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

• Published in: Carcinogenesis (New York) 2021-11, Vol.42 (11), p.1347-1356
• Main Authors: Wang, Haoxue, Yang, Beifang, Cai, Xiaomin, Cheng, Xiang, Shen, Na, Liu, Li, Li, Jiaoyuan, Wang, Ying, He, Heng, Ying, Pingting, Li, Bin, Lu, Zequn, Yang, Nan, Wang, Xiaoyang, Zhang, Fuwei, Li, Yanmin, Wang, Wenzhuo, Ning, Caibo, Zhu, Ying, Chang, Jiang, Miao, Xiaoping, Tian, Jianbo, Zhong, Rong
• Format: Article
• Language: English
• Subjects: Antisense Elements (Genetics) - genetics; Carcinoma, Hepatocellular - genetics; Carcinoma, Hepatocellular - pathology; Cell Line, Tumor; Enhancer Elements, Genetic; HLA-DQ beta-Chains - genetics; HLA-DQ beta-Chains - metabolism; Humans; Liver Neoplasms - genetics; Liver Neoplasms - pathology; Polymorphism, Single Nucleotide; Promoter Regions, Genetic; Quantitative Trait Loci; RNA, Long Noncoding - genetics
• ISSN: 0143-3334; 1460-2180
• DOI: 10.1093/carcin/bgab095

Abstract Substantial evidence highlighted the critical role of long non-coding RNAs (lncRNA) in driving hepatocarcinogenesis. We hypothesized that functional variants in genome-wide association studies (GWASs) associated loci might alter the expression levels of lncRNAs and contribute to the development of hepatocellular carcinoma (HCC). Here, we prioritized potentially cis-expression quantitative trait loci-based single nucleotide polymorphism (SNP)-lncRNA association together with the physical interaction by the analyses from Hi-C data in GWAS loci of chronic hepatitis B 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 (odds ratio = 1.26, 95% CI = 1.11 to 1.43, P = 4.14 × 10−4). Luciferase reporter assays and electrophoretic mobility shift assays showed that rs2647046 A allele significantly increased transcriptional activity via influencing transcript factor 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. After prioritizing SNPs by expression quantitative trait loci analysis and Hi-C data, we identified that SNP rs2647046 with modulating HLA-DQB1-AS1 expression is associated with HCC risk. By functional assays, HLA-DQB1-AS1 promotes cell proliferation and confers HCC risk by long-range SNP.