Epipolymorphisms associated with the clinical outcome of autoimmune arthritis affect CD4+ T cell activation pathways (expression)

Multifactorial diseases, including autoimmune juvenile idiopathic arthritis (JIA), result from a complex interplay between genetics and environment. Epigenetic mechanisms are believed to integrate such gene-environment interactions, fine-tuning gene expression and possibly contributing to immune system dysregulation. Although anti-TNF therapy has strongly increased JIA remission rates, it is not curative and up to 80% of patients flare upon treatment withdrawal. Thus, a crucial unmet medical and scientific need is to understand the immunological mechanisms associated with remission or flare to inform clinical decisions. Here, we explored the CD4+ T cell DNA methylome of 68 poly-articular and extended oligo-articular JIA patients, before and after anti-TNF therapy withdrawal, to identify features associated with maintenance of inactive disease (ID). Individual CpG sites were clustered in coherent modules without a priori knowledge of their function through network analysis. The methylation level of several CpG modules, specifically those enriched in CpG sites belonging to genes that mediate T cell activation, uniquely correlated with clinical activity. Differences in DNA methylation were already detectable at the time of therapy discontinuation, suggesting epigenetic predisposition. RNA profiling also detected differences in T cell activation markers, including HLA-DR, but, overall, its sensitivity was lower than epigenetic profiling. Changes to the T cell activation signature at the protein level were detectable by flow cytometry, confirming the biological relevance of the observed alterations in methylation. Our work proposes, for the first time, epigenetic discrimination between clinical activity states, and reveals T cell-related biological functions tied to, and possibly predicting and/or causing, clinical outcome. We measured gene expression (single replicates) in 125 CD4+ T cell samples form 68 randomly selected patients recruited in the trial “Determining Predictors of Safe Discontinuation of Anti-TNF Treatment in JIA” (ID: NCT00792233). At baseline (T0), patients were in clinical remission on medication, i.e., they maintained ID, for at least 6 months under treatment (anti-TNF). Therapy was withdrawn for eight months, after which (Tend) patients were stratified by clinical activity in patients maintaining ID or not (NO ID). Flares were tested at the time of flare (Tend), and therapy was then reintroduced.