Hepatocellular carcinoma risk variant modulates lncRNA HLA-DQB1-AS1 expression via a long-range enhancer-promoter interaction.

Abstract

Substantial evidence highlighted the critical role of long noncoding RNAs (lncRNA) in driving hepatocarcinogenesis. We hypothesized that functional variants in Genome-wide association studies (GWAS) associated loci might alter the expression levels of lncRNAs and contribute to the development of hepatocellular carcinoma (HCC). Here, we prioritized potentially cis-eQTL-based SNP-lncRNA association together with the physical interaction by the analyses from Hi-C data in GWAS loci of chronic hepatitis B (CHB) and HCC. Subsequently, by leveraging two stage case-control study (1738 hepatitis B (HBV) related HCC cases and 1988 HBV persistent carriers) and biological assays, we identified that rs2647046 was significantly associated with HCC risk (OR = 1.26, 95%CI = 1.11-1.43, P =\u20094.14×10 -4). Luciferase reporter assays and EMSA assays showed that rs2647046 A allele significantly increased transcriptional activity via influencing TF binding affinity. Allele-specific chromosome conformation capture assays revealed that enhancer with rs2647046 interacted with the HLA-DQB1-AS1 promoter to allele-specifically influence its expression by CTCF-mediated long-range loop. Cell proliferation assays indicated that HLA-DQB1-AS1 is a potential oncogene in HCC. Our study showed HLA-DQB1-AS1 regulated by a causal SNP in a long-range interaction manner conferred the susceptibility to HCC, suggesting an important mechanism of modulating lncRNA expression for risk-associated SNPs in the etiology of HCC.