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Luque-Tévar M, Perez-Sanchez C, Patiño-Trives AM, Barbarroja N, Arias de la Rosa I, Abalos-Aguilera MC, Marin-Sanz JA, Ruiz-Vilchez D, Ortega-Castro R, Font P, Lopez-Medina C, Romero-Gomez M, Rodriguez-Escalera C, Perez-Venegas J, Ruiz-Montesinos MD, Dominguez C, Romero-Barco C, Fernandez-Nebro A, Mena-Vazquez N, Marenco JL, Uceda-Montañez J, Toledo-Coello MD, Aguirre MA, Escudero-Contreras A, Collantes-Estevez E, Lopez-Pedrera C. Integrative Clinical, Molecular, and Computational Analysis Identify Novel Biomarkers and Differential Profiles of Anti-TNF Response in Rheumatoid Arthritis. Front Immunol 2021; 12:631662. [PMID: 33833756 PMCID: PMC8022208 DOI: 10.3389/fimmu.2021.631662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/15/2021] [Indexed: 12/29/2022] Open
Abstract
Background: This prospective multicenter study developed an integrative clinical and molecular longitudinal study in Rheumatoid Arthritis (RA) patients to explore changes in serologic parameters following anti-TNF therapy (TNF inhibitors, TNFi) and built on machine-learning algorithms aimed at the prediction of TNFi response, based on clinical and molecular profiles of RA patients. Methods: A total of 104 RA patients from two independent cohorts undergoing TNFi and 29 healthy donors (HD) were enrolled for the discovery and validation of prediction biomarkers. Serum samples were obtained at baseline and 6 months after treatment, and therapeutic efficacy was evaluated. Serum inflammatory profile, oxidative stress markers and NETosis-derived bioproducts were quantified and miRNomes were recognized by next-generation sequencing. Then, clinical and molecular changes induced by TNFi were delineated. Clinical and molecular signatures predictors of clinical response were assessed with supervised machine learning methods, using regularized logistic regressions. Results: Altered inflammatory, oxidative and NETosis-derived biomolecules were found in RA patients vs. HD, closely interconnected and associated with specific miRNA profiles. This altered molecular profile allowed the unsupervised division of three clusters of RA patients, showing distinctive clinical phenotypes, further linked to the TNFi effectiveness. Moreover, TNFi treatment reversed the molecular alterations in parallel to the clinical outcome. Machine-learning algorithms in the discovery cohort identified both, clinical and molecular signatures as potential predictors of response to TNFi treatment with high accuracy, which was further increased when both features were integrated in a mixed model (AUC: 0.91). These results were confirmed in the validation cohort. Conclusions: Our overall data suggest that: 1. RA patients undergoing anti-TNF-therapy conform distinctive clusters based on altered molecular profiles, which are directly linked to their clinical status at baseline. 2. Clinical effectiveness of anti-TNF therapy was divergent among these molecular clusters and associated with a specific modulation of the inflammatory response, the reestablishment of the altered oxidative status, the reduction of NETosis, and the reversion of related altered miRNAs. 3. The integrative analysis of the clinical and molecular profiles using machine learning allows the identification of novel signatures as potential predictors of therapeutic response to TNFi therapy.
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Affiliation(s)
- Maria Luque-Tévar
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Carlos Perez-Sanchez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Alejandra Mª Patiño-Trives
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Nuria Barbarroja
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Ivan Arias de la Rosa
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Mª Carmen Abalos-Aguilera
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Juan Antonio Marin-Sanz
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Desiree Ruiz-Vilchez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Rafaela Ortega-Castro
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Pilar Font
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Clementina Lopez-Medina
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain.,Hospital Universitario de Jaen, Jaén, Spain.,Hospital Universitario Virgen Macarena, Sevilla, Spain.,Hospital Clínico Universitario, Malaga, Spain.,Hospital Regional Universitario de Malaga, Malaga, Spain.,Hospital Universitario Virgen de Valme, Sevilla, Spain.,Hospital Universitario de Jerez de la Frontera, Cádiz, Spain
| | - Montserrat Romero-Gomez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | | | | | | | | | | | | | | | | | | | | | - M Angeles Aguirre
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Alejandro Escudero-Contreras
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Eduardo Collantes-Estevez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
| | - Chary Lopez-Pedrera
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Reina Sofia, Universidad de Cordoba, Córdoba, Spain
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