Recurrent Targeted Genes of Hepatitis B Virus in the Liver Cancer Genomes Identified by a Next-Generation Sequencing–Based Approach

Abstract

Integration of the viral DNA into host chromosomes was found in most of the hepatitis B virus (HBV)–related hepatocellular carcinomas (HCCs). Here we devised a massive anchored parallel sequencing (MAPS) method using next-generation sequencing to isolate and sequence HBV integrants. Applying MAPS to 40 pairs of HBV–related HCC tissues (cancer and adjacent tissues), we identified 296 HBV integration events corresponding to 286 unique integration sites (UISs) with precise HBV–Human DNA junctions. HBV integration favored chromosome 17 and preferentially integrated into human transcript units. HBV targeted genes were enriched in GO terms: cAMP metabolic processes, T cell differentiation and activation, TGF beta receptor pathway, ncRNA catabolic process, and dsRNA fragmentation and cellular response to dsRNA. The HBV targeted genes include 7 genes (PTPRJ, CNTN6, IL12B, MYOM1, FNDC3B, LRFN2, FN1) containing IPR003961 (Fibronectin, type III domain), 7 genes (NRG3, MASP2, NELL1, LRP1B, ADAM21, NRXN1, FN1) containing IPR013032 (EGF-like region, conserved site), and three genes (PDE7A, PDE4B, PDE11A) containing IPR002073 (3′, 5′-cyclic-nucleotide phosphodiesterase). Enriched pathways include hsa04512 (ECM-receptor interaction), hsa04510 (Focal adhesion), and hsa04012 (ErbB signaling pathway). Fewer integration events were found in cancers compared to cancer-adjacent tissues, suggesting a clonal expansion model in HCC development. Finally, we identified 8 genes that were recurrent target genes by HBV integration including fibronectin 1 (FN1) and telomerase reverse transcriptase (TERT1), two known recurrent target genes, and additional novel target genes such as SMAD family member 5 (SMAD5), phosphatase and actin regulator 4 (PHACTR4), and RNA binding protein fox-1 homolog (C. elegans) 1 (RBFOX1). Integrating analysis with recently published whole-genome sequencing analysis, we identified 14 additional recurrent HBV target genes, greatly expanding the HBV recurrent target list. This global survey of HBV integration events, together with recently published whole-genome sequencing analyses, furthered our understanding of the HBV–related HCC.

Genetic Profiling of Cancers of the Digestive System: Biological Insights and Clinical Implications

“…Interestingly, the same group very recently showed clonal integration of adenoassociated virus type 2 (AAV2) in known driver genes [41] , such as CCNA2, CCNE1, and TERT, among others, opening up another chapter of our understanding of HCC development. These data are in line with reports describing HBV insertions in TERT and MLL4, respectively [42,43] . While the precise functional role of many of these genetic aberrations and in particular for mutated genes that execute epigenetic regulation, as well as for alterations in the NRF2/KEAP1 pathway involved in the cellular oxidative stress response, remains to be explored in the next years, these data provide important insights into HCC carcinogenesis that will hopefully be clinically exploitable in the near future.…”

DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences

“…This study, together with a recent global survey of HBV integration events (Ding et al 2012;Fujimoto et al 2012;Jiang et al 2012;Sung et al 2012;Toh et al 2013), provides a foundation for the further experimentation and mechanistic understanding of HBV-HCC.…”

“…HBV-HCCs have been analyzed by comprehensive genome sequencing and highresolution genome mapping (Kan et al 2013;Li and Mao 2013;Nakagawa and Shibata 2013). Moreover, the recent deep sequencing of HBV DNA in patients with HCC revealed increased integration events, structural alterations, and sequence variations (Ding et al 2012;Fujimoto et al 2012;Jiang et al 2012;Sung et al 2012;Toh et al 2013). A recent study identified a viral-human chimeric fusion transcript, HBx-LINE1, that functions like a long noncoding RNA to promote HCC (Lau et al 2014).…”

Reduced Expression of DNA Damage Repair Genes High Mobility Group Box1 and Poly(ADP-ribose) Polymerase1 in Inactive Carriers of Hepatitis B Virus Infection-A Possible Stage of Viral Integration

“…19 A recent study employing next generation sequencing technique has identified 286 unique HBV integration sites (UISs) with precise HBV-human DNA junctions suggesting a clonal expansion process during HCC development. 31 It is also known that HBV encodes HBX and preS2/S truncated proteins which may have transforming activity 32 and may interfere with DNA repair. 33 Despite the reported evidence of HBV integrants in almost all the human chromosomes favored by host cellular DNA damage and the potential role of HBV integration in development of HCC, 17 status of host DNA damage repair mechanisms has not been elucidated in HBV mediated disease.…”