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Deep sequencing of the hepatitis B virus in hepatocellular carcinoma patients reveals enriched integration events, structural alterations and sequence variations
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2013 (English)In: Carcinogenesis, ISSN 0143-3334, E-ISSN 1460-2180, Vol. 34, no 4, 787-798 p.Article in journal (Refereed) Published
Abstract [en]

Chronic hepatitis B virus (HBV) infection is epidemiologically associated with hepatocellular carcinoma (HCC), but its role in HCC remains poorly understood due to technological limitations. In this study, we systematically characterize HBV in HCC patients. HBV sequences were enriched from 48 HCC patients using an oligo-bead-based strategy, pooled together and sequenced using the FLX-Genome-Sequencer. In the tumors, preferential integration of HBV into promoters of genes (P < 0.001) and significant enrichment of integration into chromosome 10 (P < 0.01) were observed. Integration into chromosome 10 was significantly associated with poorly differentiated tumors (P < 0.05). Notably, in the tumors, recurrent integration into the promoter of the human telomerase reverse transcriptase (TERT) gene was found to correlate with increased TERT expression. The preferred region within the HBV genome involved in integration and viral structural alteration is at the 3'-end of hepatitis B virus X protein (HBx), where viral replication/transcription initiates. Upon integration, the 3'-end of the HBx is often deleted. HBxhuman chimeric transcripts, the most common type of chimeric transcripts, can be expressed as chimeric proteins. Sequence variation resulting in non-conservative amino acid substitutions are commonly observed in HBV genome. This study highlights HBV as highly mutable in HCC patients with preferential regions within the host and virus genome for HBV integration/structural alterations.

Place, publisher, year, edition, pages
2013. Vol. 34, no 4, 787-798 p.
Keyword [en]
Amino Acid Substitution, Base Sequence, Carcinoma, Hepatocellular, Cell Line, Chromosomes, Human, Pair 10, DNA, Viral, Genetic Variation, Hepatitis B virus, Hepatitis B, Chronic, High-Throughput Nucleotide Sequencing, Humans, Liver Neoplasms, Promoter Regions, Genetic, Sequence Analysis, DNA, Telomerase, Trans-Activators, Virus Integration
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Medical and Health Sciences
Identifiers
URN: urn:nbn:se:kth:diva-146831DOI: 10.1093/carcin/bgs406ISI: 000317401200007Scopus ID: 2-s2.0-84875932668OAI: oai:DiVA.org:kth-146831DiVA: diva2:725515
Note

QC 20140616

Available from: 2014-06-16 Created: 2014-06-16 Last updated: 2017-12-05Bibliographically approved

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