Recurrent Targeted Genes of Hepatitis B Virus in the Liver Cancer Genomes Identified by a Next-Generation Sequencing–Based Approach

English version České info

Integration of the viral DNA into host chromosomes was found in most of the hepatitis B virus (HBV)–related hepatocellular carcinomas (HCCs). Here we devised a massive anchored parallel sequencing (MAPS) method using next-generation sequencing to isolate and sequence HBV integrants. Applying MAPS to 40 pairs of HBV–related HCC tissues (cancer and adjacent tissues), we identified 296 HBV integration events corresponding to 286 unique integration sites (UISs) with precise HBV–Human DNA junctions. HBV integration favored chromosome 17 and preferentially integrated into human transcript units. HBV targeted genes were enriched in GO terms: cAMP metabolic processes, T cell differentiation and activation, TGF beta receptor pathway, ncRNA catabolic process, and dsRNA fragmentation and cellular response to dsRNA. The HBV targeted genes include 7 genes (PTPRJ, CNTN6, IL12B, MYOM1, FNDC3B, LRFN2, FN1) containing IPR003961 (Fibronectin, type III domain), 7 genes (NRG3, MASP2, NELL1, LRP1B, ADAM21, NRXN1, FN1) containing IPR013032 (EGF-like region, conserved site), and three genes (PDE7A, PDE4B, PDE11A) containing IPR002073 (3′, 5′-cyclic-nucleotide phosphodiesterase). Enriched pathways include hsa04512 (ECM-receptor interaction), hsa04510 (Focal adhesion), and hsa04012 (ErbB signaling pathway). Fewer integration events were found in cancers compared to cancer-adjacent tissues, suggesting a clonal expansion model in HCC development. Finally, we identified 8 genes that were recurrent target genes by HBV integration including fibronectin 1 (FN1) and telomerase reverse transcriptase (TERT1), two known recurrent target genes, and additional novel target genes such as SMAD family member 5 (SMAD5), phosphatase and actin regulator 4 (PHACTR4), and RNA binding protein fox-1 homolog (C. elegans) 1 (RBFOX1). Integrating analysis with recently published whole-genome sequencing analysis, we identified 14 additional recurrent HBV target genes, greatly expanding the HBV recurrent target list. This global survey of HBV integration events, together with recently published whole-genome sequencing analyses, furthered our understanding of the HBV–related HCC.

Vyšlo v časopise: Recurrent Targeted Genes of Hepatitis B Virus in the Liver Cancer Genomes Identified by a Next-Generation Sequencing–Based Approach. PLoS Genet 8(12): e32767. doi:10.1371/journal.pgen.1003065
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003065

Souhrn

Zdroje

1. ParkinDM (2006) The global health burden of infection-associated cancers in the year 2002. Int J Cancer 118: 3030–3044.

2. SzmunessW (1978) Hepatocellular carcinoma and the hepatitis B virus: evidence for a causal association. Prog Med Virol 24: 40–69.

3. MurakamiY, SaigoK, TakashimaH, MinamiM, OkanoueT, et al. (2005) Large scaled analysis of hepatitis B virus (HBV) DNA integration in HBV related hepatocellular carcinomas. Gut 54: 1162–1168.

4. TokinoT, MatsubaraK (1991) Chromosomal sites for hepatitis B virus integration in human hepatocellular carcinoma. J Virol 65: 6761–6764.

5. FeitelsonMA, LeeJ (2007) Hepatitis B virus integration, fragile sites, and hepatocarcinogenesis. Cancer Lett 252: 157–170.

6. MarchioA, PineauP, MeddebM, TerrisB, TiollaisP, et al. (2000) Distinct chromosomal abnormality pattern in primary liver cancer of non-B, non-C patients. Oncogene 19: 3733–3738.

7. GarciaM, de TheH, TiollaisP, SamarutJ, DejeanA (1993) A hepatitis B virus pre-S-retinoic acid receptor beta chimera transforms erythrocytic progenitor cells in vitro. Proc Natl Acad Sci U S A 90: 89–93.

8. WangJ, ZindyF, ChenivesseX, LamasE, HengleinB, et al. (1992) Modification of cyclin A expression by hepatitis B virus DNA integration in a hepatocellular carcinoma. Oncogene 7: 1653–1656.

9. HorikawaI, BarrettJC (2001) cis-Activation of the human telomerase gene (hTERT) by the hepatitis B virus genome. J Natl Cancer Inst 93: 1171–1173.

10. FerberMJ, MontoyaDP, YuC, AdercaI, McGeeA, et al. (2003) 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.

11. GilletNA, MalaniN, MelamedA, GormleyN, CarterR, et al. (2011) The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones. Blood 117: 3113–3122.

12. BradyT, RothSL, MalaniN, WangGP, BerryCC, et al. (2011) A method to sequence and quantify DNA integration for monitoring outcome in gene therapy. Nucleic Acids Research 39: e72–e72.

13. KoudijsMJ, KlijnC, van der WeydenL, KoolJ, Ten HoeveJ, et al. (2011) High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors. Genome Res 21: 2181–2189.

14. SungWK, ZhengH, LiS, ChenR, LiuX, et al. (2012) Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet doi:10.1038/ng.2295.

15. JiangZ, JhunjhunwalaS, LiuJ, HavertyPM, KennemerMI, et al. (2012) The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res 22: 593–601.

16. FujimotoA, TotokiY, AbeT, BoroevichKA, HosodaF, et al. (2012) Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet doi:10.1038/ng.2291.

17. WangGP, CiuffiA, LeipzigJ, BerryCC, BushmanFD (2007) HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res 17: 1186–1194.

18. JeungJU, ChoSK, ShinJS (2005) A partial-complementary adapter for an improved and simplified ligation-mediated suppression PCR technique. J Biochem Biophys Methods 64: 110–120.

19. ShaginDA, LukyanovKA, VagnerLL, MatzMV (1999) Regulation of average length of complex PCR product. Nucleic Acids Res 27: e23.

20. ShamayM, AgamiR, ShaulY (2001) HBV integrants of hepatocellular carcinoma cell lines contain an active enhancer. Oncogene 20: 6811–6819.

21. YooJK, KimJ, ChoiSJ, NohHM, KwonYD, et al. (2012) Discovery and Characterization of Novel MicroRNAs During Endothelial Differentiation of Human Embryonic Stem Cells. Stem Cells Dev 21: 2049–2057.

22. MasonWS, LiuC, AldrichCE, LitwinS, YehMM (2010) Clonal expansion of normal-appearing human hepatocytes during chronic hepatitis B virus infection. J Virol 84: 8308–8315.

23. MinamiM, PoussinK, BrechotC, PaterliniP (1995) A novel PCR technique using Alu-specific primers to identify unknown flanking sequences from the human genome. Genomics 29: 403–408.

24. TamoriA, YamanishiY, KawashimaS, KanehisaM, EnomotoM, et al. (2005) Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clin Cancer Res 11: 5821–5826.

25. Paterlini-BrechotP, SaigoK, MurakamiY, ChamiM, GozuacikD, et al. (2003) Hepatitis B virus-related insertional mutagenesis occurs frequently in human liver cancers and recurrently targets human telomerase gene. Oncogene 22: 3911–3916.

26. MinamiM, DaimonY, MoriK, TakashimaH, NakajimaT, et al. (2005) Hepatitis B virus-related insertional mutagenesis in chronic hepatitis B patients as an early drastic genetic change leading to hepatocarcinogenesis. Oncogene 24: 4340–4348.

27. KengVW, VillanuevaA, ChiangDY, DupuyAJ, RyanBJ, et al. (2009) A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma. Nat Biotechnol 27: 264–274.

28. BrechotC, GozuacikD, MurakamiY, Paterlini-BrechotP (2000) Molecular bases for the development of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Semin Cancer Biol 10: 211–231.

29. WuX, LiY, CriseB, BurgessSM (2003) Transcription start regions in the human genome are favored targets for MLV integration. Science 300: 1749–1751.

30. BushmanF, LewinskiM, CiuffiA, BarrS, LeipzigJ, et al. (2005) Genome-wide analysis of retroviral DNA integration. Nat Rev Microbiol 3: 848–858.

31. MitchellRS, BeitzelBF, SchroderAR, ShinnP, ChenH, et al. (2004) Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol 2: e234 doi:10.1371/journal.pbio.0020234.

32. HansenLJ, TennantBC, SeegerC, GanemD (1993) Differential activation of myc gene family members in hepatic carcinogenesis by closely related hepatitis B viruses. Mol Cell Biol 13: 659–667.

33. FourelG, TrepoC, BougueleretL, HengleinB, PonzettoA, et al. (1990) Frequent activation of N-myc genes by hepadnavirus insertion in woodchuck liver tumours. Nature 347: 294–298.

34. WangJ, ChenivesseX, HengleinB, BrechotC (1990) Hepatitis B virus integration in a cyclin A gene in a hepatocellular carcinoma. Nature 343: 555–557.

35. BerasainC, PatilD, PeraraE, HuangSM, MoulyH, et al. (1998) Oncogenic activation of a human cyclin A2 targeted to the endoplasmic reticulum upon hepatitis B virus genome insertion. Oncogene 16: 1277–1288.

36. DejeanA, BougueleretL, GrzeschikKH, TiollaisP (1986) Hepatitis B virus DNA integration in a sequence homologous to v-erb-A and steroid receptor genes in a hepatocellular carcinoma. Nature 322: 70–72.

37. GraefE, CaselmannWH, WellsJ, KoshyR (1994) Insertional activation of mevalonate kinase by hepatitis B virus DNA in a human hepatoma cell line. Oncogene 9: 81–87.

38. GraefE, CaselmannWH, HofschneiderPH, KoshyR (1995) Enzymatic properties of overexpressed HBV-mevalonate kinase fusion proteins and mevalonate kinase proteins in the human hepatoma cell line PLC/PRF/5. Virology 208: 696–703.

39. PineauP, MarchioA, TerrisB, MatteiMG, TuZX, et al. (1996) A t(3;8) chromosomal translocation associated with hepatitis B virus intergration involves the carboxypeptidase N locus. J Virol 70: 7280–7284.

40. ChamiM, GozuacikD, SaigoK, CapiodT, FalsonP, et al. (2000) Hepatitis B virus-related insertional mutagenesis implicates SERCA1 gene in the control of apoptosis. Oncogene 19: 2877–2886.

41. SaigoK, YoshidaK, IkedaR, SakamotoY, MurakamiY, et al. (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.

42. PankovR, YamadaKM (2002) Fibronectin at a glance. J Cell Sci 115: 3861–3863.

43. LongcopeC, FeminoA, JohnstonJO (1988) Inhibition of peripheral aromatization in baboons by an enzyme-activated aromatase inhibitor (MDL 18,962). Endocrinology 122: 2007–2011.

44. ZhangX, LiuS, HuT, HeY, SunS (2009) Up-regulated microRNA-143 transcribed by nuclear factor kappa B enhances hepatocarcinoma metastasis by repressing fibronectin expression. Hepatology 50: 490–499.

45. TomlinsSA, RhodesDR, PernerS, DhanasekaranSM, MehraR, et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310: 644–648.

46. TomlinsSA, LaxmanB, VaramballyS, CaoX, YuJ, et al. (2008) Role of the TMPRSS2-ERG gene fusion in prostate cancer. Neoplasia 10: 177–188.