Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by persistent synovial inflammation and progressive joint destruction. Although N6-methyladenosine (m⁶A) modification is increasingly recognized as an important epitranscriptomic regulatory mechanism, its role in RA remains incompletely understood. This study integrated transcriptomic analysis, m⁶A methylome profiling, and functional experiments to investigate the potential role of m⁶A-associated growth arrest-specific 6 (GAS6) in RA.

Synovial tissue samples from patients with RA and healthy controls (HC) were subjected to mRNA sequencing, and m⁶A-related integrative analysis was performed using public epitranscriptomic datasets. Peripheral blood mononuclear cells (PBMCs) and serum samples were collected from patients with RA and HC subjects. The expression levels of GAS6 and MER proto-oncogene, tyrosine kinase (MERTK) were measured by quantitative real-time PCR (qRT-PCR) and Western blotting, and the levels of interleukin (IL)-1β, IL-6, IL-10, and transforming growth factor-β1 (TGF-β1) were determined by enzyme-linked immunosorbent assay (ELISA). Small interfering RNA (siRNA) was used to silence GAS6 and MERTK in rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS). Cell viability, apoptosis, migration, and protein expression were evaluated using Cell Counting Kit-8 (CCK-8), flow cytometry, wound-healing assay, immunofluorescence staining, and Western blotting.

Integrated multi-omics analysis identified 323 genes with both differential expression and altered m⁶A modification, mainly enriched in efferocytosis-related pathways, T helper 17 cell differentiation, and cellular senescence. Among these candidates, GAS6 showed prominent m⁶A hypermethylation and significant upregulation, suggesting a potential epitranscriptomic association. GAS6 was closely linked to the efferocytosis-related receptors MERTK and AXL in pathway and interaction analyses. In patients with RA, GAS6 and MERTK expression levels were significantly increased and were associated with inflammatory burden and disease activity. Functional experiments further showed that silencing GAS6 or MERTK inhibited the pathogenic phenotype of RA-FLS, including excessive proliferation, migration, pro-inflammatory cytokine production, and resistance to apoptosis.

Aberrant m⁶A modification may act as an important epitranscriptomic regulator in RA and is associated with activation of the GAS6/MERTK signaling axis. In the stromal context of RA-FLS, this axis may contribute to synovial inflammation and pathological progression. These findings provide new insight into the context-dependent role of the m⁶A-GAS6/MERTK pathway in RA and suggest that it may represent a potential biomarker and therapeutic target warranting further mechanistic investigation.