Project Summary Juvenile idiopathic arthritis (JIA) is a diverse family of inflammatory arthritides that begin in childhood. Genome-wide association studies in the most common phenotype, seronegative oligoarticular plus polyarticular JIA (sometimes for simplicity termed “polygoJIA”), have identified 27 non-HLA loci associated with disease risk. GWAS of the most destructive variant, systemic JIA, has defined additional loci. Each of these “hits” marks a biological pathway in the pathogenesis of JIA. 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 have so far provided limited insight into JIA biology. To address this roadblock, our lab has recently developed two novel experimental methods. SNP-seq interrogates candidate regulatory variants using enzymatic restriction followed by next-generation sequencing to identify those that bind transcription factors and other regulatory proteins. Flanking Restriction Enhanced Pulldown (FREP) is an efficient method to pull down the associated protein(s) for identification by mass spectrometry, thereby linking disease-associated variants to particular cellular pathways. This tandem strategy allows us to bridge the gap between GWAS and mechanism. The hypothesis underlying this proposal is that experimental dissection of genetic associations will identify new mechanisms and thus new potential therapeutic targets in JIA. In Aim I, we will pursue SNP-seq + FREP to identify novel DNA-protein associations that drive polygoJIA risk. We screened 1,223 genetic polymorphisms in close linkage disequilibrium with 27 polygoJIA risk loci and identified multiple strong candidate functional variants, including several validated experimentally using techniques including electrophoretic mobility shift, luciferase and CRISPR. We will confirm these high-probability variants and then extend the work to other SNP-seq hits. In Aim II, beginning with an independent SNP-seq screen of the TRAF1/C5 locus, we will employ FREP and other upstream and downstream validation approaches to define how this locus drives risk of polygoJIA. We will employ SNP-seq + FREP to interrogate recently- available GWAS findings in systemic JIA to define mechanisms in this unique, highly-inflammatory disease. Together, these studies will allow us to identify DNA-protein associations that drive the pathogenesis of JIA.