Prioritizing Parkinson’s disease risk genes in genome-wide association loci

Abstract

Recent advancements in Parkinson's disease (PD) drug development have been significantly driven by genetic research. Importantly, drugs supported by genetic evidence are more likely to be approved. While genome-wide association studies (GWAS) are a powerful tool to nominate genomic regions associated with certain traits or diseases, pinpointing the causal biologically relevant gene is often challenging. Our aim was to prioritize genes underlying PD GWAS signals. The polygenic priority score (PoPS) is a similarity-based gene prioritization method that integrates genome-wide information from MAGMA gene-level association tests and more than 57,000 gene-level features, including gene expression, biological pathways, and protein-protein interactions. We applied PoPS to data from the largest published PD GWAS in East Asian- and European-ancestries. We identified 120 independent associations with P < 5x10-8 and prioritized 46 PD genes across these loci based on their PoPS scores, distance to the GWAS signal, and presence of non-synonymous variants in the credible set. Alongside well-established PD genes (e.g., TMEM175 and VPS13C), some of which are targeted in ongoing clinical trials (i.e., SNCA, LRRK2, and GBA1), we prioritized genes with a plausible mechanistic link to PD pathogenesis (e.g., RIT2, BAG3, and SCARB2). Many of these genes hold potential for drug repurposing or novel therapeutic developments for PD (i.e., FYN, DYRK1A, NOD2, CTSB, SV2C, and ITPKB). Additionally, we prioritized potentially druggable genes that are relatively unexplored in PD (XPO1, PIK3CA, EP300, MAP4K4, CAMK2D, NCOR1, and WDR43). We prioritized a high-confidence list of genes with strong links to PD pathogenesis that may represent our next-best candidates for disease-modifying therapeutics. We hope our findings stimulate further investigations and preclinical work to facilitate PD drug development programs.