Genetic predisposition to colon and rectal adenocarcinoma is mediated by a super-enhancer polymorphism co-activating CD9 and PLEKHG6

Background: Genome-wide association studies (GWASs) have identified dozens of loci associated with colon and rectal adenocarcinoma risk. As tissue-specific super-enhancers (SEs) play important roles in tumorigenesis, we systematically investigate SEs and inner variants in established GWAS loci to decipher the underlying biological mechanisms. Methods: Through a comprehensive bioinformatics analysis on multi-omics data, we screen potential single nucleotide polymorphisms (SNPs) in cancer-specific SEs, and then subject them to a two-stage case-control study totally containing 4929 cases and 7083 controls of Chinese population. A series of functional assays including reporter gene assays, electrophoretic mobility shift assays (EMSAs), CRISPR-cas9 genome editing, chromosome conformation capture (3C) assays and cell proliferation experiments are performed to characterize the variant9s molecular consequence and target genes. Results: The SNP rs11064124 in 12p13.31 is found significantly associated with the risk of colon and rectal adenocarcinoma with an odds ratio (OR) being 0.87 (95% confidence intervals (CI) = 0.82-0.92, P = 8.67E-06). The protective rs11064124-G weakens the binding affinity with vitamin D receptor (VDR), and increases the enhancer9s activity and interactions with two target genes9 promoters, thus co-activates the transcription of CD9 and PLEKHG6 which are both putative tumor suppressor genes for colon and rectal adenocarcinoma. Conclusions: Our integrative study highlights a SE polymorphism rs11064124, and two susceptibility genes CD9 and PLEKHG6 in 12p13.31 for colon and rectal adenocarcinoma. Impact: These findings suggest a novel insight for genetic pathogenesis of colon and rectal adenocarcinoma, involving transcriptional co-activation of diverse susceptibility genes via the SE element as a gene regulation hub.