Ex vivo JAK and TNF inhibitor-modulated immune signatures guide first-line therapy selection in rheumatoid arthritis.
7 affiliations
- 1IMIBIC/Reina Sofia Hospital/University of Cordoba, Córdoba, Spain.
- 2Department of Cell Biology, Immunology and Physiology, Agrifood Campus of International Excellence, University of Córdoba, ceiA3, Córdoba, Spain.
- 3Cobiomic Bioscience, EBT IMIBIC/UCO, Córdoba, Spain.
- 4Rheumatology and Immuno-Mediated Diseases Research Group (IRIDIS), Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
- 5Center for Genomics and Oncological Research (GENYO), Granada, Spain.
- 6Institute for Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
- 7IMIBIC/Reina Sofia Hospital/University of Cordoba, Córdoba, Spain. [email protected].
Abstract
Background
Rheumatoid arthritis (RA) is a heterogeneous autoimmune disease for which selecting the most appropriate first targeted therapy remains challenging. We integrated ex vivo immune-cell functional assays, targeted proteomics, clinical outcomes, and a three-dimensional (3D) synovial model to identify treatment-associated molecular signatures and evaluate their relationship with subsequent response to Janus kinase inhibitors (JAKi) or tumour necrosis factor inhibitors (TNFi).Methods
Peripheral blood mononuclear cells and neutrophils from 48 b/tsDMARDs-naïve RA patients were cultured with autologous serum and treated ex vivo with Baricitinib or Etanercept to assess proliferation, adhesion, NETosis, and 92 inflammation-related proteins. The resulting JAKi- and TNFi-modulated protein signatures were subsequently evaluated in pretreatment serum from four independent RA treatment cohorts (n = 223; naïve and non-naïve). Unsupervised clustering was used to identify molecular subgroups, which were related to longitudinal DAS28-CRP outcomes at 3, 6, and 12 months. Logistic regression, neural network, and random forest models were evaluated using repeated nested cross-validation in naïve patients to discriminate treatment-specific 6-month remission outcomes. In a subset of naïve remission achievers, paired baseline and 6-month sera were applied to a 3D synovial micromass model.Results
Ex vivo JAKi and TNFi comparably modulated immune cell functions but induced distinct protein signatures with limited overlap. When evaluated in pretreatment baseline serum, these signatures stratified b/tsDMARD-naïve patients into clusters with different baseline inflammatory profiles and treatment-specific ΔDAS28-CRP. High baseline expression of a drug-specific signature was associated with remission with the corresponding therapy and failure to achieve remission with the alternative treatment. Under repeated nested cross-validation, logistic regression showed the highest mean discrimination among the models, with an AUC of 0.70 (SD, 0.03; empirical 2.5th-97.5th percentile, 0.65-0.75) for distinguishing treatment-specific remission outcomes in b/tsDMARD-naïve RA. In remission achievers, 6-month sera from either therapy significantly reduced synovial lining thickness in 3D micromasses versus baseline.Conclusion
Ex vivo-derived JAKi- and TNFi-associated immune-related protein signatures, integrated within a machine-learning framework, showed moderate discriminatory ability for treatment-specific remission patterns in b/tsDMARD-naïve RA and, together with complementary evidence of reduced synovial lining thickness in remission achievers, support further investigation of biomarker-informed selection between JAKi and TNFi as first targeted therapies.
Related
- Integrative proteomic and machine learning strategies identify key biomarkers associated with response to JAK inhibitor in rheumatoid arthritis.
- Sustained pain improvement and IL-12-related biomarker changes in rheumatoid arthritis patients initiating baricitinib or TNF inhibitor therapy
- Integrated Transcriptomic and Single-Cell Analysis Reveals Shared Macrophage-Associated Inflammatory Signatures in MASLD/NAFLD and Rheumatoid Arthritis
- Renal function–adjusted initial JAK inhibitor dosing and outcomes in rheumatoid arthritis: from the ANSWER cohort study
- Characteristic central nervous system fingerprints and related molecular signatures in difficult-to-treat rheumatoid arthritis.
BibTeX
@article{corrales2026vivo,
title = {{Ex vivo JAK and TNF inhibitor-modulated immune signatures guide first-line therapy selection in rheumatoid arthritis.}},
author = {Sagrario Corrales and Carlos Pérez-Sánchez and Tomas Cerdó and Christian Merlo and Beatriz Malvar-Fernández and Samuel García and Laura Muñoz-Barrera and Ismael Sanchez-Pareja and Lydia Formanti and Elena Moreno-Caño and Rafaela Ortega-Castro and Jerusalén Calvo and Concepción Aranda-Varela and Lourdes Ladehesa and Pilar Font and M Carmen Abalos-Aguilera and Desirée Ruiz-Vilchez and Mª Ángeles Aguirre and Nuria Barbarroja and Marta E Alarcon-Riquelme and Alejandro Escudero-Contreras and Chary López-Pedrera},
journal = {Biomarker research},
year = {2026},
month = oct,
doi = {10.1186/s40364-026-01029-4},
url = {https://europepmc.org/article/MED/42907925},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Ex vivo JAK and TNF inhibitor-modulated immune signatures guide first-line therapy selection in rheumatoid arthritis.
AU - Sagrario Corrales
AU - Carlos Pérez-Sánchez
AU - Tomas Cerdó
AU - Christian Merlo
AU - Beatriz Malvar-Fernández
AU - Samuel García
AU - Laura Muñoz-Barrera
AU - Ismael Sanchez-Pareja
AU - Lydia Formanti
AU - Elena Moreno-Caño
AU - Rafaela Ortega-Castro
AU - Jerusalén Calvo
AU - Concepción Aranda-Varela
AU - Lourdes Ladehesa
AU - Pilar Font
AU - M Carmen Abalos-Aguilera
AU - Desirée Ruiz-Vilchez
AU - Mª Ángeles Aguirre
AU - Nuria Barbarroja
AU - Marta E Alarcon-Riquelme
AU - Alejandro Escudero-Contreras
AU - Chary López-Pedrera
PY - 2026
DA - 2026/10/22
JO - Biomarker research
DO - 10.1186/s40364-026-01029-4
UR - https://europepmc.org/article/MED/42907925
AB - Background Rheumatoid arthritis (RA) is a heterogeneous autoimmune disease for which selecting the most appropriate first targeted therapy remains challenging. We integrated ex vivo immune-cell functional assays, targeted proteomics, clinical outcomes, and a three-dimensional (3D) synovial model to identify treatment-associated molecular signatures and evaluate their relationship with subsequent response to Janus kinase inhibitors (JAKi) or tumour necrosis factor inhibitors (TNFi).Methods Peripheral blood mononuclear cells and neutrophils from 48 b/tsDMARDs-naïve RA patients were cultured with autologous serum and treated ex vivo with Baricitinib or Etanercept to assess proliferation, adhesion, NETosis, and 92 inflammation-related proteins. The resulting JAKi- and TNFi-modulated protein signatures were subsequently evaluated in pretreatment serum from four independent RA treatment cohorts (n = 223; naïve and non-naïve). Unsupervised clustering was used to identify molecular subgroups, which were related to longitudinal DAS28-CRP outcomes at 3, 6, and 12 months. Logistic regression, neural network, and random forest models were evaluated using repeated nested cross-validation in naïve patients to discriminate treatment-specific 6-month remission outcomes. In a subset of naïve remission achievers, paired baseline and 6-month sera were applied to a 3D synovial micromass model.Results Ex vivo JAKi and TNFi comparably modulated immune cell functions but induced distinct protein signatures with limited overlap. When evaluated in pretreatment baseline serum, these signatures stratified b/tsDMARD-naïve patients into clusters with different baseline inflammatory profiles and treatment-specific ΔDAS28-CRP. High baseline expression of a drug-specific signature was associated with remission with the corresponding therapy and failure to achieve remission with the alternative treatment. Under repeated nested cross-validation, logistic regression showed the highest mean discrimination among the models, with an AUC of 0.70 (SD, 0.03; empirical 2.5th-97.5th percentile, 0.65-0.75) for distinguishing treatment-specific remission outcomes in b/tsDMARD-naïve RA. In remission achievers, 6-month sera from either therapy significantly reduced synovial lining thickness in 3D micromasses versus baseline.Conclusion Ex vivo-derived JAKi- and TNFi-associated immune-related protein signatures, integrated within a machine-learning framework, showed moderate discriminatory ability for treatment-specific remission patterns in b/tsDMARD-naïve RA and, together with complementary evidence of reduced synovial lining thickness in remission achievers, support further investigation of biomarker-informed selection between JAKi and TNFi as first targeted therapies.
SN - 2050-7771
ER -