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Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

Nature Genetics volume 44, pages 765–769 (2012)Cite this article

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Abstract

To survey hepatitis B virus (HBV) integration in liver cancer genomes, we conducted massively parallel sequencing of 81 HBV-positive and 7 HBV-negative hepatocellular carcinomas (HCCs) and adjacent normal tissues. We found that HBV integration is observed more frequently in the tumors (86.4%) than in adjacent liver tissues (30.7%). Copy-number variations (CNVs) were significantly increased at HBV breakpoint locations where chromosomal instability was likely induced. Approximately 40% of HBV breakpoints within the HBV genome were located within a 1,800-bp region where the viral enhancer, X gene and core gene are located. We also identified recurrent HBV integration events (in ≥4 HCCs) that were validated by RNA sequencing (RNA-seq) and Sanger sequencing at the known and putative cancer-related TERT, MLL4 and CCNE1 genes, which showed upregulated gene expression in tumor versus normal tissue. We also report evidence that suggests that the number of HBV integrations is associated with patient survival.

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Figure 1: Visualization of HBV integration breakpoints in the HCC and HBV genomes.
Figure 2: Overall statistics for HBV integration events in HCC tumors.
Figure 3: Mapping of HBV breakpoint integration sites.
Figure 4: Influence of HBV integration on gene expression in HCC.
Figure 5: Clinical correlation analysis of HBV integration in HCC.

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NCBI Reference Sequence

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Acknowledgements

We gratefully acknowledge Y.-K. Mak and the clinical team of the Division of Hepatobiliary and Pancreatic Surgery (HBP) at Queen Mary Hospital. This study was funded by the Asian Cancer Research Group (ACRG), a not-for-profit organization formed by Eli Lilly, Merck and Pfizer. We thank S. Friend and G. Jin for initiating the establishment of ACRG. We are grateful to former and present members of ACRG, especially K. Blanchard, Y. Turpaz, J. Sedgwick, G. Tucker-Kellogg, G. Gilliland, P. Shaw, N. Gibson and S. Adams.

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Author notes

  1. John M Luk

    Present address: Present address: Department of Oncology, Roche R&D Center (China) Ltd., Shanghai, China.,

  2. Wing-Kin Sung, Hancheng Zheng, Shuyu Li, Ronghua Chen and Xiao Liu: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Surgery, University of Hong Kong, Hong Kong

    Wing-Kin Sung, Nikki P Lee, Kwong F Wong, Angela M Liu, Ronnie T Poon, Sheung Tat Fan, Kwong L Chan & John M Luk

  2. School of Computing, National University of Singapore (NUS), Singapore

    Wing-Kin Sung & Chandana Tennakoon

  3. NUS Graduate School for Integrative Sciences & Engineering, National University of Singapore, Singapore

    Wing-Kin Sung & Chandana Tennakoon

  4. Department of Computational & Systems Biology, Genome Institute of Singapore, Singapore

    Wing-Kin Sung, Wah H Lee, Pramila N Ariyaratne & Fabianus H Mulawadi

  5. Beijing Genomics Institute, Shenzhen, China

    Hancheng Zheng, Xiao Liu, Yingrui Li, Zhuolin Gong, Yujie Hu, Zhao Lin, Guan Wang, Qinghui Zhang & Jun Wang

  6. Eli Lilly & Co., Indianapolis, Indiana, USA

    Shuyu Li, Thomas D Barber, Wen-Chi Chou, Amit Aggarwal & Christoph Reinhard

  7. Merck Research Laboratories, Boston, Massachusetts, USA

    Ronghua Chen, Ke Hao, Wei Zhou, Chunsheng Zhang, James Hardwick, Carolyn Buser & Hongyue Dai

  8. Department of Pharmacology, NUS, Singapore

    Kwong F Wong, Angela M Liu & John M Luk

  9. Department of Surgery, NUS, Singapore

    Kwong F Wong, Angela M Liu & John M Luk

  10. Cancer Science Institute, NUS, Singapore

    Kwong F Wong, Angela M Liu & John M Luk

  11. Asian Cancer Research Group, Inc., Wilmington, Delaware, USA

    James Hardwick & Mao Mao

  12. Pfizer Oncology, San Diego, California, USA

    Jiangchun Xu, Zhengyan Kan & Mao Mao

  13. Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Jun Wang

  14. The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark

    Jun Wang

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  1. Wing-Kin Sung
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Corresponding authors

Correspondence to Christoph Reinhard, Jun Wang or John M Luk.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Table 1 and Supplementary Note (PDF 1422 kb)

Supplementary Table 2

Summary of sequencing depth and coverage of 88 (TU/AN) pairs of HCC. (XLS 46 kb)

Supplementary Table 3

Characterization of 399 HBV integration breakpoints identified in HCC. (XLS 139 kb)

Supplementary Table 4

Validation result for the HBV integration sites. (XLS 40 kb)

Supplementary Table 5

Correlation analysis of HBV integration (cutoff = 1 to 6) with various clinic-pathological parameters of HCC patients (n = 83). (XLSX 13 kb)

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Sung, WK., Zheng, H., Li, S. et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet 44, 765–769 (2012). https://doi.org/10.1038/ng.2295

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