Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach

PLoS Genet. 2012;8(12):e1003065. doi: 10.1371/journal.pgen.1003065. Epub 2012 Dec 6.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Carcinoma, Hepatocellular / genetics
  • Carcinoma, Hepatocellular / virology*
  • Cell Differentiation
  • Chromosome Mapping
  • Chromosomes, Human, Pair 17 / genetics
  • DNA, Viral / genetics
  • DNA, Viral / isolation & purification
  • Genome, Human
  • Hepatitis B virus* / genetics
  • Hepatitis B virus* / isolation & purification
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Liver Neoplasms / genetics*
  • Liver Neoplasms / virology
  • Telomerase / genetics
  • Virus Integration

Substances

  • DNA, Viral
  • Telomerase

Grants and funding

This work was supported by grants 2007DFC30360 and 2004CB518707 from the MOST, China, and the Science Fund for Creative Research Groups of the National Natural Science Foundation of China (81121002), and by the joint research center of the Hangzhou Proprium Biotechnology and Zhejiang University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.