARY MEDICINE 2015; 9:1-7. [PMID: 26056507 PMCID: PMC4444491 DOI: 10.4137/ccrpm.s23283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/10/2015] [Accepted: 03/13/2015] [Indexed: 01/03/2023]
Abstract
Interstitial lung disease (ILD) is a chronic, progressive fibrotic lung disease with a dismal prognosis. ILD of unknown etiology is referred to as idiopathic interstitial pneumonia (IIP), which is sporadic in the majority of cases. ILD is frequently accompanied by rheumatoid arthritis (RA), systemic sclerosis (SSc), polymyositis/dermatomyositis (PM/DM), and other autoimmune diseases, and is referred to as collagen vascular disease-associated ILD (CVD-ILD). Susceptibility to ILD is influenced by genetic and environmental factors. Recent advances in radiographic imaging techniques such as high-resolution computed tomography (CT) scanning as well as high-throughput genomic analyses have provided insights into the genetics of ILD. These studies have repeatedly revealed an association between IIP (sporadic and familial) and a single nucleotide polymorphism (SNP) in the promoter region of the mucin 5B (MUC5B). HLA-DRB1*11 alleles have been reported to correlate with ILD in European patients with SSc, whereas in Japanese patients with RA, the HLA-DR2 serological group was identified. The aim of this review is to describe the genetic background of sporadic IIP, CVD-ILD, drug-induced-ILD (DI-ILD), pneumoconiosis, and hypersensitivity pneumonitis. The genetics of ILD is still in progress. However, this information will enhance the understanding of the pathogenesis of ILD and aid the identification of novel therapeutic targets for personalized medicine in future.
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Affiliation(s)
- Hiroshi Furukawa
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, Sagamihara, Japan
| | - Shomi Oka
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, Sagamihara, Japan
| | - Kota Shimada
- Department of Rheumatic Diseases, Tokyo Metropolitan Tama Medical Center, Fuchu, Japan
| | - Naoyuki Tsuchiya
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shigeto Tohma
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, Sagamihara, Japan
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Herzog EL, Mathur A, Tager AM, Feghali-Bostwick C, Schneider F, Varga J. Review: interstitial lung disease associated with systemic sclerosis and idiopathic pulmonary fibrosis: how similar and distinct? Arthritis Rheumatol 2014; 66:1967-78. [PMID: 24838199 PMCID: PMC4340472 DOI: 10.1002/art.38702] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/08/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Erica L. Herzog
- Erica L. Herzog, MD, Aditi Mathur, MD: Yale School of Medicine, New Haven, Connecticut
| | - Aditi Mathur
- Erica L. Herzog, MD, Aditi Mathur, MD: Yale School of Medicine, New Haven, Connecticut
| | - Andrew M. Tager
- Andrew M. Tager, MD: Harvard Medical School and Massachusetts General Hospital, Boston
| | | | - Frank Schneider
- Frank Schneider, MD: University of Pittsburgh, Pittsburgh, Pennsylvania
| | - John Varga
- John Varga, MD: Northwestern University Feinberg School of Medicine, Chicago, Illinois
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34
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Dobrota R, Mihai C, Distler O. Personalized Medicine in Systemic Sclerosis: Facts and Promises. Curr Rheumatol Rep 2014; 16:425. [DOI: 10.1007/s11926-014-0425-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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López-Isac E, Bossini-Castillo L, Simeon CP, Egurbide MV, Alegre-Sancho JJ, Callejas JL, Roman-Ivorra JA, Freire M, Beretta L, Santaniello A, Airó P, Lunardi C, Hunzelmann N, Riemekasten G, Witte T, Kreuter A, Distler JHW, Schuerwegh AJ, Vonk MC, Voskuyl AE, Shiels PG, van Laar JM, Fonseca C, Denton C, Herrick A, Worthington J, Assassi S, Koeleman BP, Mayes MD, Radstake TRDJ, Martin J. A genome-wide association study follow-up suggests a possible role for PPARG in systemic sclerosis susceptibility. Arthritis Res Ther 2014; 16:R6. [PMID: 24401602 PMCID: PMC3978735 DOI: 10.1186/ar4432] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 12/18/2013] [Indexed: 02/06/2023] Open
Abstract
Introduction A recent genome-wide association study (GWAS) comprising a French cohort of systemic sclerosis (SSc) reported several non-HLA single-nucleotide polymorphisms (SNPs) showing a nominal association in the discovery phase. We aimed to identify previously overlooked susceptibility variants by using a follow-up strategy. Methods Sixty-six non-HLA SNPs showing a P value <10-4 in the discovery phase of the French SSc GWAS were analyzed in the first step of this study, performing a meta-analysis that combined data from the two published SSc GWASs. A total of 2,921 SSc patients and 6,963 healthy controls were included in this first phase. Two SNPs, PPARG rs310746 and CHRNA9 rs6832151, were selected for genotyping in the replication cohort (1,068 SSc patients and 6,762 healthy controls) based on the results of the first step. Genotyping was performed by using TaqMan SNP genotyping assays. Results We observed nominal associations for both PPARG rs310746 (PMH = 1.90 × 10-6, OR, 1.28) and CHRNA9 rs6832151 (PMH = 4.30 × 10-6, OR, 1.17) genetic variants with SSc in the first step of our study. In the replication phase, we observed a trend of association for PPARG rs310746 (P value = 0.066; OR, 1.17). The combined overall Mantel-Haenszel meta-analysis of all the cohorts included in the present study revealed that PPARG rs310746 remained associated with SSc with a nominal non-genome-wide significant P value (PMH = 5.00 × 10-7; OR, 1.25). No evidence of association was observed for CHRNA9 rs6832151 either in the replication phase or in the overall pooled analysis. Conclusion Our results suggest a role of PPARG gene in the development of SSc.
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Mayes M, Bossini-Castillo L, Gorlova O, Martin J, Zhou X, Chen W, Assassi S, Ying J, Tan F, Arnett F, Reveille J, Guerra S, Teruel M, Carmona F, Gregersen P, Lee A, López-Isac E, Ochoa E, Carreira P, Simeón C, Castellví I, González-Gay M, Zhernakova A, Padyukov L, Alarcón-Riquelme M, Wijmenga C, Brown M, Beretta L, Riemekasten G, Witte T, Hunzelmann N, Kreuter A, Distler JH, Voskuyl AE, Schuerwegh AJ, Hesselstrand R, Nordin A, Airó P, Lunardi C, Shiels P, van Laar JM, Herrick A, Worthington J, Denton C, Wigley FM, Hummers LK, Varga J, Hinchcliff ME, Baron M, Hudson M, Pope JE, Furst DE, Khanna D, Phillips K, Schiopu E, Segal BM, Molitor JA, Silver RM, Steen VD, Simms RW, Lafyatis RA, Fessler BJ, Frech TM, AlKassab F, Docherty P, Kaminska E, Khalidi N, Jones HN, Markland J, Robinson D, Broen J, Radstake TR, Fonseca C, Koeleman BP, Martin J, Ortego-Centeno N, Ríos R, Callejas J, Navarrete N, García Portales R, Camps M, Fernández-Nebro A, González-Escribano M, Sánchez-Román J, García-Hernández F, Castillo M, Aguirre M, Gómez-Gracia I, Fernández-Gutiérrez B, Rodríguez-Rodríguez L, Vicente E, Andreu J, Fernández de Castro M, García de la Peña P, López-Longo F, Martínez L, Fonollosa V, Espinosa G, Tolosa C, Pros A, Rodríguez Carballeira M, Narváez F, Rubio Rivas M, Ortiz Santamaría V, Díaz B, Trapiella L, Freire M, Sousa A, Egurbide M, Fanlo Mateo P, Sáez-Comet L, Díaz F, Hernández V, Beltrán E, Román-Ivorra J, Grau E, Alegre Sancho J, Blanco García F, Oreiro N, Fernández Sueiro L. Immunochip analysis identifies multiple susceptibility loci for systemic sclerosis. Am J Hum Genet 2014; 94:47-61. [PMID: 24387989 DOI: 10.1016/j.ajhg.2013.12.002] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 12/03/2013] [Indexed: 12/12/2022] Open
Abstract
In this study, 1,833 systemic sclerosis (SSc) cases and 3,466 controls were genotyped with the Immunochip array. Classical alleles, amino acid residues, and SNPs across the human leukocyte antigen (HLA) region were imputed and tested. These analyses resulted in a model composed of six polymorphic amino acid positions and seven SNPs that explained the observed significant associations in the region. In addition, a replication step comprising 4,017 SSc cases and 5,935 controls was carried out for several selected non-HLA variants, reaching a total of 5,850 cases and 9,401 controls of European ancestry. Following this strategy, we identified and validated three SSc risk loci, including DNASE1L3 at 3p14, the SCHIP1-IL12A locus at 3q25, and ATG5 at 6q21, as well as a suggested association of the TREH-DDX6 locus at 11q23. The associations of several previously reported SSc risk loci were validated and further refined, and the observed peak of association in PXK was related to DNASE1L3. Our study has increased the number of known genetic associations with SSc, provided further insight into the pleiotropic effects of shared autoimmune risk factors, and highlighted the power of dense mapping for detecting previously overlooked susceptibility loci.
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