Functional characterization of the novel GWAS-identified GP2 coding variant

In a meta-analysis of three GWASs in the Japanese population, we identified a novel locus at 16p12.3 significantly associated with pancreatic cancer susceptibility. A series of experiments were performed to explore the functional impact of the nonsynonymous lead SNP rs78193826 of the GP2 gene at 16p12.3 on global gene expression. Based on CRISPR-Cas9-induced mutation, RNA-seq, and GSEA analyses, we demonstrated that the functional relevance of rs78193826 may involve modulation of KRAS activity. GP2-expressing pancreatic cancer cell line PaTu 8988s was used for functional characterizations of the lead SNP rs78193826. The genome-edited PaTu 8988s cell line (GP2_V282M) was generated through mutation induced by CRISPR-Cas9-mediated homologous recombination. Control cell line (GP2_WT) was obtained from clones without induced mutation by the same plasmid transfection. RNA-seq was performed using two biological replicates in each of GP2_V282M and GP2_WT groups. Differentially expressed genes between the two groups were identified using GFOLD. The GSEA was performed using the MSigDB v6.2 collections - H and C6.