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Ortiz-Fernández L, Carmona EG, Kerick M, Lyons P, Carmona FD, López Mejías R, Khor CC, Grayson PC, Tombetti E, Jiang L, Direskeneli H, Saruhan-Direskeneli G, Callejas-Rubio JL, Vaglio A, Salvarani C, Hernández-Rodríguez J, Cid MC, Morgan AW, Merkel PA, Burgner D, Smith KG, Gonzalez-Gay MA, Sawalha AH, Martin J, Marquez A. Identification of new risk loci shared across systemic vasculitides points towards potential target genes for drug repurposing. Ann Rheum Dis 2023; 82:837-847. [PMID: 36797040 PMCID: PMC10314028 DOI: 10.1136/ard-2022-223697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/04/2023] [Indexed: 02/18/2023]
Abstract
OBJECTIVES The number of susceptibility loci currently associated with vasculitis is lower than in other immune-mediated diseases due in part to small cohort sizes, a consequence of the low prevalence of vasculitides. This study aimed to identify new genetic risk loci for the main systemic vasculitides through a comprehensive analysis of their genetic overlap. METHODS Genome-wide data from 8467 patients with any of the main forms of vasculitis and 29 795 healthy controls were meta-analysed using ASSET. Pleiotropic variants were functionally annotated and linked to their target genes. Prioritised genes were queried in DrugBank to identify potentially repositionable drugs for the treatment of vasculitis. RESULTS Sixteen variants were independently associated with two or more vasculitides, 15 of them representing new shared risk loci. Two of these pleiotropic signals, located close to CTLA4 and CPLX1, emerged as novel genetic risk loci in vasculitis. Most of these polymorphisms appeared to affect vasculitis by regulating gene expression. In this regard, for some of these common signals, potential causal genes were prioritised based on functional annotation, including CTLA4, RNF145, IL12B, IL5, IRF1, IFNGR1, PTK2B, TRIM35, EGR2 and ETS2, each of which has key roles in inflammation. In addition, drug repositioning analysis showed that several drugs, including abatacept and ustekinumab, could be potentially repurposed in the management of the analysed vasculitides. CONCLUSIONS We identified new shared risk loci with functional impact in vasculitis and pinpointed potential causal genes, some of which could represent promising targets for the treatment of vasculitis.
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Affiliation(s)
| | - Elio G Carmona
- Institute of Parasitology and Biomedicine "López- Neyra", CSIC, Granada, Spain
- Unidad de Enfermedades Autoinmunes Sistémicas, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria de Granada ibs.GRANADA, Granada, Spain
| | - Martin Kerick
- Institute of Parasitology and Biomedicine "López- Neyra", CSIC, Granada, Spain
| | - Paul Lyons
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Francisco David Carmona
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Raquel López Mejías
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Santander, Spain
| | - Chiea Chuen Khor
- Duke-NUS Medical School, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Peter C Grayson
- Systemic Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, Maryland, USA
| | - Enrico Tombetti
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences L. Sacco, Milan University, Milan, Italy
| | - Lindi Jiang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
- Evidence-Based Medicine Center, Fudan University, Shanghai, China
| | - Haner Direskeneli
- Department of Internal Medicine, Division of Rheumatology, Marmara University, Faculty of Medicine, Istanbul, Turkey
| | | | - José-Luis Callejas-Rubio
- Systemic Autoimmune Diseases Unit, San Cecilio University Hospital, Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Augusto Vaglio
- Department of Biomedical Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
- Nephrology and Dialysis Unit, Meyer Children's Hospital, Florence, Italy
| | - Carlo Salvarani
- Rheumatology Unit, Azienda USL-IRCCS di Reggio Emilia and Azienda Ospedaliero - Universitaria di Modena, Università di Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Jose Hernández-Rodríguez
- Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Maria Cinta Cid
- Department of Autoimmune Diseases, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ann W Morgan
- School of Medicine and Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre and NIHR Leeds Medtech and In vitro Diagnostics Co-Operative, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Peter A Merkel
- Division of Rheumatology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Epidemiology, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Burgner
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Department of General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Kenneth Gc Smith
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Miguel Angel Gonzalez-Gay
- Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, University of Cantabria, Santander, Spain
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Javier Martin
- Institute of Parasitology and Biomedicine "López- Neyra", CSIC, Granada, Spain
| | - Ana Marquez
- Institute of Parasitology and Biomedicine "López- Neyra", CSIC, Granada, Spain
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Barturen G, Babaei S, Català-Moll F, Martínez-Bueno M, Makowska Z, Martorell-Marugán J, Carmona-Sáez P, Toro-Domínguez D, Carnero-Montoro E, Teruel M, Kerick M, Acosta-Herrera M, Le Lann L, Jamin C, Rodríguez-Ubreva J, García-Gómez A, Kageyama J, Buttgereit A, Hayat S, Mueller J, Lesche R, Hernandez-Fuentes M, Juarez M, Rowley T, White I, Marañón C, Gomes Anjos T, Varela N, Aguilar-Quesada R, Garrancho FJ, López-Berrio A, Rodriguez Maresca M, Navarro-Linares H, Almeida I, Azevedo N, Brandão M, Campar A, Faria R, Farinha F, Marinho A, Neves E, Tavares A, Vasconcelos C, Trombetta E, Montanelli G, Vigone B, Alvarez-Errico D, Li T, Thiagaran D, Blanco Alonso R, Corrales Martínez A, Genre F, López Mejías R, Gonzalez-Gay MA, Remuzgo S, Ubilla Garcia B, Cervera R, Espinosa G, Rodríguez-Pintó I, De Langhe E, Cremer J, Lories R, Belz D, Hunzelmann N, Baerlecken N, Kniesch K, Witte T, Lehner M, Stummvoll G, Zauner M, Aguirre-Zamorano MA, Barbarroja N, Castro-Villegas MC, Collantes-Estevez E, de Ramon E, Díaz Quintero I, Escudero-Contreras A, Fernández Roldán MC, Jiménez Gómez Y, Jiménez Moleón I, Lopez-Pedrera R, Ortega-Castro R, Ortego N, Raya E, Artusi C, Gerosa M, Meroni PL, Schioppo T, De Groof A, Ducreux J, Lauwerys B, Maudoux AL, Cornec D, Devauchelle-Pensec V, Jousse-Joulin S, Jouve PE, Rouvière B, Saraux A, Simon Q, Alvarez M, Chizzolini C, Dufour A, Wynar D, Balog A, Bocskai M, Deák M, Dulic S, Kádár G, Kovács L, Cheng Q, Gerl V, Hiepe F, Khodadadi L, Thiel S, de Rinaldis E, Rao S, Benschop RJ, Chamberlain C, Dow ER, Ioannou Y, Laigle L, Marovac J, Wojcik J, Renaudineau Y, Borghi MO, Frostegård J, Martín J, Beretta L, Ballestar E, McDonald F, Pers JO, Alarcón-Riquelme ME. Integrative Analysis Reveals a Molecular Stratification of Systemic Autoimmune Diseases. Arthritis Rheumatol 2021; 73:1073-1085. [PMID: 33497037 DOI: 10.1002/art.41610] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/01/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Clinical heterogeneity, a hallmark of systemic autoimmune diseases, impedes early diagnosis and effective treatment, issues that may be addressed if patients could be classified into groups defined by molecular pattern. This study was undertaken to identify molecular clusters for reclassifying systemic autoimmune diseases independently of clinical diagnosis. METHODS Unsupervised clustering of integrated whole blood transcriptome and methylome cross-sectional data on 955 patients with 7 systemic autoimmune diseases and 267 healthy controls was undertaken. In addition, an inception cohort was prospectively followed up for 6 or 14 months to validate the results and analyze whether or not cluster assignment changed over time. RESULTS Four clusters were identified and validated. Three were pathologic, representing "inflammatory," "lymphoid," and "interferon" patterns. Each included all diagnoses and was defined by genetic, clinical, serologic, and cellular features. A fourth cluster with no specific molecular pattern was associated with low disease activity and included healthy controls. A longitudinal and independent inception cohort showed a relapse-remission pattern, where patients remained in their pathologic cluster, moving only to the healthy one, thus showing that the molecular clusters remained stable over time and that single pathogenic molecular signatures characterized each individual patient. CONCLUSION Patients with systemic autoimmune diseases can be jointly stratified into 3 stable disease clusters with specific molecular patterns differentiating different molecular disease mechanisms. These results have important implications for future clinical trials and the study of nonresponse to therapy, marking a paradigm shift in our view of systemic autoimmune diseases.
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Affiliation(s)
- Guillermo Barturen
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | | | | | - Manuel Martínez-Bueno
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | | | - Jordi Martorell-Marugán
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - Pedro Carmona-Sáez
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - Daniel Toro-Domínguez
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - Elena Carnero-Montoro
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - María Teruel
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - Martin Kerick
- Institute of Parasitology and Biomedicine "López Neyra", Spanish National Research Council, Granada, Spain
| | - Marialbert Acosta-Herrera
- Institute of Parasitology and Biomedicine "López Neyra", Spanish National Research Council, Granada, Spain
| | - Lucas Le Lann
- Université de Brest, Centre Hospitalier Universitaire de Brest, INSERM, and Labex IGO, Brest, France
| | - Christophe Jamin
- Université de Brest, Centre Hospitalier Universitaire de Brest, INSERM, and Labex IGO, Brest, France
| | | | | | | | | | | | | | | | | | | | | | | | - Concepción Marañón
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - Tania Gomes Anjos
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - Nieves Varela
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | | | | | | | | | | | | | | | | | - Ana Campar
- Centro Hospitalar do Porto, Porto, Portugal
| | | | | | | | | | | | | | - Elena Trombetta
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gaia Montanelli
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Barbara Vigone
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Tianlu Li
- Bellvitge Biomedical Research Institute, Barcelona, Spain
| | | | - Ricardo Blanco Alonso
- Hospital Universitario Marqués de Valdecilla, IDIVAL, Universidad de Cantabria, Santander, Spain
| | | | - Fernanda Genre
- Hospital Universitario Marqués de Valdecilla, IDIVAL, Universidad de Cantabria, Santander, Spain
| | - Raquel López Mejías
- Hospital Universitario Marqués de Valdecilla, IDIVAL, Universidad de Cantabria, Santander, Spain
| | - Miguel A Gonzalez-Gay
- Hospital Universitario Marqués de Valdecilla, IDIVAL, Universidad de Cantabria, Santander, Spain
| | - Sara Remuzgo
- Hospital Universitario Marqués de Valdecilla, IDIVAL, Universidad de Cantabria, Santander, Spain
| | - Begoña Ubilla Garcia
- Hospital Universitario Marqués de Valdecilla, IDIVAL, Universidad de Cantabria, Santander, Spain
| | - Ricard Cervera
- Hospital Clínic and Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Gerard Espinosa
- Hospital Clínic and Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Ignasi Rodríguez-Pintó
- Hospital Clínic and Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Ellen De Langhe
- Katholieke Universiteit Leuven and Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Jonathan Cremer
- Katholieke Universiteit Leuven and Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Rik Lories
- Katholieke Universiteit Leuven and Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Doreen Belz
- Klinikum der Universitaet zu Koeln, Cologne, Germany
| | | | | | | | | | | | | | | | | | - Nuria Barbarroja
- Reina Sofia University Hospital and University of Cordoba, Cordoba, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aurélie De Groof
- Université Catholique de Louvain and Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Julie Ducreux
- Université Catholique de Louvain and Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Bernard Lauwerys
- Université Catholique de Louvain and Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Anne-Lise Maudoux
- Université Catholique de Louvain and Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Divi Cornec
- Université de Brest, Centre Hospitalier Universitaire de Brest, INSERM, and Labex IGO, Brest, France
| | | | - Sandrine Jousse-Joulin
- Université de Brest, Centre Hospitalier Universitaire de Brest, INSERM, and Labex IGO, Brest, France
| | | | - Bénédicte Rouvière
- Université de Brest, Centre Hospitalier Universitaire de Brest, INSERM, and Labex IGO, Brest, France
| | - Alain Saraux
- Université de Brest, Centre Hospitalier Universitaire de Brest, INSERM, and Labex IGO, Brest, France
| | - Quentin Simon
- Université de Brest, Centre Hospitalier Universitaire de Brest, INSERM, and Labex IGO, Brest, France
| | | | | | | | | | | | | | | | | | | | | | - Qingyu Cheng
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Velia Gerl
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Falk Hiepe
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | - Silvia Thiel
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | | | | | | | | | | | - Laurence Laigle
- Institut de Recherches Internationales Servier, Suresnes, France
| | | | | | - Yves Renaudineau
- Université de Brest, Centre Hospitalier Universitaire de Brest, INSERM, and Labex IGO, Brest, France
| | | | | | - Javier Martín
- Institute of Parasitology and Biomedicine "López Neyra", Spanish National Research Council, Granada, Spain
| | - Lorenzo Beretta
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | - Jacques-Olivier Pers
- Université de Brest, Centre Hospitalier Universitaire de Brest, INSERM, and Labex IGO, Brest, France
| | - Marta E Alarcón-Riquelme
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain, and Karolinska Institutet, Stockholm, Sweden
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