Cancer Letters
Volume 286, Issue 1 , Pages 89-95 , 1 December 2009

Systematic -omics analysis of HBV-associated liver diseases

  • Wei Sun

      Affiliations

    • State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 33 Life Science Park, Beijing 102206, China
    • Equally contributed.
    • ,
  • Fan Zhong

      Affiliations

    • Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, 220 Handan Road, Shanghai 200032, China
    • Equally contributed.
    • ,
  • Lianteng Zhi

      Affiliations

    • State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 33 Life Science Park, Beijing 102206, China
    • Equally contributed.
    • ,
  • Gangqiao Zhou

      Affiliations

    • State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 33 Life Science Park, Beijing 102206, China
    • Corresponding Author InformationCorresponding authors. Address: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 33 Life Science Park, Beijing 102206, China. Tel.: +86 10 68177417 (F. He).
    • ,
  • Fuchu He

      Affiliations

    • State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 33 Life Science Park, Beijing 102206, China
    • Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, 220 Handan Road, Shanghai 200032, China
    • Corresponding Author InformationCorresponding authors. Address: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, 33 Life Science Park, Beijing 102206, China. Tel.: +86 10 68177417 (F. He).

Received 29 February 2008 ,Revised 25 November 2008 ,Accepted 2 December 2008.

References 

  1. Hyodo N, Tajimi M, Ugajin T, Nakamura I, Imawari M. Frequencies of interferon-gamma and interleukin-10 secreting cells in peripheral blood mononuclear cells and liver infiltrating lymphocytes in chronic hepatitis B virus infection. Hepatol. Res. 2003;27:109–116
  2. Thursz MR, Kwiatkowski D, Allsopp CE, Greenwood BM, Thomas HC, Hill AV. Association between an MHC class II allele and clearance of hepatitis B virus in the Gambia. New Engl. J. Med. 1995;332:1065–1069
  3. Ben-Ari Z, Mor E, Papo O, Kfir B, Sulkes J, Tambur AR, et al. Cytokine gene polymorphisms in patients infected with hepatitis B virus. Am. J. Gastroenterol. 2003;98:144–150
  4. Kim YJ, Lee HS, Yoon JH, Kim CY, Park MH, Kim LH, et al. Association of TNF-alpha promoter polymorphisms with the clearance of hepatitis B virus infection. Hum. Mol. Genet. 2003;12:2541–2546
  5. Thomas HC, Foster GR, Sumiya M, McIntosh D, Jack DL, Turner MW, et al. Mutation of gene of mannose-binding protein associated with chronic hepatitis B viral infection. Lancet. 1996;348:1417–1419
  6. Bellamy R, Ruwende C, Corrah T, McAdam KP, Thursz M, Whittle HC, et al. Tuberculosis and chronic hepatitis B virus infection in Africans and variation in the vitamin D receptor gene. J. Infect. Dis. 1999;179:721–724
  7. Deng G, Zhou G, Zhai Y, Li S, Li X, Li Y, et al. Association of estrogen receptor alpha polymorphisms with susceptibility to chronic hepatitis B virus infection. Hepatology. 2004;40:318–326
  8. Thursz M. Pros and cons of genetic association studies in hepatitis B. Hepatology. 2004;40:284–286
  9. Maini MK, Boni C, Lee CK, Larrubia JR, Reignat S, Ogg GS, et al. The role of virus-specific CD8(+) cells in liver damage and viral control during persistent hepatitis B virus infection. J. Exp. Med. 2000;191:1269–1280
  10. Xu XW, Lu MH, Tan DM. Association between tumour necrosis factor gene polymorphisms and the clinical types of patients with chronic hepatitis B virus infection. Clin. Microbiol. Infect. 2005;11:52–56
  11. Yuen MF, Lau CS, Lau YL, Wong WM, Cheng CC, Lai CL. Mannose binding lectin gene mutations are associated with progression of liver disease in chronic hepatitis B infection. Hepatology. 1999;29:1248–1251
  12. Chong WP, To YF, Ip WK, Yuen MF, Poon TP, Wong WH, et al. Mannose-binding lectin in chronic hepatitis B virus infection. Hepatology. 2005;42:1037–1045
  13. Liu C, Cheng B. Association of polymorphisms of human leucocyte antigen-DQA1 and DQB1 alleles with chronic hepatitis B virus infection, liver cirrhosis and hepatocellular carcinoma in Chinese. Int. J. Immunogenet. 2007;34:373–378
  14. Deng G, Zhou G, Zhang R, Zhai Y, Zhao W, Yan Z, et al. Regulatory polymorphisms in the promoter of CXCL10 Gene and disease progression in male hepatitis B virus carriers. Gastroenterology. 2008;134:716–726
  15. Cougot D, Neuveut C, Buendia MA. HBV induced carcinogenesis. J. Clin. Virol. 2005;34(Suppl. 1):S75–S78
  16. Jicai Z, Zongtao Y, Jun L, Haiping L, Jianmin W, Lihua H. Persistent infection of hepatitis B virus is involved in high rate of p16 methylation in hepatocellular carcinoma. Mol. Carcinogen. 2006;45:530–536
  17. Kummee P, Tangkijvanich P, Poovorawan Y, Hirankarn N. Association of HLA-DRB1*13 and TNF-alpha gene polymorphisms with clearance of chronic hepatitis B infection and risk of hepatocellular carcinoma in Thai population. J. Viral Hepatitis. 2007;14:841–848
  18. Hirankarn N, Kimkong I, Kummee P, Tangkijvanich P, Poovorawan Y. Interleukin-1beta gene polymorphism associated with hepatocellular carcinoma in hepatitis B virus infection. World J. Gastroenterol. 2006;12:776–779
  19. Yu MW, Yang SY, Pan IJ, Lin CL, Liu CJ, Liaw YF, et al. Polymorphisms in XRCC1 and glutathione S-transferase genes and hepatitis B-related hepatocellular carcinoma. J. Natl. Cancer Inst. 2003;95:1485–1488
  20. Shin HD, Park BL, Kim LH, Jung JH, Kim JY, Yoon JH, et al. Interleukin 10 haplotype associated with increased risk of hepatocellular carcinoma. Hum. Mol. Genet. 2003;12:901–906
  21. Yu MW, Yang YC, Yang SY, Cheng SW, Liaw YF, Lin SM, et al. Hormonal markers and hepatitis B virus-related hepatocellular carcinoma risk: a nested case-control study among men. J. Natl. Cancer Inst. 2001;93:1644–1651
  22. Wu HC, Wang Q, Wang LW, Yang HI, Ahsan H, Tsai WY, et al. Polycyclic aromatichydrocarbon- and aflatoxin-albumin adducts, hepatitis B virus infection and hepatocellular carcinoma in Taiwan. Cancer Lett. 2007;252:104–114
  23. Jung YJ, Kim YJ, Kim LH, Lee SO, Park BL, Shin HD, et al. Putative association of Fas and FasL gene polymorphisms with clinical outcomes of hepatitis B virus infection. Intervirology. 2007;50:369–376
  24. Migita K, Miyazoe S, Maeda Y, Daikoku M, Abiru S, Ueki T, et al. Cytokine gene polymorphisms in Japanese patients with hepatitis B virus infection–association between TGF-beta1 polymorphisms and hepatocellular carcinoma. J. Hepatol. 2005;42:505–510
  25. Zhai Y, Zhou G, Deng G, Xie W, Dong X, Zhang X, et al. Estrogen receptor alpha polymorphisms associated with susceptibility to hepatocellular carcinoma in hepatitis B virus carriers. Gastroenterology. 2006;130:2001–2009
  26. Tamori A, Yamanishi Y, Kawashima S, Kanehisa M, Enomoto M, Tanaka H, et al. Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clin. Cancer Res. 2005;11:5821–5826
  27. Saigo K, Yoshida K, Ikeda R, Sakamoto Y, Murakami Y, Urashima T, 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. 2008;29:703–708
  28. Iizuka N, Oka M, Yamada-Okabe H, Mori N, Tamesa T, Okada T, et al. Differential gene expression in distinct virologic types of hepatocellular carcinoma: association with liver cirrhosis. Oncogene. 2003;22:3007–3014
  29. Lee S, Kim S. Gene regulations in HBV-related liver cirrhosis closely correlate with disease severity. J. Biochem. Mol. Biol. 2007;40:814–824
  30. Iizuka N, Tsunedomi R, Tamesa T, Okada T, Sakamoto K, Hamaguchi T, et al. Involvement of c-myc-regulated genes in hepatocellular carcinoma related to genotype-C hepatitis B virus. J. Cancer Res. Clin. Oncol. 2006;132:473–481
  31. Lopes AR, Kellam P, Das A, Dunn C, Kwan A, Turner J, et al. Bim-mediated deletion of antigen-specific CD8 T cells in patients unable to control HBV infection. J. Clin. Invest. 2008;118:1835–1845
  32. Barone M, Spano D, D’Apolito M, Centra M, Lasalandra C, Capasso M, et al. Gene expression analysis in HBV transgenic mouse liver: a model to study early events related to hepatocarcinogenesis. Mol. Med. 2006;12:115–123
  33. Hajjou M, Norel R, Carver R, Marion P, Cullen J, Rogler LE, et al. cDNA microarray analysis of HBV transgenic mouse liver identifies genes in lipid biosynthetic and growth control pathways affected by HBV. J. Med. Virol. 2005;77:57–65
  34. Li Y, Wan D, Wei W, Su J, Cao J, Qiu X, et al. Candidate genes responsible for human hepatocellular carcinoma identified from differentially expressed genes in hepatocarcinogenesis of the tree shrew (Tupaia belangeri chinesis). Hepatol. Res. 2008;38:85–95
  35. Ryu HM, Park SG, Yea SS, Jang WH, Yang YI, Jung G. Gene expression analysis of primary normal human hepatocytes infected with human hepatitis B virus. World J. Gastroenterol. 2006;12:4986–4995
  36. Pan XB, Wei L, Chen HS, Liu F, Gao Y. Liver-derived cell lines QSG-7701 and HepG2 support different HBV replication patterns. Arch. Virol. 2007;152:1159–1173
  37. Zhang Q, Wang Y, Wei L, Jiang D, Wang JH, Rao HY, et al. Role of ISGF3 in modulating the anti-hepatitis B virus activity of interferon-alpha in vitro. J. Gastroenterol. Hepatol. 2007;
  38. Yoon SY, Kim JM, Oh JH, Jeon YJ, Lee DS, Kim JH, et al. Gene expression profiling of human HBV- and/or HCV-associated hepatocellular carcinoma cells using expressed sequence tags. Int. J. Oncol. 2006;29:315–327
  39. Xu XR, Huang J, Xu ZG, Qian BZ, Zhu ZD, Yan Q, et al. Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Proc. Natl. Acad. Sci. USA. 2001;98:15089–15094
  40. Ng RK, Lau CY, Lee SM, Tsui SK, Fung KP, Waye MM. cDNA microarray analysis of early gene expression profiles associated with hepatitis B virus X protein-mediated hepatocarcinogenesis. Biochem. Biophys. Res. Commun. 2004;322:827–835
  41. Sidorkiewicz M, Jais JP, Tralhao G, Morosan S, Giannini C, Brezillon N, et al. Gene modulation associated with inhibition of liver regeneration in hepatitis B virus X transgenic mice. World J. Gastroenterol. 2008;14:574–581
  42. Han J, Yoo HY, Choi BH, Rho HM. Selective transcriptional regulations in the human liver cell by hepatitis B viral X protein. Biochem. Biophys. Res. Commun. 2000;272:525–530
  43. Wu CG, Salvay DM, Forgues M, Valerie K, Farnsworth J, Markin RS, et al. Distinctive gene expression profiles associated with hepatitis B virus x protein. Oncogene. 2001;20:3674–3682
  44. Wu CG, Forgues M, Siddique S, Farnsworth J, Valerie K, Wang XW. SAGE transcript profiles of normal primary human hepatocytes expressing oncogenic hepatitis B virus X protein. Faseb J. 2002;16:1665–1667
  45. Hu Z, Zhang Z, Kim JW, Huang Y, Liang TJ. Altered proteolysis and global gene expression in hepatitis B virus X transgenic mouse liver. J. Virol. 2006;80:1405–1413
  46. Kuo CY, Wang JC, Wu CC, Hsu SL, Hwang GY. Effects of hepatitis B virus X protein (HBx) on cell-growth inhibition in a CCL13-HBx stable cell line. Intervirology. 2008;51:26–32
  47. Liu X, Wang L, Zhang S, Lin J, Feitelson MA, Gao H, et al. Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses. Carcinogenesis. 2008;29:1207–1214
  48. Honda M, Kaneko S, Kawai H, Shirota Y, Kobayashi K. Differential gene expression between chronic hepatitis B and C hepatic lesion. Gastroenterology. 2001;120:955–966
  49. Lee CF, Ling ZQ, Zhao T, Lee KR. Distinct expression patterns in hepatitis B virus- and hepatitis C virus-infected hepatocellular carcinoma. World J. Gastroenterol. 2008;14:6072–6077
  50. Honda M, Yamashita T, Ueda T, Takatori H, Nishino R, Kaneko S. Different signaling pathways in the livers of patients with chronic hepatitis B or chronic hepatitis C. Hepatology. 2006;44:1122–1138
  51. Iizuka N, Oka M, Yamada-Okabe H, Mori N, Tamesa T, Okada T, et al. Comparison of gene expression profiles between hepatitis B virus- and hepatitis C virus-infected hepatocellular carcinoma by oligonucleotide microarray data on the basis of a supervised learning method. Cancer Res. 2002;62:3939–3944
  52. Okabe H, Satoh S, Kato T, Kitahara O, Yanagawa R, Yamaoka Y, et al. Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: identification of genes involved in viral carcinogenesis and tumor progression. Cancer Res. 2001;61:2129–2137
  53. Murakami Y, Yasuda T, Saigo K, Urashima T, Toyoda H, Okanoue T, et al. Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene. 2006;25:2537–2545
  54. Sells MA, Chen ML, Acs G. Production of hepatitis B virus particles in Hep G2 cells transfected with cloned hepatitis B virus DNA. Proc. Natl. Acad. Sci. USA. 1987;84:1005–1009
  55. Tong A, Wu L, Lin Q, Lau QC, Zhao X, Li J, et al. Proteomic analysis of cellular protein alterations using a hepatitis B virus-producing cellular model. Proteomics. 2008;8:2012–2023
  56. Liu K, Qian L, Li W, Deng X, Chen X, Sun W, et al. Two-dimensional blue native/SDS PAGE analysis reveals HSPs chaperone machinery involved in HBV production in HepG2.2.15 cells. Mol. Cell Proteomics. 2008;
  57. Yang F, Yan S, He Y, Wang F, Song S, Guo Y, et al. Expression of hepatitis B virus proteins in transgenic mice alters lipid metabolism and induces oxidative stress in the liver. J. Hepatol. 2008;48:12–19
  58. He Y, Yang F, Wang F, Song SX, Li DA, Guo YJ, et al. The upregulation of expressed proteins in HepG2 cells transfected by the recombinant plasmid-containing HBx gene. Scand J. Immunol. 2007;65:249–256
  59. Tan TL, Chen WN. A proteomics analysis of cellular proteins associated with HBV genotype-specific HBX: potential in identification of early diagnostic markers for HCC. J. Clin. Virol. 2005;33:293–298
  60. Cui F, Wang Y, Wang J, Wei K, Hu J, Liu F, et al. The up-regulation of proteasome subunits and lysosomal proteases in hepatocellular carcinomas of the HBx gene knockin transgenic mice. Proteomics. 2006;6:498–504
  61. Kawakami T, Tateishi K, Yamano Y, Ishikawa T, Kuroki K, Nishimura T. Protein identification from product ion spectra of peptides validated by correlation between measured and predicted elution times in liquid chromatography/mass spectrometry. Proteomics. 2005;5:856–864
  62. Zhao C, Fang CY, Tian XC, Wang L, Yang PY, Wen YM. Proteomic analysis of hepatitis B surface antigen positive transgenic mouse liver and decrease of cyclophilin A. J. Med. Virol. 2007;79:1478–1484
  63. Lim SO, Park SJ, Kim W, Park SG, Kim HJ, Kim YI, et al. Proteome analysis of hepatocellular carcinoma. Biochem. Biophys. Res. Commun. 2002;291:1031–1037
  64. Liang CR, Leow CK, Neo JC, Tan GS, Lo SL, Lim JW, et al. Proteome analysis of human hepatocellular carcinoma tissues by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics. 2005;5:2258–2271
  65. Zhang D, Lim SG, Koay ES. Proteomic identification of down-regulation of oncoprotein DJ-1 and proteasome activator subunit 1 in hepatitis B virus-infected well-differentiated hepatocellular carcinoma. Int. J. Oncol. 2007;31:577–584
  66. Li C, Tan YX, Zhou H, Ding SJ, Li SJ, Ma DJ, et al. Proteomic analysis of hepatitis B virus-associated hepatocellular carcinoma: identification of potential tumor markers. Proteomics. 2005;5:1125–1139
  67. Yi X, Luk JM, Lee NP, Peng J, Leng X, Guan XY, et al. Association of mortalin (HSPA9) with liver cancer metastasis and prediction for early tumor recurrence. Mol. Cell Proteomics. 2008;7:315–325
  68. Sun W, Xing B, Sun Y, Du X, Lu M, Hao C, et al. Proteome analysis of hepatocellular carcinoma by two-dimensional difference gel electrophoresis: novel protein markers in hepatocellular carcinoma tissues. Mol. Cell Proteomics. 2007;6:1798–1808
  69. Li C, Hong Y, Tan YX, Zhou H, Ai JH, Li SJ, et al. Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry. Mol. Cell Proteomics. 2004;3:399–409
  70. Ai J, Tan Y, Ying W, Hong Y, Liu S, Wu M, et al. Proteome analysis of hepatocellular carcinoma by laser capture microdissection. Proteomics. 2006;6:538–546
  71. Wang HY. Laser capture microdissection in comparative proteomic analysis of hepatocellular carcinoma. Methods Cell Biol. 2007;82:689–707
  72. Kim W, Oe Lim S, Kim JS, Ryu YH, Byeon JY, Kim HJ, et al. Comparison of proteome between hepatitis B virus- and hepatitis C virus-associated hepatocellular carcinoma. Clin. Cancer Res. 2003;9:5493–5500
  73. He QY, Lau GK, Zhou Y, Yuen ST, Lin MC, Kung HF, et al. Serum biomarkers of hepatitis B virus infected liver inflammation: a proteomic study. Proteomics. 2003;3:666–674
  74. Steel LF, Shumpert D, Trotter M, Seeholzer SH, Evans AA, London WT, et al. A strategy for the comparative analysis of serum proteomes for the discovery of biomarkers for hepatocellular carcinoma. Proteomics. 2003;3:601–609
  75. Feng JT, Liu YK, Song HY, Dai Z, Qin LX, Almofti MR, et al. Heat-shock protein 27: a potential biomarker for hepatocellular carcinoma identified by serum proteome analysis. Proteomics. 2005;5:4581–4588
  76. Comunale MA, Mattu TS, Lowman MA, Evans AA, London WT, Semmes OJ, et al. Comparative proteomic analysis of de-N-glycosylated serum from hepatitis B carriers reveals polypeptides that correlate with disease status. Proteomics. 2004;4:826–838
  77. Fernandez-Irigoyen J, Santamaria E, Sesma L, Munoz J, Riezu JI, Caballeria J, et al. Oxidation of specific methionine and tryptophan residues of apolipoprotein A-I in hepatocarcinogenesis. Proteomics. 2005;5:4964–4972
  78. Block TM, Comunale MA, Lowman M, Steel LF, Romano PR, Fimmel C, et al. Use of targeted glycoproteomics to identify serum glycoproteins that correlate with liver cancer in woodchucks and humans. Proc. Natl. Acad. Sci. USA. 2005;102:779–784
  79. Poon TC, Hui AY, Chan HL, Ang IL, Chow SM, Wong N, et al. Prediction of liver fibrosis and cirrhosis in chronic hepatitis B infection by serum proteomic fingerprinting: a pilot study. Clin. Chem. 2005;51:328–335
  80. Cui J, Kang X, Dai Z, Huang C, Zhou H, Guo K, et al. Prediction of chronic hepatitis B, liver cirrhosis and hepatocellular carcinoma by SELDI-based serum decision tree classification. J. Cancer Res. Clin. Oncol. 2007;133:825–834
  81. He QY, Zhu R, Lei T, Ng MY, Luk JM, Sham P, et al. Toward the proteomic identification of biomarkers for the prediction of HBV related hepatocellular carcinoma. J. Cell Biochem. 2008;103:740–752
  82. Feng JT, Liu YK, Dai Z, Zhou HJ, Song HY, Qin LX, et al. Screening hepatocellular carcinoma autoantibodies by serological proteome analysis. Zhonghua Gan Zang Bing Za Zhi. 2005;13:832–835
  83. Ranish JA, Hahn S, Lu Y, Yi EC, Li XJ, Eng J, et al. Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat. Genet. 2004;36:707–713
  84. Giglia-Mari G, Coin F, Ranish JA, Hoogstraten D, Theil A, Wijgers N, et al. A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat. Genet. 2004;36:714–719
  85. Lin B, White JT, Lu W, Xie T, Utleg AG, Yan X, et al. Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. Cancer Res. 2005;65:3081–3091
  86. Dihal AA, van der Woude H, Hendriksen PJ, Charif H, Dekker LJ, Ijsselstijn L, et al. Transcriptome and proteome profiling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms,increased mitochondrial fatty acid degradation and decreased glycolysis. Proteomics. 2008;8:45–61
  87. Minagawa H, Honda M, Miyazaki K, Tabuse Y, Teramoto R, Yamashita T, et al. Comparative proteomic and transcriptomic profiling of the human hepatocellular carcinoma. Biochem. Biophys. Res. Commun. 2008;366:186–192
  88. Ying W, Jiang Y, Guo L, Hao Y, Zhang Y, Wu S, et al. A dataset of human fetal liver proteome identified by subcellular fractionation and multiple protein separation and identification technology. Mol. Cell Proteomics. 2006;5:1703–1707
  89. He F. Human liver proteome project: plan, progress, and perspectives. Mol. Cell Proteomics. 2005;4:1841–1848
  90. Clish CB, Davidov E, Oresic M, Plasterer TN, Lavine G, Londo T, et al. Integrative biological analysis of the APOE*3-leiden transgenic mouse. Omics. 2004;8:3–13

PII: S0304-3835(08)00932-4

doi: 10.1016/j.canlet.2008.12.002

Cancer Letters
Volume 286, Issue 1 , Pages 89-95 , 1 December 2009

Article Tools