Post-GWAS functional studies reveal an RA-associated CD40 induced NF-kB signal transduction and transcriptional regulation network targeted by class II HDAC inhibitors.

Currently, it remains difficult to identify which SNPs identified by GWAS are functional, and how various functional SNPs (fSNPs) interact and contribute to disease susceptibility. GWAS have identified a CD40 locus that is associated with rheumatoid arthritis (RA). We previously used two techniques developed in our lab, SNP-seq and FREP-MS, to determine that the RA risk gene RBPJ regulates CD40 expression via a fSNP at the RA-associated CD40 locus. In the present work, by applying the same approach, we report the identification of 6 proteins that regulate RBPJ expression via binding to two fSNPs on the RA-associated RBPJ locus. Using these findings, together with published data, we constructed an RA-associated signal transduction and transcriptional regulation network (STTRN) that functionally connects multiple RA-associated risk genes via transcriptional regulation networks linked by CD40-induced NF-kB signaling. Remarkably, this STTRN provides insight into the potential mechanism of action for the histone deacetylase (HDAC) inhibitor givinostat, an approved therapy for systemic juvenile idiopathic arthritis (SJIA). Thus, generation of disease-associated STTRNs based on post-GWAS functional studies is demonstrated as a novel and effective approach to apply GWAS for mechanistic studies and target identification.