Background: Rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and SLE with antiphospholipid syndrome (SLE+APS) are complex autoimmune disorders characterized by overlapping yet distinct clinical features. Understanding the molecular underpinnings of these conditions is crucial for developing targeted therapies.

Objectives: To elucidate the shared and distinct gene expression profiles linked to specific clinical features in rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and SLE with antiphospholipid syndrome (SLE+APS) through comparative transcriptomic analysis of immune cells.

Methods: Advanced computational methods were employed to integrate transcriptomic and clinical data from peripheral blood mononuclear cells of 257 RA patients, 66 SLE patients, -including 20 with SLE+APS-, obtained via RNA sequencing. This involved aligning gene expression data to a reference genome, normalizing the data, and annotating genes. Gene Set Variation Analysis (GSVA) then identified pathway-level alterations by analysing predefined gene sets rather than individual genes, enabling single-sample pathway enrichment analysis. Unsupervised hierarchical clustering of the resulting altered transcriptomic profiles subsequently identified distinct patient subgroups and gene modules. Finally, correlation and association analyses explored the relationships between these gene modules and clinical parameters.

Results: Unsupervised clustering of the transcriptomic data identified three distinct clusters (C1, C2, C3), each demonstrating unique gene expression patterns across 11 gene modules, indicative of varying biological pathways and cellular functions. Patients from all conditions were evenly distributed among the clusters. Clinically, C1 was associated with increased cardiovascular risk in RA, higher disease activity and renal involvement in SLE, and prevalent thrombotic events in SLE+APS. C2 was characterized by high disease activity and pulmonary involvement in RA and increased cardiovascular risk in SLE and SLE+APS. C3 displayed an intermediate profile with autoantibody positivity across all three conditions and significant renal involvement, thrombosis, and abortions in SLE+APS. Gene profile analysis highlighted that C2 showed heightened activity in modules related to myeloid cells, inflammation, and interferon responses, whereas C1 and C3 showed increased T and B cell activity; C1 further displayed increased platelet signaling, and C3 enhanced immunoregulation modules. Common alterations in integrin-mediated cell adhesion and signaling were observed across all clusters. In addition to the alteration in gene signatures linked to specific clinical features in each disease, several shared genomic modules were found to correlate with common clinical profiles across these disorders:

• Cell Cycle Regulation correlated with disease activity indices in RA and SLE.

• Integrin-mediated cell adhesion was linked to cardiovascular risk RA and APS+SLE.

• Myeloid cells activity was associated with cardiovascular risk in SLE and APS+SLE.

Conversely, specific gene modules showed unique but distinctive correlations with clinical features in various diseases:

• Inflammatory Network and interferon response correlated positively with disease activity in RA and cardiovascular risk in SLE.

• T Cell Activity negatively correlated with disease activity in RA and complement C3 levels in SLE.

• B Cell Activity was associated with pulmonary involvement in RA and autoantibody positivity in SLE.

• Immunoregulation was linked to joint erosion in RA and autoantibody positivity in SLE and SLE+APS

Conclusion: The identification of distinct transcriptomic clusters underscores the molecular heterogeneity in RA, SLE, and SLE+APS, primarily driven by inflammation and immune dysregulation. These findings reveal both shared and unique genomic characteristics associated with clinical manifestations, providing new insights into disease-specific mechanisms and potential therapeutic targets. Supported by EU/EFPIA IMI-JU 3TR, ISCIII (PI21/00591, PI21/00959, CD21/00187 and RICOR-21/0002/0033), co-financed by European Union, and MINECO (RYC2021-033828-I/PID2022-141500OA-I00).

REFERENCES: NIL.

Acknowledgements: NIL.

Disclosure of Interests: None declared.

© The Authors 2025. This abstract is an open access article published in Annals of Rheumatic Diseases under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ ). Neither EULAR nor the publisher make any representation as to the accuracy of the content. The authors are solely responsible for the content in their abstract including accuracy of the facts, statements, results, conclusion, citing resources etc.