Integrative functional screen of genomic loci uncovers CCND2 and its genetic regulatory mechanism in colorectal cancer development

Abstract

Although genome-wide association studies (GWASs) have identified dozens of loci associated with colorectal cancer (CRC) susceptibility, the causal genes or risk variants within these loci and their biological functions often remain elusive. Recently, the genomic locus 12p13.32, with the tag SNP rs10774214, was identified as a crucial CRC risk locus in Asian populations. However, the functional mechanism of this region has not been fully elucidated. Here, we applied a high-throughput RNA interference (RNAi) approach in CRC cell lines to interrogate the function of genes in this genomic region. Multiple genes were found to affect cell functions, with CCND2 having the most significant effect as an oncogene. Moreover, overexpressed CCND2 could promote CRC cell proliferation. Subsequently, by integrating a fine-mapping analysis and multi-ancestry large-scale population cohorts consisting of 14,358 CRC cases and 34,251 healthy controls, we identified a regulatory variant rs4477507-T that contributed to an increased CRC risk in populations from China (OR = 1.16, 95%CI = 1.11-1.22, P = 4.45×10-10) and Europe (OR = 1.17, 95%CI = 1.12-1.21, P = 1.65×10-14). Functional characterization of the variant demonstrated that it could act as an allele-specific enhancer to distally facilitate the expression of CCND2 mediated by the transcription factor TEAD4. Overall, our study underscores the essential role of CCND2 in CRC development and delineates its regulatory mechanism mediated by rs4477507, establishing an epidemiological and biological link between genetic variation and CRC pathogenesis.

Keywords: CCND2; Colorectal cancer; Enhancer-promoter interaction; GWAS; High-throughput RNA interference.