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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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