Feature genes of hepatitis B virus-positive hepatocellular carcinoma, established by its molecular discrimination approach using prediction analysis of microarray

Biochimica et Biophysica Acta - Molecular Basis of Disease

Volumn 1739, Issue 1, 2004, Pages 50-61

  Kim, Bu Yeo ^a   Lee, Je Geun ^a   Park, Sunhoo ^a   Ahn, Jae Yeon ^a   Ju, Yeun Jin ^a   Chung, Jin Haeng ^a   Han, Chul Ju ^a   Jeong, Sook Hyang ^a   Yeom, Young Il ^b   Kim, Sangsoo ^b   Lee, Yong Sung ^c   Kim, Chang Min ^d   Eom, Eun Mi ^e   Lee, Dong Hee ^e   Choi, Kang Yell ^f   Cho, Myung Haing ^g   Suh, Kyung Suk ^g   Choi, Dong Wook ^a   Lee, Kee Ho ^a  

^a Korea Institute of Radiation and Medical Science   (South Korea)

^b Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^c Hanyang University   (South Korea)

^d National Cancer Center   (South Korea)

^e Ewha Womans University   (South Korea)

^f Yonsei University   (South Korea)

^g Seoul National University   (South Korea)

Author keywords

Hepatocellular carcinoma; Learning; Microarray; Prediction

Indexed keywords

ARTICLE; CLINICAL FEATURE; CONTROLLED STUDY; DNA MICROARRAY; DOWN REGULATION; HEPATITIS B; HEPATITIS B VIRUS; HUMAN; LIVER CELL CARCINOMA; MAJOR CLINICAL STUDY; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; REPRODUCIBILITY; STATISTICAL ANALYSIS; UPREGULATION; VALIDATION PROCESS;

HEPATITIS B VIRUS;

EID: 10644291862     PISSN: 09254439     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbadis.2004.07.004     Document Type: Article

References (58)

1. K. Okuda Hepatocellular carcinoma J. Hepatol. 32 2000 225 237
2. P.E. Jackson, G.S. Qian, M.D. Friesen, Y.R. Zhu, P. Lu, J.B. Wang, Y. Wu, T.W. Kensler, B. Vogelstein, and J.D. Groopman Specific p53 mutations detected in plasma and tumors of hepatocellular carcinoma patients by electrospray ionization mass spectrometry Cancer Res. 61 2001 33 35
3. K. Taniguchi, L.R. Roberts, I.N. Aderca, X. Dong, C. Qian, L.M. Murphy, D.M. Nagorney, L.J. Burgart, P.C. Roche, D.I. Smith, J.A. Ross, and W. Liu Mutational spectrum of beta-catenin, AXIN1, and AXIN2 in hepatocellular carcinomas and hepatoblastomas Oncogene 21 2002 4863 4871
4. S. Satoh, Y. Daigo, Y. Furukawa, T. Kato, N. Miwa, T. Nishiwaki, T. Kawasoe, H. Ishiguro, M. Fujita, T. Tokino, Y. Sasaki, S. Imaoka, M. Murata, T. Shimano, Y. Yamaoka, and Y. Nakamura AXIN1 mutations in hepatocellular carcinoma and growth suppression in cancer cells by virus-mediated transfer of AXIN1 Nat. Genet. 24 2000 245 250
5. L.F. Qin, and I.O. Ng Expression of p27Kip1 and p21WAF1/CIP1 in primary hepatocellular carcinoma: Clinicopathologic correlation and survival analysis Hum. Pathol. 32 2001 778 785
6. A. Tannapfel, D. Grund, A. Katalinic, D. Uhlmann, F. Kockerling, U. Haugwitz, M. Wasner, J. Hauss, K. Engeland, and C. Wittekind Decreased expression of p27 protein is associated with advanced tumor stage in hepatocellular carcinoma Int. J. Cancer 89 2000 350 355
7. A.A. Alizadeh, M.B. Eisen, R.E. Davis, C. Ma, I.S. Lossos, A. Rosenwald, J.C. Boldrick, H. Sabet, T. Tran, X. Yu, J.I. Powell, L. Yang, G.E. Marti, T. Moore, J. Hudson Jr., L. Lu, D.B. Lewis, R. Tibshirani, G. Sherlock, W.C. Chan, T.C. Greiner, D.D. Weisenburger, J.O. Armitage, R. Warnke, R. Levy, W. Wilson, M.R. Grever, J.C. Byrd, D. Botstein, P.O. Brown, and L.M. Staudt Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling Nature 403 2000 503 511
8. H. Okabe, S. Satoh, T. Kato, O. Kitahara, R. Yanagawa, Y. Yamaoka, T. Tsunoda, Y. Furukawa, and Y. Nakamura 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. 61 2001 2129 2137
9. X. Chen, S.T. Cheung, S. So, S.T. Fan, C. Barry, J. Higgins, K.M. Lai, J. Ji, S. Dudoit, I.O. Ng, M. Van de Rijn, D. Botstein, and P.O. Brown Gene expression patterns in human liver cancers Mol. Biol. Cell 13 2002 1929 1939
10. T.R. Golub, D.K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J.P. Mesirov, H. Coller, M.L. Loh, J.R. Downing, M.A. Caligiuri, C.D. Bloomfield, and E.S. Lander Molecular classification of cancer: class discovery and class prediction by gene expression monitoring Science 286 1999 531 537
11. S. Ramaswamy, P. Tamayo, R. Rifkin, S. Mukherjee, C.H. Yeang, M. Angelo, C. Ladd, M. Reich, E. Latulippe, J.P. Mesirov, T. Poggio, W. Gerald, M. Loda, E.S. Lander, and T.R. Golub Multiclass cancer diagnosis using tumor gene expression signatures Proc. Natl. Acad. Sci. U. S. A. 98 2001 15149 15154
12. R. Tibshirani, T. Hastie, B. Narasimhan, and G. Chu Diagnosis of multiple cancer types by shrunken centroids of gene expression Proc. Natl. Acad. Sci. U. S. A. 99 2002 6567 6572
13. M.A. Shipp, K.N. Ross, P. Tamayo, A.P. Weng, J.L. Kutok, R.C. Aguiar, M. Gaasenbeek, M. Angelo, M. Reich, G.S. Pinkus, T.S. Ray, M.A. Koval, K.W. Last, A. Norton, T.A. Lister, J. Mesirov, D.S. Neuberg, E.S. Lander, J.C. Aster, and T.R. Golub Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning Nat. Med. 8 2002 68 74
14. N. Iizuka, M. Oka, H. Yamada-Okabe, N. Mori, T. Tamesa, T. Okada, N. Takemoto, A. Tangoku, K. Hamada, H. Nakayama, T. Miyamoto, S. Uchimura, and Y. Hamamoto 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. 62 2002 3939 3944
15. N. Iizuka, M. Oka, H. Yamada-Okabe, M. Nishida, Y. Maeda, N. Mori, T. Takao, T. Tamesa, A. Tangoku, H. Tabuchi, K. Hamada, H. Nakayama, H. Ishitsuka, T. Miyamoto, A. Hirabayashi, S. Uchimura, and Y. Hamamoto Oligonucleotide microarray for prediction of early intrahepatic recurrence of hepatocellular carcinoma after curative resection Lancet 361 2003 923 929
16. B. Ewing, L. Hillier, M.C. Wendl, and P. Green Base-calling of automated sequencer traces using phred. I. Accuracy Assessment Genome Res. 8 1998 175 185
17. Y.H. Yang, S. Dudoit, P. Luu, D.M. Lin, V. Peng, J. Ngai, and T.P. Speed Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res. 30 2002 e15
18. M.B. Eisen, P.T. Spellman, P.O. Brown, and D. Botstein Cluster analysis and display of genome-wide expression patterns Proc. Natl. Acad. Sci. U. S. A. 95 1998 14863 14868
19. V.G. Tusher, R. Tibshirani, and G. Chu Significance analysis of microarrays applied to the ionizing radiation response Proc. Natl. Acad. Sci. U. S. A. 98 2001 5116 5121
20. C.J. Huberty Applied Discriminant Analysis 1994 John Wiley and Sons New York
21. Q.H. Ye, L.X. Qin, M. Forgues, P. He, J.W. Kim, A.C. Peng, R. Simon, Y. Li, A.I. Robles, Y. Chen, Z.C. Ma, Z.Q. Wu, S.L. Ye, Y.K. Liu, Z.Y. Tang, and X.W. Wang Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning Nat. Med. 9 2003 416 423
22. S. Varambally, S.M. Dhanasekaran, M. Zhou, T.R. Barrette, C. Kumar-Sinha, M.G. Sanda, D. Ghosh, K.J. Pienta, R.G. Sewalt, A.P. Otte, M.A. Rubin, and A.M. Chinnaiyan The polycomb group protein EZH2 is involved in progression of prostate cancer Nature 419 2002 624 629
23. M.W. Smith, Z.N. Yue, G.K. Geiss, N.Y. Sadovnikova, V.S. Carter, L. Boix, C.A. Lazaro, G.B. Rosenberg, R.E. Bumgarner, N. Fausto, J. Bruix, and M.G. Katze Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma Cancer Res. 63 2003 859 864
24. L. Xu, L. Hui, S. Wang, J. Gong, Y. Jin, Y. Wang, Y. Ji, X. Wu, Z. Han, and G. Hu Expression profiling suggested a regulatory role of liver-enriched transcription factors in human hepatocellular carcinoma Cancer Res. 61 2001 3176 3181
25. X.R. Xu, J. Huang, Z.G. Xu, B.Z. Qian, Z.D. Zhu, Q. Yan, T. Cai, X. Zhang, H.S. Xiao, J. Qu, F. Liu, Q.H. Huang, Z.H. Cheng, N.G. Li, J.J. Du, W. Hu, K.T. Shen, G. Lu, G. Fu, M. Zhong, S.H. Xu, W.Y. Gu, W. Huang, X.T. Zhao, G.X. Hu, J.R. Gu, Z. Chen, and Z.G. Han 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. U. S. A. 98 2001 15089 15094
26. D. Tackels-Horne, M.D. Goodman, A.J. Williams, D.J. Wilson, T. Eskandari, L.M. Vogt, J.F. Boland, U. Scherf, and J.G. Vockley Identification of differentially expressed genes in hepatocellular carcinoma and metastatic liver tumors by oligonucleotide expression profiling Cancer 92 2001 395 405
27. J.S. Lee, and S.S. Thorgeirsson Functional and genomic implications of global gene expression profiles in cell lines from human hepatocellular cancer Hepatology 35 2002 1134 1143
28. C.R. Graveel, T. Jatkoe, S.J. Madore, A.L. Holt, and P.J. Farnham Expression profiling and identification of novel genes in hepatocellular carcinomas Oncogene 20 2001 2704 2712
29. S.T. Cheung, X. Chen, X.Y. Guan, S.Y. Wong, L.S. Tai, I.O. Ng, S. So, and S.T. Fan Identify metastasis-associated genes in hepatocellular carcinoma through clonality delineation for multinodular tumor Cancer Res. 62 2002 4711 4721
30. N. Iizuka, M. Oka, H. Yamada-Okabe, N. Mori, T. Tamesa, T. Okada, N. Takemoto, K. Hashimoto, A. Tangoku, K. Hamada, H. Nakayama, T. Miyamoto, S. Uchimura, and Y. Hamamoto Differential gene expression in distinct virologic types of hepatocellular carcinoma: association with liver cirrhosis Oncogene 22 2003 3007 3014
31. A. Tannapfel, K. Anhalt, P. Hausermann, F. Sommerer, M. Benicke, D. Uhlmann, H. Witzigmann, J. Hauss, and C. Wittekind Identification of novel proteins associated with hepatocellular carcinomas using protein microarrays J. Pathol. 201 2003 238 249
32. J.W. Kim, Q. Ye, M. Forgues, Y. Chen, A. Budhu, J. Sime, L.J. Hofseth, R. Kaul, and X.W. Wang Cancer-associated molecular signature in the tissue samples of patients with cirrhosis Hepatology 39 2004 518 527
33. G.P. Sawiris, C.A. Sherman-Baust, K.G. Becker, C. Cheadle, D. Teichberg, and P.J. Morin Development of a highly specialized cDNA array for the study and diagnosis of epithelial ovarian cancer Cancer Res. 62 2002 2923 2928
34. K. Li, T. Prow, S.M. Lemon, and M.R. Beard Cellular response to conditional expression of hepatitis C virus core protein in Huh7 cultured human hepatoma cells Hepatology 35 2002 1237 1246
35. J.M. Markert, C.M. Fuller, G.Y. Gillespie, J.K. Bubien, L.A. McLean, R.L. Hong, K. Lee, S.R. Gullans, T.B. Mapstone, and D.J. Benos Differential gene expression profiling in human brain tumors Physiol. Genomics 5 2001 21 33
36. J.M. Kolesar, S.C. Pritchard, K.M. Kerr, K. Kim, M.C. Nicolson, and H. McLeod Evaluation of NQO1 gene expression and variant allele in human NSCLC tumors and matched normal lung tissue Int. J. Oncol. 21 2002 1119 1124
37. A. Strassburg, C.P. Strassburg, M.P. Manns, and R.H. Tukey Differential gene expression of NAD(P)H:quinone oxidoreductase and NRH:quinone oxidoreductase in human hepatocellular and biliary tissue Mol. Pharmacol. 61 2002 320 325
38. M.T. Smith, Y. Wang, E. Kane, S. Rollinson, J.L. Wiemels, E. Roman, P. Roddam, R. Cartwright, and G. Morgan Low NAD(P)H:quinone oxidoreductase 1 activity is associated with increased risk of acute leukemia in adults Blood 97 2001 1422 1426
39. Y. Chen, J. Wang, M.M. Fraig, J. Metcalf, W.R. Turner, N.K. Bissada, D.K. Watson, and C.W. Schweinfest Defects of DNA mismatch repair in human prostate cancer Cancer Res. 61 2001 4112 4121
40. M. Korabiowska, U. Brinck, H. Dengler, J. Stachura, A. Schauer, and M. Droese Analysis of the DNA mismatch repair proteins expression in malignant melanomas Anticancer Res. 20 2000 4499 4505
41. Y. Midorikawa, S. Ishikawa, H. Iwanari, T. Imamura, H. Sakamoto, K. Miyazono, T. Kodama, M. Makuuchi, and H. Aburatani Glypican-3, overexpressed in hepatocellular carcinoma, modulates FGF2 and BMP-7 signaling Int. J. Cancer 103 2003 455 465
42. Z.W. Zhu, H. Friess, L. Wang, M. Abou-Shady, A. Zimmermann, A.D. Lander, M. Korc, J. Kleeff, and M.W. Buchler Enhanced glypican-3 expression differentiates the majority of hepatocellular carcinomas from benign hepatic disorders Gut 48 2001 558 564
43. M. Kinoshita, and M. Miyata Underexpression of mRNA in human hepatocellular carcinoma focusing on eight loci Hepatology 36 2002 433 438
44. S. Gill, D. Peston, B.K. Vonderhaar, and S. Shousha Expression of prolactin receptors in normal, benign, and malignant breast tissue: an immunohistological study J. Clin. Pathol. 54 2001 956 960
45. A. Glasow, L.C. Horn, S.E. Taymans, C.A. Stratakis, P.A. Kelly, U. Kohler, J. Gillespie, B.K. Vonderhaar, and S.R. Bornstein Mutational analysis of the PRL receptor gene in human breast tumors with differential PRL receptor protein expression J. Clin. Endocrinol. Metab. 86 2001 3826 3832
46. T. Garcia-Caballero, H.M. Mertani, A. Lambert, R. Gallego, M. Fraga, E. Pintos, J. Forteza, M. Chevallier, P.E. Lobie, B.K. Vonderhaar, A. Beiras, and G. Morel Increased expression of growth hormone and prolactin receptors in hepatocellular carcinomas Endocrine 12 2000 265 271
47. M. Kochetkova, O.L. McKenzie, A.J. Bais, J.M. Martin, G.A. Secker, R. Seshadri, J.A. Powell, S.J. Hinze, A.E. Gardner, H.E. Spendlove, N.J. O'Callaghan, A.M. Cleton-Jansen, C. Cornelisse, S.A. Whitmore, J. Crawford, G. Kremmidiotis, G.R. Sutherland, and D.F. Callen CBFA2T3 (MTG16) is a putative breast tumor suppressor gene from the breast cancer loss of heterozygosity region at 16q24.3 Cancer Res. 62 2002 4599 4604
48. J.A. Powell, A.E. Gardner, A.J. Bais, S.J. Hinze, E. Baker, S. Whitmore, J. Crawford, M. Kochetkova, H.E. Spendlove, N.A. Doggett, G.R. Sutherland, D.F. Callen, and G. Kremmidiotis Sequencing, transcript identification, and quantitative gene expression profiling in the breast cancer loss of heterozygosity region 16q24.3 reveal three potential tumor-suppressor genes Genomics 80 2002 303 310
49. A. Chetcuti, S. Margan, S. Mann, P. Russell, D. Handelsman, J. Rogers, and Q. Dong Identification of differentially expressed genes in organ-confined prostate cancer by gene expression array Prostate 47 2001 132 140
50. J. Hasskarl, and K. Munger Id proteins-tumor markers or oncogenes? Cancer Biol. Ther. 1 2002 91 96
51. S.L. Winski, Y. Koutalos, D.L. Bentley, and D. Ross Subcellular localization of NAD(P)H:quinone oxidoreductase 1 in human cancer cells Cancer Res. 62 2002 1420 1424
52. N. Siegelmann-Danieli, and K.H. Buetow Significance of genetic variation at the glutathione S-transferase M1 and NAD(P)H:quinone oxidoreductase 1 detoxification genes in breast cancer development Oncology 62 2002 39 45
53. G. Asher, J. Lotem, R. Kama, L. Sachs, and Y. Shaul NQO1 stabilizes p53 through a distinct pathway Proc. Natl. Acad. Sci. U. S. A. 99 2002 3099 3104
54. R.M. Alani, A.Z. Young, and C.B. Shifflett Id1 regulation of cellular senescence through transcriptional repression of p16/Ink4a Proc. Natl. Acad. Sci. U. S. A. 98 2001 7812 7816
55. M.M. de las Alas, S. Aebi, D. Fink, S.B. Howell, and G. Los Loss of DNA mismatch repair: effects on the rate of mutation to drug resistance J. Natl. Cancer Inst. 89 1997 1537 1541
56. H.J. Mackay, D. Cameron, M. Rahilly, M.J. Mackean, J. Paul, S.B. Kaye, and R. Brown Reduced MLH1 expression in breast tumors after primary chemotherapy predicts disease-free survival J. Clin. Oncol. 18 2000 87 93
57. H. Dong, N. Toyoda, H. Yoneyama, M. Kurachi, T. Kasahara, Y. Kobayashi, H. Inadera, S. Hashimoto, and K. Matsushima Gene expression profile analysis of the mouse liver during bacteria-induced fulminant hepatitis by a cDNA microarray system Biochem. Biophys. Res. Commun. 298 2002 675 686
58. S. Kloehn, C. Otte, M. Korsanke, T. Arendt, A. Clemens, A. Glasow, S.R. Bornstein, U.R. Folsch, and H. Monig Expression and distribution of the prolactin receptor in normal rat liver and in experimental liver cirrhosis Horm. Metab. Res. 33 2001 394 401