Genome - Wide Association Of HBV - Associated Liver Diseases

Hepatitis B virus(HBV) infection is one of the major infectious diseases with more than 250 million chronic carriers worldwide. The prevalence of HBV infection is high in China, meanwhile, HBV infection may cause a broad spectrum of liver diseases, which is a potential serious threat to public health of China. The clinical outcome of HBV infection shows obvious individual differences. Only a fraction of subjects infected with HBV will develop chronic HBV infection, cirrhosis and hepatocellular carcinoma(HCC). For example, most adults who are infected with HBV, will spontaneously recovered. Only a fraction of these persons will develop chronic infections. Moreover, only a fraction of chronic HBV carriers will develop HCC. The segregation analyses and twin studies strongly suggest that genetic susceptibility plays an important role in the progress of HBV-related liver diseases. Systematically identifying susceptibility loci for HBV-related liver diseases will be of great significance for the prevention and treatment of these diseases. Genome-wide association study(GWAS) has emerged as a powerful and successful tool to identify susceptibility loci for common diseases. To identify loci underlying HBV-related diseases(persistent HBV infection and HBV-related HCC), we performed two GWASs.Recently, several genome-wide association studies(GWASs) have identified single nucleotide polymorphisms(SNPs) at eight loci linking genetic susceptibility to persistent HBV infection in populations of Asia ancestry, including HLA-DP(index rs3077 and rs9277535), HLA-DQ(rs2856718 and rs7453920), HLA-C(rs3130542), EHMT2(rs652888), TCF19(rs1419881), CFB(rs12614) and two non-HLA loci UBE2L3(rs4821116) and CD40(rs1883832). To identify novel genetic loci involved in persistent HBV infection, we performed a GWAS among Chinese populations. GWAS scan was performed in 1,251 persistently HBV infected subjects(PIs, cases) and 1,057 spontaneously recovered subjects(SRs, controls), followed by replications in four independent populations totally consisting of 3,905 PIs and 3,356 SRs. We replicated the previously reported HLA-DP and HLA-DQ at 6p21.32, CFB at 6p21.33 and CD40 at 20q13.12. Additionally, previously identified HLA alleles were replicated in the present study. We identified two novel SNP, rs9277934 in COL11A2 gene at 6p21.33(OR = 0.81, P = 6.0 × 10-11) and rs7000921 at 8p21.3(OR = 0.78, P = 3.2 × 10-12), were identified to be strongly associated with persistent HBV infection, which reached the genome-wide significant threshold of 5 × 10-8. We found no appreciable variation of the effect of both SNPs on persistent HBV infection across the subgroups stratified by age or gender.The SNP rs9277934 in COL11A2 gene at 6p21.33 was a nonsynonymous SNP(Glu276Lys). Several studies have suggested that collagen related pathway might play a role in immune regulation, suggesting COL11A2 gene may be the candidate gene at 6p21.33 for persistent HBV infection. The SNP rs7000921 was at intergenic region at 8p21.3. We identified significant expression quantitative trait locus(eQTL) associations for INTS10 gene at 8p21.3, suggesting that INTS10 gene may be the candidate gene at 8p21.3 for persistent HBV infection. We further demonstrated that INST10 suppresses HBV replication in liver cells. Based on mRNA expression profiles of liver tissues, we obseverd significant up-regulation of the retinoic acid-inducible gene-I-like receptor(RLR) signaling pathway in samples with high INTS10 expression. This suggested that INST10 suppresses HBV replication through RLR signaling pathway. We further demonstrated that INST10 could suppresse HBV replication through IRF3. We also observed that the plasma INTS10 is significantly downregulated in PIs compared to SRs, and negatively correlated with the HBV DNA levels. These results suggested that INTS10 may be an antiviral gene.In conclusion, these findings highlight two novel potential antiviral genes COL11A2 and INTS10 in the clearance of HBV infection, which may provide new insights for prevention and treatment of persistent HBV infection.In additional, using genome-wide association study(GWAS) strategy, we and others identified single nucleotide polymorphisms(SNPs) at chromosome 1p36.22, 2q32.3, 6p21.32 and 21q21.3 to be significantly associated with HBV-related HCC. However, the identified loci only explain a fraction of the heritability of HBV-related HCC, and additional genetic risk factors remain to be discovered. To identify new genetic susceptibility loci for HBV-related HCC, we carried out a GWAS among Chinese populations, using a combination of family trios-based and case/control-based designs.GWAS scan. GWAS scan was performed in 205 HBV-related HCC proband-parent trios(consisting of 615 individuals) combined with 348 chronic HBV carriers with HCC(cases) and 359 chronic HBV carriers without HCC(controls) in our previous GWAS. We replicated the previously reported SNPs at KIF1 B, HLA-DQA1/DRB1, HLA-DQ and BACH2. We noted that many SNPs, which were associated with other HBV-related phenotypes, were also significantly associated with HBV-related HCC, suggesting existence of shared genetic risk factors among these HBV-related phenotypes. We then selected 14 novel loci which were identified to be significantly associated with HBV-related HCC in the discovery GWAS stage for replication. Through a two-stage replication totally consisting of 2,280 cases and 2,004 controls, we newly identified a signal within the CDK14 gene at 7q21.13(index rs10273859) to be significantly associated with susceptibility to HBV-related HCC(OR = 1.30, P = 2.63 × 10-8), which reached the genome-wide significant threshold of 5 × 10-8. We found no appreciable variation of the effect of rs10272859 on HBV-related HCC across the subgroups stratified by age or gender. This SNP was also shown to be significantly associated with the survival of patients with HCC. Furthermore, we observed that the at-risk allele of rs10272859[G] was associated with higher mRNA expression of CDK14 in HCC tissues. Chromosome conformation capture analyses confirmed the interaction between the promoter region of CDK14 and the risk-associated SNPs at 7q21.13 in liver cells.Our findings suggest that the CDK14 gene at 7q21.13 confers susceptibility to HBV-related HCC. The variants at 7q21.13 may help to define high-risk populations of HCC.