Abnormal DNA methylation pattern and expression of DNA methyltransferase 1 promote synovitis and bone destruction in rheumatoid arthritis

Background Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by synovial hyperplasia and joint destruction, in which fibroblast-like synoviocytes (FLS) play a pivotal role. However, the epigenetic mechanisms underlying FLS activation remain incompletely understood. Methods DNA methylation chip sequencing and transcriptome sequencing were performed on FLS of RA and Osteoarthritis (OA) patients, then analyzed the role of DNA methylation in RA-FLS. DNA methyltransferase 1 (DNMT1) is the major enzyme regulating DNA methylation. In in vitro and in vivo experiments, the effects of inhibiting DNMT1 on FLS function and CIA mouse synovitis were detected. Results Compared with OA-FLS, RA-FLS exhibited 353 upregulated and 144 downregulated genes, mainly enriched in extracellular matrix organization, angiogenesis, and inflammatory signaling pathways such as PI3K-AKT, MAPK, and JAK-STAT. DNA methylation analysis identified 2550 hypermethylated and 3300 hypomethylated genes, which were enriched in pathways associated with cell proliferation, migration, and apoptosis. Integration of transcriptomic and methylation data revealed 96 methylation-regulated differentially expressed genes (MeDEGs), involving Rap1, mTOR, and Hippo signaling. Among key regulators, DNA methyltransferase 1 (DNMT1) was markedly up-regulated in RA-FLS. Functional validation showed that DNMT1 knock-down significantly suppressed RA-FLS proliferation, migration, invasion, induced G2/M cell-cycle arrest and reduced pro-inflammatory cytokine secretion. In collagen-induced arthritis (CIA) mouse model, pharmacological inhibition of DNMT1 alleviated joint inflammation and bone erosion without significant systemic toxicity. Conclusions Our findings demonstrate that aberrant DNA methylation contributes to RA-FLS activation, with DNMT1 serving as a key epigenetic driver of their “tumor-like” phenotype. Targeting DNMT1 may represent a promising therapeutic strategy for RA.