Among the most significantly enriched pathways and processes we detected in the synovial tissues were those implicated in the epigenetic regulation of gene expression, including “SIRT1 negatively regulates rRNA expression”, “nucleosome”, and “RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function.” RUNX1 is associated with the susceptibility risk for RA [21,22] and was recently shown to epigenetically regulate gene expression, contributing to reduced disease severity in autoimmune arthritis [23]. Here, SIRT1 is linked to rheumatoid arthritis.