Massively parallel reporter assay (MPRA) combined with bayesian fine mapping approaches prioritize variants associated with multiple sclerosis (MS) from genome wide association studies (GWAS) with a potential functional role and interaction with environmental factors

Multiple Sclerosis is a complex autoimmune disorder. Large-scale Genome-Wide Association Studies (GWAS) have detected 200 MS risk loci. Linkage Disequilibrium (LD) represents a limitation of GWAS in pinpointing likely causative variants among the large number of associated SNPs, thus further evaluations are required such as Fine-Mapping and MPRA. Functionally informed fine mapping was performed using Paintor and CaviarBF on 36 known MS regions showing a significant replication in an Italian cohort with genotypes imputated against the HCR panel (5903 individuals, 4259 MS, and 1644 HC), and overlapping with at least one drug target gene (Drug-Gene Interaction database v4.2 (DGIdb). We also used the Open Targets Genetics tool for variant-to-gene mapping. For five regions, we functionally analyzed all the SNPs in LD (r2> 0.77) with the lead SNP using the Massively Parallel Reporter Assay (MPRA). We applied the mpralm tool to obtain a (LogFC) which gives the difference in the expression of variants. MotifbreakR and MEME suite allowed the selection of TF that bind in the presence of a specific allele. Following the described pipeline, MPRA was able to distinguish, 8 variants (replicated in two separate experiments) as potential variants influencing their target gene expression.We identified variants altering the expression of 4 different genes out of the 5 tested through preferential binding of TF. MEF2B binding on Rs1883832 and AHR binding to RS6974022 the CD40 gene with Iscalimab as a drug, TCF4, and E2F4 binding on 3 variants with VEGF-B as a target gene, VEGF154 and CONBERCEPT as drugs. TGIF2 and PROX1 binding with 2 variants with IFNGR2 gene as a target, and INTERFERON GAMMA-1B as a drug. TBX3 binding on 1 variant targeting the TEC gene with Capivarsetib as a drug. Using the MPRA to test the influence of MS-associated environmental factors we were able to identify 2 variants that change their effect on gene expression in the presence of the EBNA2 1.2 variant.