In the present study, we demonstrated for the first time that VDR, PPAR-γ, and LC-3 participate in a functional module of autophagy (a functional module is a group of genes that are tightly associated through multiple feedback loops) and are significantly upregulated in RA synovial tissues, although autophagic flux was unexpectedly severely impaired. Here, MAP1LC3A is linked to rheumatoid arthritis.