Palmitoylation is a key post-translational modification with emerging implications in immunotherapy research. Despite recent advances, the role of palmitoylation in regulating rheumatoid arthritis (RA)-associated immune cells remains unexplored. Additionally, the effects of DNA methylation on RA-associated gene expression have not yet been fully characterized. 

This study aimed to employ Mendelian randomization (MR) to dissect the genetic pathways linking palmitoylation, DNA methylation, immune modulation, and RA. We integrated RA GWAS data from the Finngen database, palmitoylation gene data from eQTLGen, DNA methylation data from the UKB, and immune cell data from the GWAS Catalog. Two-sample MR and mediation analyses were performed to assess the causal relationships between palmitoylation genes, RA, and immune cells. 

Our analysis revealed that high expression of ZDHHC5, ZDHHC13, ZDHHC14, and ZDHHC18 increased RA risk. Mediation analysis revealed that DNA methylation at cg06216065 modulates ZDHHC18 expression, mediating 77.4% of its effect on RA progression. ZDHHC18 expression also influenced immune cells (e.g., CD3 on TD CD4+ and CD28- CD8br), mediating substantial effects on RA risk (68.6%–82.6%). Sensitivity analyses confirmed the robustness of these results. 

ZDHHC18, which is regulated by DNA methylation, plays a crucial role in RA pathogenesis through immune cell modulation. These findings highlight ZDHHC18 as a potential diagnostic and therapeutic target in RA.