Analysis of viral integration reveals new insights of oncogenic mechanism in HBV-infected intrahepatic cholangiocarcinoma and combined hepatocellular-cholangiocarcinoma

Abstract

Background Integration of HBV DNA into the human genome could progressively contribute to hepatocarcinogenesis. Both intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC) are known to be associated with HBV infection. However, the integration of HBV and mechanism of HBV-induced carcinogenesis in ICC and CHC remains unclear. Methods 41 patients with ICC and 20 patients with CHC were recruited in the study. We conducted HIVID analysis on these 61 samples to identify HBV integration sites in both the tumor tissues and adjacent non-tumor liver tissues. To further explore the effect of HBV integration on gene alteration, we selected paired tumors and adjacent non-tumor liver tissues from 3 ICC and 4 CHC patients for RNA-seq and WGS. Results We detected 493 HBV integration sites in ICC patients, of which 417 were from tumor samples and 76 were from non-tumor samples. And 246 HBV integration sites were detected in CHC patients, of which 156 were located in the genome of tumor samples and 90 were in non-tumor samples. Recurrent HBV integration events were detected in ICC including TERT, ZMAT4, MET, ANKFN1, PLXNB2, and in CHC like TERT, ALKBH5. Together with our established data of HBV-infected hepatocellular carcinoma, we found that HBV preferentially integrates into the specific regions which may affect the gene expression and regulation in cells and involved in carcinogenesis. We further performed genomic and transcriptomic sequencing of three ICC and four CHC patients, and found that HBV fragments could integrate near some important oncogene like TERT, causing large-scale genome variations on nearby genomic sequences, and at the same time changing the expression level of the oncogenes. Conclusion Comparative analysis demonstrates numerous newly discovered mutational events in ICC and CHC resulting from HBV insertions in the host genome. Our study provides an in-depth biological and clinical insights into HBV-induced ICC and CHC.

Genomic Analysis of Amphioxus Reveals a Wide Range of Fragments Homologous to Viral Sequences

“…Statistical significance was assessed by computing either the p value or the adjusted p value (using the Bonferroni method) based on the chi-squared (X 2 ) test. This test was selected because it enables comparison of the observed frequency distribution of a categorical variable with an expected frequency distribution that follows a specific theoretical distribution, as previously reported in the literature [53][54][55][56].…”

HBV Infection and Host Interactions: The Role in Viral Persistence and Oncogenesis

“…The recurrently targeted genes (RTGs) potentially involved in genomic integration processes are numerous [96,97]. However, Péneau et al [98] analyzed the characteristics of the HBV integrations involved in hepatocarcinogenesis, showing that, in HCC tumor cells, the genomic integration occurs more frequently at the level of three specific genes: telomerase reverse transcriptase (TERT), cyclin E1 (CCNE1), and KMT2B.…”

Mutational Landscape of Cholangiocarcinoma According to Different Etiologies: A Review

“…As for HCC, recent studies suggest that HBV integration is not a random event, but preferentially occurs in the promoter region of target genes [38]. A molecular analysis of 41 HBV-associated iCCAs identified most recurrent HBV integration events in TERT (10%), ZMAT4 (5%), MET (5%), ANKFN1 (5%), and PLXNB2 (5%) genes [39]. Another molecular analysis of a largest population study of 108 HBV-associated iCCAs reported the occurrence of HBV insertion in 41.7% of cases, with recurrent integration sites in TERT, FN1, FAT2, BRD9, ABCA12 and NBPF20 genes [40].…”