title: Deep sequencing of the hepatitis B virus in hepatocellular carcinoma patients reveals enriched integration events, structural alterations and sequence variations.
abstract: 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. HBx-human 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.
authors.affiliation: Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
authors.forename: Soo Ting
authors.initials: ST
authors.lastname: Toh
authors.forename: Yu
authors.initials: Y
authors.lastname: Jin
authors.forename: Lizhen
authors.initials: L
authors.lastname: Liu
authors.forename: Jingbo
authors.initials: J
authors.lastname: Wang
authors.forename: Farbod
authors.initials: F
authors.lastname: Babrzadeh
authors.forename: Baback
authors.initials: B
authors.lastname: Gharizadeh
authors.forename: Mostafa
authors.initials: M
authors.lastname: Ronaghi
authors.forename: Han Chong
authors.initials: HC
authors.lastname: Toh
authors.forename: Pierce Kah-Hoe
authors.initials: PK
authors.lastname: Chow
authors.forename: Alexander Y-F
authors.initials: AY
authors.lastname: Chung
authors.forename: London L-P-J
authors.initials: LL
authors.lastname: Ooi
authors.forename: Caroline G-L
authors.initials: CG
authors.lastname: Lee
mesh_terms: D019943:Amino Acid Substitution; D001483:Base Sequence; D006528:Carcinoma, Hepatocellular / Q000150:complications / Q000235:genetics / Q000821:virology*; D002460:Cell Line; D002879:Chromosomes, Human, Pair 10 / Q000821:virology; D004279:DNA, Viral / Q000235:genetics; D014644:Genetic Variation; D006515:Hepatitis B virus / Q000235:genetics*; D019694:Hepatitis B, Chronic / Q000150:complications; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics / Q000821:virology*; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D019098:Telomerase / Q000096:biosynthesis / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics; D054334:Viral Regulatory and Accessory Proteins; D016662:Virus Integration / Q000235:genetics
chemical_list: D004279:DNA, Viral; D015534:Trans-Activators; D054334:Viral Regulatory and Accessory Proteins; C057628:hepatitis B virus X protein; C509186:TERT protein, human; D019098:Telomerase