Integrative genomic analyses revealed colorectal cancer susceptibility genes in risk loci identified in genome-wide association studies

Genome-wide association studies (GWAS) have identified approximately 50 loci associated with colorectal cancer (CRC) risk. However, the target genes and underlying mechanisms are largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using data from the Genotype-Tissue Expression (GTEx), The Cancer Genome Atlas (TCGA), and the Colonomics projects. We identified 24 putative target genes for 17 index SNPs at Benjamini-Hochberg adjusted P < 0.05 in at least one of the datasets. By analyzing functional genomic data, our result further indicated that 18 genes (75%) showed evidence of cis-regulation by putative functional SNPs via promoter or enhancer-promoter interactions. We next performed in vitro functional assays for three genes, TMBIM1, AAMP, and CABLES2, and confirmed that they play a vital role in colorectal carcinogenesis via disruption of cell behavior. Furthermore, our results indicate that silencing CABLES2 can promote the PI3K/AKT pathway. Our study reveals new candidate susceptibility genes and provides novel insight into the biological mechanisms for CRC development. We conducted RNA-sequencing in the CABLES2 shRNA-1 and control vehicle cells with two technical replicates