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Gogulska Z, Smolenska Z, Turyn J, Zdrojewski Z, Chmielewski M. Metabolomics in systemic sclerosis. Rheumatol Int 2024:10.1007/s00296-024-05628-y. [PMID: 38981905 DOI: 10.1007/s00296-024-05628-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/28/2024] [Indexed: 07/11/2024]
Abstract
Systemic sclerosis is a rare autoimmune condition leading to incurable complications. Therefore fast and precise diagnosis is crucial to prevent patient death and to maintain quality of life. Unfortunately, currently known biomarkers do not meet this need. To address this problem researchers use diverse approaches to elucidate the underlying aberrations. One of the methods applied is metabolomics. This modern technique enables a comprehensive assessment of multiple compound concentrations simultaneously. As it has been gaining popularity, we found it necessary to summarize metabolomic studies presented so far in a narrative review. We found 11 appropriate articles. All of the researchers found significant differences between patients and control groups, whereas the reported findings were highly inconsistent. Additionally, we have found the investigated groups in most studies were scarcely described, and the inclusion/exclusion approach was diverse. Therefore, further study with meticulous patient assessment is necessary.
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Affiliation(s)
- Zuzanna Gogulska
- Department of Rheumatology, Clinical Immunology, Geriatrics and Internal Medicine, Medical University of Gdansk, Gdansk, Poland.
| | - Zaneta Smolenska
- Department of Rheumatology, Clinical Immunology, Geriatrics and Internal Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Jacek Turyn
- Department of Biochemistry, Medical University of Gdansk, Gdansk, Poland
| | - Zbigniew Zdrojewski
- Department of Rheumatology, Clinical Immunology, Geriatrics and Internal Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Michał Chmielewski
- Department of Rheumatology, Clinical Immunology, Geriatrics and Internal Medicine, Medical University of Gdansk, Gdansk, Poland
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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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Chairta PP, Nicolaou P, Christodoulou K. Enrichr in silico analysis of MS-based extracted candidate proteomic biomarkers highlights pathogenic pathways in systemic sclerosis. Sci Rep 2023; 13:1934. [PMID: 36732374 PMCID: PMC9894849 DOI: 10.1038/s41598-023-29054-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Systemic sclerosis (SSc) is a rheumatic disease characterised by vasculopathy, inflammation and fibrosis. Its aetiopathogenesis is still unknown, and the pathways/mechanisms of the disease are not clarified. This study aimed to perform in silico analysis of the already Mass Spectrometry (MS)-based discovered biomarkers of SSc to extract possible pathways/mechanisms implicated in the disease. We recorded all published candidate MS-based found biomarkers related to SSc. We then selected a number of the candidate biomarkers using specific criteria and performed pathway and cellular component analyses using Enrichr. We used PANTHER and STRING to assess the biological processes and the interactions of the recorded proteins, respectively. Pathway analysis extracted several pathways that are associated with the three different stages of SSc pathogenesis. Some of these pathways are also related to other diseases, including autoimmune diseases. We observe that these biomarkers are located in several cellular components and implicated in many biological processes. STRING analysis showed that some proteins interact, creating significant clusters, while others do not display any evidence of an interaction. All these data highlight the complexity of SSc, and further investigation of the extracted pathways/biological processes and interactions may help study the disease from a different angle.
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Affiliation(s)
- Paraskevi P Chairta
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
| | - Paschalis Nicolaou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
| | - Kyproula Christodoulou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus.
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Chepy A, Vivier S, Bray F, Ternynck C, Meneboo JP, Figeac M, Filiot A, Guilbert L, Jendoubi M, Rolando C, Launay D, Dubucquoi S, Marot G, Sobanski V. Effects of Immunoglobulins G From Systemic Sclerosis Patients in Normal Dermal Fibroblasts: A Multi-Omics Study. Front Immunol 2022; 13:904631. [PMID: 35844491 PMCID: PMC9276964 DOI: 10.3389/fimmu.2022.904631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Autoantibodies (Aabs) are frequent in systemic sclerosis (SSc). Although recognized as potent biomarkers, their pathogenic role is debated. This study explored the effect of purified immunoglobulin G (IgG) from SSc patients on protein and mRNA expression of dermal fibroblasts (FBs) using an innovative multi-omics approach. Dermal FBs were cultured in the presence of sera or purified IgG from patients with diffuse cutaneous SSc (dcSSc), limited cutaneous SSc or healthy controls (HCs). The FB proteome and transcriptome were explored using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and microarray assays, respectively. Proteomic analysis identified 3,310 proteins. SSc sera and purified IgG induced singular protein profile patterns. These FB proteome changes depended on the Aab serotype, with a singular effect observed with purified IgG from anti-topoisomerase-I autoantibody (ATA) positive patients compared to HC or other SSc serotypes. IgG from ATA positive SSc patients induced enrichment in proteins involved in focal adhesion, cadherin binding, cytosolic part, or lytic vacuole. Multi-omics analysis was performed in two ways: first by restricting the analysis of the transcriptomic data to differentially expressed proteins; and secondly, by performing a global statistical analysis integrating proteomics and transcriptomics. Transcriptomic analysis distinguished 764 differentially expressed genes and revealed that IgG from dcSSc can induce extracellular matrix (ECM) remodeling changes in gene expression profiles in FB. Global statistical analysis integrating proteomics and transcriptomics confirmed that IgG from SSc can induce ECM remodeling and activate FB profiles. This effect depended on the serotype of the patient, suggesting that SSc Aab might play a pathogenic role in some SSc subsets.
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Affiliation(s)
- Aurélien Chepy
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France, Lille, France
| | - Solange Vivier
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
| | - Fabrice Bray
- Univ. Lille, CNRS, USR 3290, Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - Camille Ternynck
- Univ. Lille, CHU Lille, ULR 2694, METRICS: Évaluation des Technologies de Santé et des Pratiques Médicales, Lille, France
| | - Jean-Pascal Meneboo
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41—UAR 2014-PLBS, Lille, France
| | - Martin Figeac
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41—UAR 2014-PLBS, Lille, France
| | - Alexandre Filiot
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
| | - Lucile Guilbert
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Institut d’Immunologie, Lille, France
| | - Manel Jendoubi
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
| | - Christian Rolando
- Univ. Lille, CNRS, USR 3290, Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, Lille, France
| | - David Launay
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France, Lille, France
- *Correspondence: David Launay,
| | - Sylvain Dubucquoi
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Institut d’Immunologie, Lille, France
| | - Guillemette Marot
- Univ. Lille, CHU Lille, ULR 2694, METRICS: Évaluation des Technologies de Santé et des Pratiques Médicales, Lille, France
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41—UAR 2014-PLBS, Lille, France
- Inria, Models for Data Analysis and Learning, Lille, France
| | - Vincent Sobanski
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE ( Institute for Translational Research) in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes Systémiques Rares du Nord et Nord-Ouest de France, Lille, France
- Institut Universitaire de France, Paris, France
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Barriga M, Benitez R, Robledo G, Caro M, O'Valle F, Campos-Salinas J, Delgado M. Neuropeptide Cortistatin Regulates Dermal and Pulmonary Fibrosis in an Experimental Model of Systemic Sclerosis. Neuroendocrinology 2022; 112:784-795. [PMID: 34649259 DOI: 10.1159/000520194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/13/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Scleroderma, or systemic sclerosis, is a complex connective tissue disorder characterized by autoimmunity, vasculopathy, and progressive fibrosis of the skin and internal organs. Because its aetiology is unknown, the identification of genes/factors involved in disease severity, differential clinical forms, and associated complications is critical for understanding its pathogenesis and designing novel treatments. Neuroendocrine mediators in the skin emerge as potential candidates. We investigated the role played by the neuropeptide cortistatin in a preclinical model of scleroderma. METHODS Dermal fibrosis was induced by repetitive intradermal injections of bleomycin in wild-type and cortistatin-deficient mice. The histopathological signs and expression of fibrotic markers were evaluated in the skin and lungs. RESULTS An inverse correlation between cortistatin levels and fibrogenic activation exists in the damaged skin and dermal fibroblasts. Bleomycin-challenged skin lesions of mice that are partially and totally deficient in cortistatin showed exacerbated histopathological signs of scleroderma, characterized by thicker and more fibrotic dermal layer, enlarged epidermis, and increased inflammatory infiltration in comparison to those of wild-type mice. Cortistatin deficiency enhanced dermal collagen deposits, connective tissue growth factor expression, loss of microvessels, and predisposition to suffer severe complications that co-occur with dermal exposition to bleomycin, including pulmonary fibrotic disease and increased mortality. Treatment with cortistatin mitigated these pathological processes. DISCUSSION/CONCLUSION We identify cortistatin as an endogenous break of skin inflammation and fibrosis. Deficiency in cortistatin could be a marker of poor prognosis of scleroderma and associated complications. Cortistatin-based therapies emerge as attractive candidates to treat severe forms of systemic sclerosis and to manage fibrosis-related side effects of bleomycin chemotherapy in oncologic patients.
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Affiliation(s)
- Margarita Barriga
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Raquel Benitez
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Gema Robledo
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Marta Caro
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Francisco O'Valle
- Pathology Department, School of Medicine, IBIMER, CIBM, University of Granada and Biosanitary Research Institute IBS-Granada, Granada, Spain
| | - Jenny Campos-Salinas
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
| | - Mario Delgado
- Institute of Parasitology and Biomedicine Lopez-Neyra IPBLN-CSIC, Granada, Spain
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