Identification of potential functional variants and genes at 18q21.1 associated with the carcinogenesis of colorectal cancer

• Published in: PLoS genetics Vol. 18; no. 2; p. e1010050
• Main Authors: Cheng, Xiaoqing, Zhang, Fenglan, Gong, Jingwen, Li, Yige, Zhou, Dan, Wang, Jing, Vong, Eu Gene, Yuan, Ying, Lai, Maode, Zhang, Dandan
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 02.02.2022; Public Library of Science (PLoS)
• Subjects: Annotations; Binding sites; Biology and Life Sciences; Cancer; Carcinogenesis; Chromosome 18; Chromosomes; Colorectal cancer; Colorectal carcinoma; Colorectal Neoplasms - genetics; Datasets; Development and progression; Disease; Epigenetics; Gene expression; Gene loci; Genetic aspects; Genetic Predisposition to Disease; Genome-wide association studies; Genome-Wide Association Study; Genomes; Health risk assessment; Humans; Linkage disequilibrium; Malignancy; Medicine and Health Sciences; mRNA; Oncology, Experimental; Polymorphism, Single Nucleotide; Risk factors; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Smad7 protein; Smooth muscle; Therapeutic targets; China
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1010050

Genome-wide association studies (GWAS) have identified more than 160 susceptibility loci for colorectal cancer (CRC). The effects of these variants, particularly their mechanisms, however, remain unclear. In this study, a comprehensive functional annotation of CRC-related GWAS signals was firstly conducted to identify the potential causal variants. We found that the SNP rs7229639 in intron 3 of SMAD7 at 18q21.1 might serve as a putative functional variant in CRC. The SNP rs7229639 is located in a region with evidence of regulatory potential. Dual-luciferase reporter assays revealed that three other SNPs (rs77544449, rs60385309 and rs72917785), in strong linkage disequilibrium (LD) with rs7229639, exhibited allele-specific enhancer activity, of which one of the target genes may conceivably be LIPG, as suggested by eQTL association data and Hi-C data. We also verified that LIPG promoted malignancy of CRC cells in vitro, with supporting clinical data indicating that LIPG is upregulated and correlated with a poor prognosis in CRC. Finally, pitavastatin was observed to exhibit an anti-CRC activity and modest inhibition of LIPG mRNA levels. Collectively, our data suggest that these functional variants at 18q21.1 are involved in the pathogenesis of CRC by modulating enhancer activity, and possibly LIPG expression, thus indicating a promising therapeutic target for CRC. The results of functional annotation in our investigation could also serve as an inventory for CRC susceptibility SNPs and offer guides for post-GWAS downstream functional studies.