Hepatocellular carcinoma‐associated single‐nucleotide variants and deletions identified by the use of genome‐wide high‐throughput analysis of hepatitis B virus

Abstract

This study investigated hepatitis B virus (HBV) single-nucleotide variants (SNVs) and deletion mutations linked with hepatocellular carcinoma (HCC). Ninety-three HCC patients and 108 non-HCC patients were enrolled for HBV genome-wide next-generation sequencing (NGS) analysis. A systematic literature review and a meta-analysis were performed to validate NGS-defined HCC-associated SNVs and deletions. The experimental results identified 60 NGS-defined HCC-associated SNVs, including 41 novel SNVs, and their pathogenic frequencies. Each SNV was specific for either genotype B (n = 24) or genotype C (n = 34), except for nt53C, which was present in both genotypes. The pathogenic frequencies of these HCC-associated SNVs showed a distinct U-shaped distribution pattern. According to the meta-analysis and literature review, 167 HBV variants from 109 publications were categorized into four levels (A-D) of supporting evidence that they are associated with HCC. The proportion of NGS-defined HCC-associated SNVs among these HBV variants declined significantly from 75% of 12 HCC-associated variants by meta-analysis (Level A) to 0% of 10 HCC-unassociated variants by meta-analysis (Level D) (P < 0.0001). PreS deletions were significantly associated with HCC, in terms of deletion index, for both genotypes B (P = 0.030) and C (P = 0.049). For genotype C, preS deletions involving a specific fragment (nt2977-3013) were significantly associated with HCC (HCC versus non-HCC, 6/34 versus 0/32, P = 0.025). Meta-analysis of preS deletions showed significant association with HCC (summary odds ratio 3.0; 95% confidence interval 2.3-3.9). Transfection of Huh7 cells showed that all of the five novel NGS-defined HCC-associated SNVs in the small surface region influenced hepatocarcinogenesis pathways, including endoplasmic reticulum-stress and DNA repair systems, as shown by microarray, real-time polymerase chain reaction and western blot analysis. Their carcinogenic mechanisms are worthy of further research. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Comparison of hepatitis B virus genotypes B and C among chronically hepatitis B virus‐infected patients who received nucleos(t)ide analogs: A multicenter retrospective study

“…[5][6][7][8][9][10][11][12] As viral factors from nucleotide sequencing analyses, core promoter mutations, precore mutations, core mutations, and Pre-S deletions have been reported. 10,13,14 Recently, the hepatitis B X protein genotype was reported to be associated with HCC development and HCC proliferation in vitro and in vivo. 15 Additionally, some single-nucleotide polymorphisms in several genes including HLA class I and II have been shown to be associated with HBV-related HCC.…”

“…Several cohorts have identified the risk factors for HBV‐related HCC, such as age, male sex, albumin, platelet counts (PLT), advanced fibrosis/liver cirrhosis, HBV DNA, and hepatitis B core‐related antigen (HBcrAg) . As viral factors from nucleotide sequencing analyses, core promoter mutations, precore mutations, core mutations, and Pre‐S deletions have been reported . Recently, the hepatitis B X protein genotype was reported to be associated with HCC development and HCC proliferation in vitro and in vivo .…”

Mechanisms and clinical behavior of hepatocellular carcinoma in HBV and HCV infection and alcoholic and non-alcoholic fatty liver disease

“…In addition to the integration mechanisms of the viral genome, specific mutations in the X regions, pre-core, core-promoter and pre-S may increase the risk of developing HCC [39,40] . Among the most frequent mutations at the nuclear promoter level, the double mutation A1762T/G1764A is closely related to the probability of developing HCC.…”

Cancer Evo-Dev, a novel hypothesis derived from studies on hepatitis B virus-induced carcinogenesis

“…The predictive value of HBV preS deletion on the occurrence of HCC in patients chronically infected with HBV has been confirmed in a prospective study [54] . Recent deep sequencing analysis has demonstrated that the preS deletions involving a specific fragment (nt2977-3013) in HBV genotype C are significantly associated with HCC [55] . These epidemiological evidences indicate that the HBV mutations including preS deletion, A1762T/G1764A, C1653T, and T1753V are the etiological factors of HBVinduced HCC.…”

“…Mutations in the preS and S regions also notably facilitate carcinogenesis. Transfection of Huh7 cells with the large S region with preS deletion has shown that HCC-associated single-nucleotide variants (SNVs) in the small surface region of HBV genome influence carcinogenesis pathways, including endoplasmic reticulum-stress and DNA repair systems [55] . The HBV large envelope protein gene fragment (preS1/ preS2/S), with F141L mutation in the preS2 region, can significantly promote the proliferation of hepatocytes by downregulating the p53 and p21 pathways and upregulating the expression of cyclin-dependent kinase 4 and cyclin A.…”