Bridging the gap between GWAS and mechanism in arthritis

PROJECT SUMMARY Juvenile idiopathic arthritis (JIA) and rheumatoid arthritis (RA) are inflammatory disease of joints that together affect >1% of the population. Genome-wide association studies (GWAS) have identified >120 non- HLA loci associated with disease risk, each marking a biological pathway confirmed by human population genetics to play a role the pathogenesis of inflammatory arthritis. Unfortunately, pinpointing these mechanisms from GWAS data has proven difficult. GWAS hits mark large segments of DNA, termed haplotypes. Most of these haplotypes contain no SNPs (single nucleotide polymorphisms) or other variants that affect coding, suggesting that most causative polymorphisms are regulatory. Finding regulatory SNPs and the proteins that bind them has proven to be exceptionally difficult, and as a result GWAS in JIA and RA have so far provided limited insight into arthritis biology. In the first cycle of this award, we developed an experimental approach to this problem that allowed us to address this roadblock, identifying pathogenic mechanisms engaged by regulatory variants at TRAF1/C5 and CD28/CTLA4/ICOS. Each solution established a novel pathway not only for arthritis biology but more broadly to mechanisms of immunoregulation, specifically a new feedback loop that limits TNF production and a previously unrecognized role for ICOS in differentiation of T peripheral helper cells. We now propose to use this approach to define new mechanisms of human arthritis mediated through T lymphocytes, testing the hypothesis that common non-coding SNPs uncover novel T cell mechanisms in inflammatory arthritis. Aim I pursues a new variant in the CD28/CTLA4/ICOS that we show regulates not only CTLA4 expression but also Treg abundance; we define the transcription factor that mediates the effect and test whether the impact on Treg abundance is driven through differentiation or stability. Aim II extends these studies first to ANKRD55/IL6ST, a risk locus for both JIA and RA that we implicate in the regulation of CD4+ effector and regulatory T cells; and then more broadly to Tregs, based on a successful massively parallel reporter assay that we will extend using SNP-seq, a novel high-throughput technique developed in the lab that interrogates candidate regulatory variants using enzymatic restriction followed by next- generation sequencing to identify those that bind transcription factors and other regulatory proteins. Together, these studies will extend the successful first cycle of this proposal, leveraging human genetics to define potentially targetable pathways that drive the pathogenesis of JIA and RA.