Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

Nature Genetics

Volumn 44, Issue 7, 2012, Pages 765-769

  Sung, Wing Kin ^a,b,c,d   Zheng, Hancheng ^e   Li, Shuyu ^f   Chen, Ronghua ^g   Liu, Xiao ^e   Li, Yingrui ^e   Lee, Nikki P ^a   Lee, Wah H ^d   Ariyaratne, Pramila N ^d   Tennakoon, Chandana ^b,c   Mulawadi, Fabianus H ^d   Wong, Kwong F ^a,b,h   Liu, Angela M ^a,b,h   Poon, Ronnie T ^a   Fan, Sheung Tat ^a   Chan, Kwong L ^a   Gong, Zhuolin ^e   Hu, Yujie ^e   Lin, Zhao ^e   Wang, Guan ^e   Zhang, Qinghui ^e   Barber, Thomas D ^f   Chou, Wen Chi ^f   Aggarwal, Amit ^f   Hao, Ke ^g   Zhou, Wei ^g   Zhang, Chunsheng ^g   Hardwick, James ^g,i   Buser, Carolyn ^g   Xu, Jiangchun ^j   Kan, Zhengyan ^j   Dai, Hongyue ^g   Mao, Mao ^i,j   Reinhard, Christoph ^f   Wang, Jun ^e,k,l   Luk, John M ^a,b,h,m   more..

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^d GENOME INSTITUTE OF SINGAPORE   (Singapore)

^e BGI SHENZHEN   (China)

^f ELI LILLY AND COMPANY   (United States)

^g MERCK RESEARCH LABORATORIES   (United States)

^h NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

ⁱ Asian Cancer Research Group Inc   (United States)

^j PFIZER INC   (United States)

^k UNIVERSITY OF COPENHAGEN   (Denmark)

^l Capital Region   (Denmark)

^m Roche R and D Center China Ltd   (China)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CANCER SURVIVAL; CCNE1 GENE; CHROMOSOMAL INSTABILITY; CONTROLLED STUDY; COPY NUMBER VARIATION; ENHANCER REGION; GENE EXPRESSION REGULATION; GENE LOCATION; GENE MAPPING; GENOME ANALYSIS; HEPATITIS B VIRUS; HUMAN; HUMAN TISSUE; LIVER; LIVER CELL CARCINOMA; MLL4 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; ONCOGENE; PRIORITY JOURNAL; REVIEW; RNA SEQUENCE; TERT GENE; UPREGULATION; VIRUS DNA CELL DNA INTERACTION; VIRUS GENE; VIRUS GENOME;

BASE SEQUENCE; CARCINOMA, HEPATOCELLULAR; CHROMOSOMAL INSTABILITY; CYCLIN E; DNA COPY NUMBER VARIATIONS; DNA, VIRAL; DNA-BINDING PROTEINS; FEMALE; HEPATITIS B VIRUS; HUMANS; LIVER NEOPLASMS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; ONCOGENE PROTEINS; RNA, VIRAL; SURVIVAL RATE; TELOMERASE; VIRUS INTEGRATION;

HEPATITIS B VIRUS;

EID: 84862999344     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2295     Document Type: Review

References (29)

1. Center, M.M. & Jemal, A. International trends in liver cancer incidence rates. Cancer Epidemiol. Biomarkers Prev. 20, 2362-2368 (2011).
2. But, D.Y., Lai, C.L. & Yuen, M.F. Natural history of hepatitis-related hepatocellular carcinoma. World J. Gastroenterol. 14, 1652-1656 (2008). (Pubitemid 351493370)
3. Ishikawa, T. Clinical features of hepatitis B virus-related hepatocellular carcinoma. World J. Gastroenterol. 16, 2463-2467 (2010).
4. Bréchot, C., Gozuacik, D., Murakami, Y. & Paterlini-Brechot, P. Molecular bases for the development of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Semin. Cancer Biol. 10, 211-231 (2000). (Pubitemid 30614221)
5. Zucman-Rossi, J. & Laurent-Puig, P. Genetic diversity of hepatocellular carcinomas and its potential impact on targeted therapies. Pharmacogenomics 8, 997-1003 (2007). (Pubitemid 47423689)
6. Gehring, A.J. et al. Profile of tumor antigen-specific CD8 T cells in patients with hepatitis B virus-related hepatocellular carcinoma. Gastroenterology 137, 682-690 (2009).
7. Shafritz, D.A., Shouval, D., Sherman, H.I., Hadziyannis, S.J. & Kew, M.C. Integration of hepatitis B virus DNA into the genome of liver cells in chronic liver disease and hepatocellular carcinoma. Studies in percutaneous liver biopsies and post-mortem tissue specimens. N. Engl. J. Med. 305, 1067-1073 (1981). (Pubitemid 12234831)
8. Koshy, R. et al. Integration of hepatitis B virus DNA: evidence for integration in the single-stranded gap. Cell 34, 215-223 (1983).
9. Brechot, C., Pourcel, C., Louise, A., Rain, B. & Tiollais, P. Presence of integrated hepatitis B virus DNA sequences in cellular DNA of human hepatocellular carcinoma. Nature 286, 533-535 (1980). (Pubitemid 10017698)
10. Chakraborty, P.R., Ruiz-Opazo, N., Shouval, D. & Shafritz, D.A. Identification of integrated hepatitis B virus DNA and expression of viral RNA in an HBsAg-producing human hepatocellular carcinoma cell line. Nature 286, 531-533 (1980). (Pubitemid 10017697)
11. Bonilla Guerrero, R. & Roberts, L.R. The role of hepatitis B virus integrations in the pathogenesis of human hepatocellular carcinoma. J. Hepatol. 42, 760-777 (2005).
12. Murakami, Y. et al. Large scaled analysis of hepatitis B virus (HBV) DNA integration in HBV related hepatocellular carcinomas. Gut 54, 1162-1168 (2005). (Pubitemid 41025914)
13. Paterlini-Bréchot, P. et al. Hepatitis B virus-related insertional mutagenesis occurs frequently in human liver cancers and recurrently targets human telomerase gene. Oncogene 22, 3911-3916 (2003). (Pubitemid 36819664)
14. Gozuacik, D. et al. Identification of human cancer-related genes by naturally occurring Hepatitis B Virus DNA tagging. Oncogene 20, 6233-6240 (2001). (Pubitemid 32964436)
15. Saigo, K. et al. Integration of hepatitis B virus DNA into the myeloid/lymphoid or mixed-lineage leukemia (MLL4) gene and rearrangements of MLL4 in human hepatocellular carcinoma. Hum. Mutat. 29, 703-708 (2008). (Pubitemid 351614595)
16. Ferber, M.J. et al. Integrations of the hepatitis B virus (HBV) and human papillomavirus (HPV) into the human telomerase reverse transcriptase (hTERT) gene in liver and cervical cancers. Oncogene 22, 3813-3820 (2003). (Pubitemid 36760744)
17. Neuveut, C., Wei, Y. & Buendia, M.A. Mechanisms of HBV-related hepatocarcinogenesis. J. Hepatol. 52, 594-604 (2010).
18. Totoki, Y. et al. High-resolution characterization of a hepatocellular carcinoma genome. Nat. Genet. 43, 464-469 (2011).
19. Li, M. et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat. Genet. 43, 828-829 (2011).
20. Furuta, T. et al. Clinicopathologic features of hepatocellular carcinoma in young patients. Cancer 66, 2395-2398 (1990).
21. Kim, J.H. et al. Clinical features and prognosis of hepatocellular carcinoma in young patients from a hepatitis B-endemic area. J. Gastroenterol. Hepatol. 21, 588-594 (2006).
22. Hao, K. et al. Predicting prognosis in hepatocellular carcinoma after curative surgery with common clinicopathologic parameters. BMC Cancer 9, 389 (2009).
23. Xu, X. et al. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat. Biotechnol. 29, 735-741 (2011).
24. Chen, Y. et al. Complete genome sequence of hepatitis B virus (HBV) from a patient with fulminant hepatitis without precore and core promoter mutations: comparison with HBV from a patient with acute hepatitis infected from the same infectious source. J. Hepatol. 38, 84-90 (2003). (Pubitemid 36078528)
25. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
26. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008). (Pubitemid 351911867)
27. Lamb, J.R. et al. Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting. PLoS ONE 6, e20090 (2011).
28. Chiang, D.Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99-103 (2009).
29. Mermel, C.H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).