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Systemic sclerosis
Genome-wide whole blood transcriptome profiling in a large European cohort of systemic sclerosis patients
  1. Lorenzo Beretta1,
  2. Guillermo Barturen2,
  3. Barbara Vigone1,
  4. Chiara Bellocchi1,3,
  5. Nicolas Hunzelmann4,
  6. Ellen De Langhe5,
  7. Ricard Cervera6,
  8. Maria Gerosa3,
  9. László Kovács7,
  10. Rafaela Ortega Castro8,
  11. Isabel Almeida9,
  12. Divi Cornec10,11,
  13. Carlo Chizzolini12,
  14. Jacques-Olivier Pers10,
  15. Zuzanna Makowska13,
  16. Ralf Lesche14,
  17. Martin Kerick15,
  18. Marta Eugenia Alarcón-Riquelme2,
  19. Javier Martin15,
  20. PRECISESADS SSc substudy group
  21. PRECISESADS Flow Cytometry study group
      1. 1 Scleroderma Unit, Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
      2. 2 GENYO, Centre for Genomics and Oncological Research Pfizer, University of Granada, Andalusian Regional Government, PTS GRANADA, Granada, Spain
      3. 3 Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
      4. 4 Klinik und Poliklinik für Dermatologie und Venerologie, Uniklinik Köln, Köln, Germany
      5. 5 Division of Rheumatology, University Hospitals Leuven and Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium
      6. 6 Department of Autoimmune Diseases, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
      7. 7 Department of Rheumatology and Immunology, University of Szeged, Faculty of Medicine, Szeged, Hungary
      8. 8 Servicio de Reumatologia, Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica IMIBIC, Córdoba, Spain
      9. 9 Serviço de Imunologia EX-CICAP, Centro Hospitalar e Universitário do Porto, Porto, Portugal
      10. 10 UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, Inserm, Labex IGO, Brest, France
      11. 11 Rheumatology Department, Cavale Blanche Hospital, Brest, France
      12. 12 Immunology & Allergy, University Hospital and School of Medicine (HCUGE), Geneva, Switzerland
      13. 13 Bayer Pharma AG, Berlin, Berlin, Germany
      14. 14 Drug Discovery, Bayer AG, Berlin, Germany
      15. 15 Instituto de Parasitologia y Biomedicina Lopez-Neyra, Granada, Spain
      1. Correspondence to Dr Lorenzo Beretta, Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan 20122, Italy; lorberimm@hotmail.com

      Abstract

      Objectives The analysis of annotated transcripts from genome-wide expression studies may help to understand the pathogenesis of complex diseases, such as systemic sclerosis (SSc). We performed a whole blood (WB) transcriptome analysis on RNA collected in the context of the European PRECISESADS project, aiming at characterising the pathways that differentiate SSc from controls and that are reproducible in geographically diverse populations.

      Methods Samples from 162 patients and 252 controls were collected in RNA stabilisers. Cases and controls were divided into a discovery (n=79+163; Southern Europe) and validation cohort (n=83+89; Central-Western Europe). RNA sequencing was performed by an Illumina assay. Functional annotations of Reactome pathways were performed with the Functional Analysis of Individual Microarray Expression (FAIME) algorithm. In parallel, immunophenotyping of 28 circulating cell populations was performed. We tested the presence of differentially expressed genes/pathways and the correlation between absolute cell counts and RNA transcripts/FAIME scores in regression models. Results significant in both populations were considered as replicated.

      Results Overall, 15 224 genes and 1277 functional pathways were available; of these, 99 and 225 were significant in both sets. Among replicated pathways, we found a deregulation in type-I interferon, Toll-like receptor cascade, tumour suppressor p53 protein function, platelet degranulation and activation. RNA transcripts or FAIME scores were jointly correlated with cell subtypes with strong geographical differences; neutrophils were the major determinant of gene expression in SSc-WB samples.

      Conclusions We discovered a set of differentially expressed genes/pathways validated in two independent sets of patients with SSc, highlighting a number of deregulated processes that have relevance for the pathogenesis of autoimmunity and SSc.

      • systemic sclerosis
      • autoimmune diseases
      • epidemiology
      http://creativecommons.org/licenses/by-nc/4.0/

      This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/.

      https://doi.org/10.1136/annrheumdis-2020-217116

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        Footnotes

        • MEA-R and JM are joint senior authors.

        • Handling editor Josef S Smolen

        • Contributors LB: data analysis, study design, manuscript drafting, revision and approval. GB: data analysis, manuscript revision and approval. BV: data acquisition, manuscript revision and approval. CB: data analysis, manuscript revision and approval. NH: data acquisition, manuscript revision and approval. EDL: data acquisition, manuscript revision and approval. LK: data acquisition, manuscript revision and approval. RC: data acquisition, manuscript revision and approval. MG: data acquisition, manuscript revision and approval. ROC: data acquisition, manuscript revision and approval. IA: data acquisition, manuscript revision and approval. DC: data acquisition, manuscript revision and approval. CC: data acquisition, manuscript revision and approval. PRECISESADS SSc substudy group, J-OP: data analysis, manuscript revision and approval. PRECISESADS Flow Cytometry study group, ZM: data analysis, manuscript revision and approval. RL: data analysis, manuscript revision and approval. MK: data analysis, manuscript revision and approval. MEA-R: study design, data analysis, manuscript revision and approval. JM: study design, data analysis, manuscript revision and approval.

        • Funding This work was supported by EU/EFPIA/Innovative Medicines Initiative Joint Undertaking PRECISESADS Grant No. 115 565.

        • Competing interests None declared.

        • Patient and public involvement Patients and/or the public were not involved in the design, or conduct, or reporting or dissemination plans of this research.

        • Patient consent for publication Not required.

        • Ethics approval The study (PRECISESADS cross-sectional cohort) was approved by the following ethic committees (including those for the author listed as collaborators in the Supplemental Material): Comitato Etico Area 2 (Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano and University of Milan); approval no. 425bis Nov 19, 2014, and no. 671_2018 Sep 19, 2018; Klinikum der Universitaet zu Koeln, Cologne, Germany. Geschaftsstelle Ethikkommission; Pôle de pathologies rhumatismales systémiques et inflammatoires, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium. Comité d'Èthique Hospitalo-Facultaire; University of Szeged, Szeged, Hungary. Csongrad Megyei Kormanyhivatal; Hospital Clinic I Provicia, Institut d’Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain. Comité Ética de Investigación Clínica del Hospital Clínic de Barcelona. Hospital Clinic del Barcelona; Servicio Andaluz de Salud, Hospital Universitario Reina Sofía Córdoba, Spain. Comité de Ética e la Investigación de Centro de Granada (CEI – Granada); Centro Hospitalar do Porto, Portugal. Comissao de ética para a Saude – CES do CHP; Centre Hospitalier Universitaire de Brest, Hospital de la Cavale Blanche, Avenue Tanguy Prigent 29609, Brest, France. Comite de Protection des Personnes Ouest VI; Hospitaux Universitaires de Genève, Switzerland. DEAS – Commission Cantonale d’ethique de la recherche Hopitaux universitaires de Geneve ; Andalusian Public Health System Biobank, Granada, Spain; Katholieke Universiteit Leuven, Belgium. Commissie Medische Ethiek UZ KU Leuven /Onderzoek; Charite, Berlin, Germany. Ethikkommission; Medizinische Hochschule Hannover, Germany. Ethikkommission.

        • Provenance and peer review Not commissioned; externally peer reviewed.

        • Data availability statement Data are available on reasonable request. Raw data are property of the PRECISESADS consortium and protected under the European General Data Protection Regulation (GDPR). Metadata and aggregated processed data are available on reasonable request to the authors and from the EGA (European Genome-phenome Archive).