The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients

Genome Research

Volumn 22, Issue 4, 2012, Pages 593-601

  Jiang, Zhaoshi ^a   Jhunjhunwala, Suchit ^a   Liu, Jinfeng ^a   Haverty, Peter M ^a   Kennemer, Michael I ^b   Guan, Yinghui ^a   Lee, William ^a   Carnevali, Paolo ^b   Stinson, Jeremy ^a   Johnson, Stephanie ^a   Diao, Jingyu ^a   Yeung, Stacy ^a   Jubb, Adrian ^a   Ye, Weilan ^a   Wu, Thomas D ^a   Kapadia, Sharookh B ^a   De Sauvage, Frederic J ^a   Gentleman, Robert C ^a   Stern, Howard M ^a   Seshagiri, Somasekar ^a   Pant, Krishna P ^b   Modrusan, Zora ^a   Ballinger, Dennis G ^b   Zhang, Zemin ^a   more..

^a GENENTECH INC   (United States)

^b Complete Genomics Inc ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CASE REPORT; COPY NUMBER VARIATION; GENE DISRUPTION; GENE EXPRESSION; GENE SEQUENCE; GENOMIC INSTABILITY; HEPATITIS B VIRUS; HUMAN; HUMAN CELL; HUMAN GENOME; HUMAN TISSUE; LIVER CELL; LIVER CELL CARCINOMA; NONHUMAN; PRIORITY JOURNAL; SOMATIC MUTATION; VIRUS CHARACTERIZATION; VIRUS DNA CELL DNA INTERACTION; VIRUS TRANSCRIPTION;

BASE SEQUENCE; BINDING SITES; CARCINOMA, HEPATOCELLULAR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; HEPATITIS B; HEPATITIS B VIRUS; HOST-PATHOGEN INTERACTIONS; HUMANS; LIVER NEOPLASMS; MALE; MOLECULAR SEQUENCE DATA; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME; VIRUS INTEGRATION;

HEPATITIS B VIRUS;

EID: 84859553856     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.133926.111     Document Type: Article

References (36)

1. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106. doi: 10.1186/gb-2010-11-10-r106.
2. Baeza N, Masuoka J, Kleihues P, Ohgaki H. 2003. AXIN1 mutations but not deletions in cerebellar medulloblastomas. Oncogene 22: 632-636. (Pubitemid 36188620)
3. Block TM, Mehta AS, Fimmel CJ, Jordan R. 2003. Molecular viral oncology of hepatocellular carcinoma. Oncogene 22: 5093-5107. (Pubitemid 37059591)
4. Bouchard MJ, Navas-Martin S. 2011. Hepatitis B and C virus hepatocarcinogenesis: Lessons learned and future challenges. Cancer Lett 305: 123-143.
5. Bréchot C, Gozuacik D, Murakami Y, Paterlini-Bréchot P. 2000. Molecular bases for the development of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Semin Cancer Biol 10: 211-231. (Pubitemid 30614221)
6. Chemin I, Zoulim F. 2009. Hepatitis B virus induced hepatocellular carcinoma. Cancer Lett 286: 52-59.
7. Crawford NP, Walker RC, Lukes L, Officewala JS, Williams RW, Hunter KW. 2008. The Diasporin Pathway: A tumor progression-related transcriptional network that predicts breast cancer survival. Clin Exp Metastasis 25: 357-369.
8. Dejean A, Sonigo P, Wain-Hobson S, Tiollais P. 1984. Specific hepatitis B virus integration in hepatocellular carcinoma DNA through a viral 11-base-pair direct repeat. Proc Natl Acad Sci 81: 5350-5354. (Pubitemid 14048745)
9. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, et al. 2010. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327: 78-81.
10. Farazi PA, DePinho RA. 2006. Hepatocellular carcinoma pathogenesis: From genes to environment. Nat Rev Cancer 6: 674-687. (Pubitemid 44286000)
11. Gozuacik D, Murakami Y, Saigo K, Chami M, Mugnier C, Lagorce D, Okanoue T, Urashima T, Bréchot C, Paterlini-Bréchot P. 2001. Identification of human cancer-related genes by naturally occurring Hepatitis B Virus DNA tagging. Oncogene 20: 6233-6240. (Pubitemid 32964436)
12. Guo W, Chen M, Yen TS, Ou JH. 1993. Hepatocyte-specific expression of the hepatitis B virus core promoter depends on both positive and negative regulation. Mol Cell Biol 13: 443-448. (Pubitemid 23006922)
13. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: An information aesthetic for comparative genomics. Genome Res 19: 1639-1645.
14. Lavanchy D. 2004. Hepatitis B virus epidemiology, disease burden, treatment, and current and emerging prevention and control measures. J Viral Hepat 11: 97-107. (Pubitemid 38365759)
15. Lee S, Lee J, Lee S-K, Lee JW. 2008. Activating signal cointegrator-2 is an essential adaptor to recruit histone H3 lysine 4 methyltransferases MLL3 and MLL4 to the liver X receptors. Mol Endocrinol 22: 1312-1319. (Pubitemid 351786992)
16. Lee J, Kim D-H, Lee S, Yang Q-H, Lee DK, Lee S-K, Roeder RG, Lee JW. 2009. A tumor suppressive coactivator complex of p53 containing ASC-2 and histone H3-lysine-4 methyltransferase MLL3 or its paralogue MLL4. Proc Natl Acad Sci 106: 8513-8518.
17. Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J, Yue P, Zhang Y, Pant KP, Bhatt D, et al. 2010. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465: 473-477.
18. Mason WS, Liu C, Aldrich CE, Litwin S, Yeh MM. 2010. Clonal expansion of normal-appearing human hepatocytes during chronic hepatitis B virus infection. J Virol 84: 8308-8315.
19. Meyerson M, Gabriel S, Getz G. 2010. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11: 685-696.
20. Michielsen P, Ho E. 2011. Viral hepatitis B and hepatocellular carcinoma. Acta Gastroenterol Belg 74: 4-8.
21. Mulyanto, Depamede SN, Wahyono A, Jirintai, Nagashima S, Takahashi M, Okamoto H. 2011. Analysis of the full-length genomes of novel hepatitis B virus subgenotypes C11 and C12 in Papua, Indonesia. J Med Virol 83: 54-64.
22. Murakami Y, Saigo K, Takashima H, Minami M, Okanoue T, Bréchot C, Paterlini-Bréchot P. 2005. Large scaled analysis of hepatitis B virus (HBV) DNA integration in HBV related hepatocellular carcinomas. Gut 54: 1162-1168. (Pubitemid 41025914)
23. Natarajan TG, Kallakury BV, Sheehan CE, Bartlett MB, Ganesan N, Preet A, Ross JS, Fitzgerald KT. 2010. Epigenetic regulator MLL2 shows altered expression in cancer cell lines and tumors from human breast and colon. Cancer Cell Int 10: 13. doi: 10.1186/1475-2867-10-13.
24. Paterlini-Bréchot P, Saigo K, Murakami Y, Chami M, Gozuacik D, Mugnier C, Lagorce D, Bréchot C. 2003. Hepatitis B virus-related insertional mutagenesis occurs frequently in human liver cancers and recurrently targets human telomerase gene. Oncogene 22: 3911-3916. (Pubitemid 36819664)
25. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin M-L, Ordóñez GR, Bignell GR, et al. 2010a. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463: 191-196.
26. Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin M-L, Beare D, Lau KW, Greenman C, et al. 2010b. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463: 184-190.
27. Raney AK, McLachlan A. 1997. Characterization of the hepatitis B virus major surface antigen promoter hepatocyte nuclear factor 3 binding site. J Gen Virol 78: 3029-3038. (Pubitemid 27480843)
28. Saigo K, Yoshida K, Ikeda R, Sakamoto Y, Murakami Y, Urashima T, Asano T, Kenmochi T, Inoue I. 2008. 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. (Pubitemid 351614595)
29. Segditsas S, Tomlinson I. 2006. Colorectal cancer and genetic alterations in the Wnt pathway. Oncogene 25: 7531-7537. (Pubitemid 44885752)
30. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, et al. 2011. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144: 27-40.
31. Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S, Tsutsumi S, Sonoda K, Totsuka H, Shirakihara T, et al. 2011. High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet 43: 464-469.
32. Wu TD, Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
33. Yu X, Mertz JE. 2001. Critical roles of nuclear receptor response elements in replication of hepatitis B virus. J Virol 75: 11354-11364. (Pubitemid 33063226)
34. Zeng W, Gouw ASH, van den Heuvel MC, Zwiers PJ, Zondervan PE, Poppema S, Zhang N, Platteel I, de Jong KP, Molema G. 2008. The angiogenic makeup of human hepatocellular carcinoma does not favor vascular endothelial growth factor/angiopoietin-driven sprouting neovascularization. Hepatology 48: 1517-1527.
35. Zöllner B, Feucht H-H, Sterneck M, Schäfer H, Rogiers X, Fischer L. 2006. Clinical reactivation after liver transplantation with an unusual minor strain of hepatitis B virus in an occult carrier. Liver Transpl 12: 1283-1289. (Pubitemid 44194598)
36. Zucman-Rossi J, Benhamouche S, Godard C, Boyault S, Grimber G, Balabaud C, Cunha AS, Bioulac-Sage P, Perret C. 2007. Differential effects of inactivated Axin1 and activated beta-catenin mutations in human hepatocellular carcinomas. Oncogene 26: 774-780. (Pubitemid 46204256)