Transcriptome analysis of hepatitis B virus-associated small hepatocellular carcinoma by serial analysis of gene expression

International Journal of Oncology

Volumn 35, Issue 1, 2009, Pages 129-137

  Kim, Jin Wook ^a   Lee, Sang Hyub ^a   Park, Young Soo ^a   Jeong, Sook Hyang ^a   Kim, Nayoung ^a   Lee, Dong Ho ^a   Lee, Hyo Suk ^b  

^a Seoul National University Bundang Hospital   (South Korea)

^b Seoul National University College of Medicine   (South Korea)

Author keywords

Hepatitis B virus; Hepatocellular carcinoma; Serial analysis of gene expression; Transcriptome

Indexed keywords

ACYL COENZYME A DESATURASE; ALDEHYDE REDUCTASE; ALPHA FETOPROTEIN; ALPHA LEVO FUCOSIDASE; BETA GALACTOSIDASE; IMMUNOGLOBULIN HEAVY CHAIN; IMMUNOGLOBULIN KAPPA CHAIN; IMMUNOGLOBULIN LAMBDA CHAIN; ONCOPROTEIN; PROTEIN GON 4; RAS PROTEIN; TESTIS SPECIFIC PROTEIN Y ENCODED LIKE 2; THYMOSIN; UNCLASSIFIED DRUG;

AGED; ARTICLE; CANCER RESEARCH; CLINICAL ARTICLE; CONTROLLED STUDY; EARLY DIAGNOSIS; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE LIBRARY; GENE OVEREXPRESSION; HEPATITIS B VIRUS; HUMAN; HUMAN TISSUE; LIVER CARCINOGENESIS; LIVER CELL CARCINOMA; MALE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SERIAL ANALYSIS OF GENE EXPRESSION; TRANSCRIPTOMICS; TUMOR VOLUME; UNINDEXED SEQUENCE; UPREGULATION;

ADULT; AGED; ASIAN CONTINENTAL ANCESTRY GROUP; CARCINOMA, HEPATOCELLULAR; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE LIBRARY; HEPATITIS B; HUMANS; KOREA; LIVER NEOPLASMS; MALE; MIDDLE AGED; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; TUMOR MARKERS, BIOLOGICAL;

EID: 67649429218     PISSN: 10196439     EISSN: 17912423     Source Type: Journal    
DOI: 10.3892/ijo_00000321     Document Type: Article

References (56)

1. Parkin DM, Bray F, Ferlay J and Pisani P: Global cancer statistics, 2002. CA Cancer J Clin 55: 74-108, 2005.
2. Zhang BH, Yang BH and Tang ZY: Randomized controlled trial of screening for hepatocellular carcinoma. J Cancer Res Clin Oncol 130: 417-422, 2004.
3. Daniele B, Bencivenga A, Megna AS and Tinessa V: Alphafetoprotein and ultrasonography screening for hepatocellular carcinoma. Gastroenterology 127: S108-S112, 2004.
4. Bruix J and Sherman M: Management of hepatocellular carcinoma. Hepatology 42: 1208-1236, 2005.
5. Marrero JA and Lok AS: Newer markers for hepatocellular carcinoma. Gastroenterology 127: S113-S119, 2004.
6. Nam SW, Park JY, Ramasamy A, et al: Molecular changes from dysplastic nodule to hepatocellular carcinoma through gene expression profiling. Hepatology 42: 809-818, 2005.
7. Iizuka N, Oka M, Yamada-Okabe H, et al: Oligonucleotide microarray for prediction of early intrahepatic recurrence of hepatocellular carcinoma after curative resection. Lancet 361: 923-929, 2003.
8. Lee JS, Chu IS, Heo J, et al: Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling. Hepatology 40: 667-676, 2004.
9. Matoba K, Iizuka N, Gondo T, et al: Tumor HLA-DR expression linked to early intrahepatic recurrence of hepatocellular carcinoma. Int J Cancer 115: 231-240, 2005.
10. Boyault S, Rickman DS, de Reynies A, et al: Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets. Hepatology 45: 42-52, 2007.
11. Smith MW, Yue ZN, Geiss GK, et al: Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma. Cancer Res 63: 859-864, 2003.
12. Patil MA, Chua MS, Pan KH, et al: An integrated data analysis approach to characterize genes highly expressed in hepatocellular carcinoma. Oncogene 24: 3737-3747, 2005.
13. Xu XR, Huang J, Xu ZG, 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 98: 15089-15094, 2001.
14. Tsai CC, Huang KW, Chen HF, et al: Gene expression analysis of human hepatocellular carcinoma by using full-length cDNA library. J Biomed Sci 13: 241-249, 2006.
15. Yoon SY, Kim JM, Oh JH, et al: Gene expression profiling of human HBV- and/or HCV-associated hepatocellular carcinoma cells using expressed sequence tags. Int J Oncol 29: 315-327, 2006.
16. Velculescu VE, Zhang L, Vogelstein B and Kinzler KW: Serial analysis of gene expression. Science 270: 484-487, 1995.
17. Lash AE, Tolstoshev CM, Wagner L, et al: SAGEmap: a public gene expression resource. Genome Res 10: 1051-1060, 2000.
18. Boon K, Osorio EC, Greenhut SF, et al: An anatomy of normal and malignant gene expression. Proc Natl Acad Sci USA 99: 11287-11292, 2002.
19. Margulies EH and Innis JW: eSAGE: managing and analysing data generated with serial analysis of gene expression (SAGE). Bioinformatics 16: 650-651, 2000.
20. Pleasance ED, Marra MA and Jones SJ: Assessment of SAGE in transcript identification. Genome Res 13: 1203-1215, 2003.
21. Audic S and Claverie JM: The significance of digital gene expression profiles. Genome Res 7: 986-995, 1997.
22. Fernandez-Velasco M, Goren N, Benito G, Blanco-Rivero J, Bosca L and Delgado C: Regional distribution of hyperpolarization-activated current (If) and hyperpolarization-activated cyclic nucleotide-gated channel mRNA expression in ventricular cells from control and hypertrophied rat hearts. J Physiol 553: 395-405, 2003.
23. Kondoh N, Wakatsuki T, Ryo A, et al: Identification and characterization of genes associated with human hepatocellular carcinogenesis. Cancer Res 59: 4990-4996, 1999.
24. Yamashita T, Kaneko S, Hashimoto S, et al: Serial analysis of gene expression in chronic hepatitis C and hepatocellular carcinoma. Biochem Biophys Res Commun 282: 647-654, 2001.
25. Blackshaw S, Kuo WP, Park PJ, et al: MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol 4: R17, 2003.
26. Baggerly KA, Deng L, Morris JS and Aldaz CM: Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics 19: 1477-1483, 2003.
27. Wong LY, Hafeman A, Boyd VL, et al: Assessing gene expression variation in normal human tissues using GeneTag, a novel, global, sensitive profiling method. J Biotechnol 101: 199-217, 2003.
28. Vencio RZ, Brentani H, Patrao DF and Pereira CA: Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE). BMC Bioinformatics 5: 119, 2004.
29. Iizuka N, Oka M, Yamada-Okabe H, 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 62: 3939-3944, 2002.
30. Mas VR, Maluf DG, Archer KJ, Yanek K, Williams B and Fisher RA: Differentially expressed genes between early and advanced hepatocellular carcinoma (HCC) as a potential tool for selecting liver transplant recipients. Mol Med 12: 97-104, 2006.
31. Wei C, Li J and Bumgarner RE: Sample size for detecting differentially expressed genes in microarray experiments. BMC Genomics 5: 87, 2004.
32. Shih JH, Michalowska AM, Dobbin K, Ye Y, Qiu TH and Green JE: Effects of pooling mRNA in microarray class comparisons. Bioinformatics 20: 3318-3325, 2004.
33. Kendziorski C, Irizarry RA, Chen KS, Haag JD and Gould MN: On the utility of pooling biological samples in microarray experiments. Proc Natl Acad Sci USA 102: 4252-4257, 2005.
34. Yamamoto M, Wakatsuki T, Hada A and Ryo A: Use of serial analysis of gene expression (SAGE) technology. J Immunol Methods 250: 45-66, 2001.
35. Su WH, Chao CC, Yeh SH, Chen DS, Chen PJ and Jou YS: OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci. Nucleic Acids Res 35: D727-D731, 2007.
36. Lu J, Lal A, Merriman B, Nelson S and Riggins G: A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips. Genomics 84: 631-636, 2004.
37. Li YJ, Xu P, Qin X, et al: A comparative analysis of the information content in long and short SAGE libraries. BMC Bioinformatics 7: 504, 2006.
38. Chen J, Sun M, Lee S, Zhou G, Rowley JD and Wang SM: Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci USA 99: 12257-12262, 2002.
39. Zhou T, Evans AA, London WT, et al: Glutathione S-transferase expression in hepatitis B virus-associated human hepatocellular carcinogenesis. Cancer Res 57: 2749-2753, 1997.
40. Coles BF and Kadlubar FF: Human alpha class glutathione Stransferases: genetic polymorphism, expression, and susceptibility to disease. Methods Enzymol 401: 9-42, 2005.
41. Sperling P, Ternes P, Zank TK and Heinz E: The evolution of desaturases. Prostaglandins Leukot Essent Fatty Acids 68: 73-95, 2003.
42. Hansen-Petrik MB, McEntee MF, Johnson BT, et al: Selective inhibition of Delta-6 desaturase impedes intestinal tumorigenesis. Cancer Lett 175: 157-163, 2002.
43. Takahashi H, Saibara T, Iwamura S, et al: Serum alpha-Lfucosidase activity and tumor size in hepatocellular carcinoma. Hepatology 19: 1414-1417, 1994.
44. Giardina MG, Matarazzo M, Morante R, et al: Serum alpha-Lfucosidase activity and early detection of hepatocellular carcinoma: a prospective study of patients with cirrhosis. Cancer 83: 2468-2474, 1998.
45. Wang JJ and Cao EH: Rapid kinetic rate assay of the serum alpha-L-fucosidase in patients with hepatocellular carcinoma by using a novel substrate. Clin Chim Acta 347: 103-109, 2004.
46. Yin YH, Li YY, Qiao H, et al: TSPY is a cancer testis antigen expressed in human hepatocellular carcinoma. Br J Cancer 93: 458-463, 2005.
47. Eichmuller S, Usener D, Dummer R, Stein A, Thiel D and Schadendorf D: Serological detection of cutaneous T-cell lymphoma-associated antigens. Proc Natl Acad Sci USA 98: 629-634, 2001.
48. Ozbun LL, You L, Kiang S, Angdisen J, Martinez A and Jakowlew SB: Identification of differentially expressed nucleolar TGF-beta1 target (DENTT) in human lung cancer cells that is a new member of the TSPY/SET/ NAP-1 superfamily. Genomics 73: 179-193, 2001.
49. Kuryshev VY, Vorobyov E, Zink D, et al: An anthropoid-specific segmental duplication on human chromosome 1q22. Genomics 88: 143-151, 2006.
50. Hsu HC, Cheng W and Lai PL: Cloning and expression of a developmentally regulated transcript MXR7 in hepatocellular carcinoma: biological significance and temporospatial distribution. Cancer Res 57: 5179-5184, 1997.
51. Zhu ZW, Friess H, Wang L, et al: Enhanced glypican-3 expression differentiates the majority of hepatocellular carcinomas from benign hepatic disorders. Gut 48: 558-564, 2001.
52. Capurro M, Wanless IR, Sherman M, et al: Glypican-3: a novel serum and histochemical marker for hepatocellular carcinoma. Gastroenterology 125: 89-97, 2003.
53. Nakatsura T, Yoshitake Y, Senju S, et al: Glypican-3, overexpressed specifically in human hepatocellular carcinoma, is a novel tumor marker. Biochem Biophys Res Commun 306: 16-25, 2003.
54. Khan S, Blackburn M, Mao DL, Huber R, Schlessinger D and Fant M: Glypican-3 (GPC3) expression in human placenta: localization to the differentiated syncytiotrophoblast. Histol Histopathol 16: 71-78, 2001.
55. Coston WM, Loera S, Lau SK, et al: Distinction of hepatocellular carcinoma from benign hepatic mimickers using Glypican-3 and CD34 immunohistochemistry. Am J Surg Pathol 32: 433-444, 2008.
56. Wang HL, Anatelli F, Zhai QJ, Adley B, Chuang ST and Yang XJ: Glypican-3 as a useful diagnostic marker that distinguishes hepatocellular carcinoma from benign hepatocellular mass lesions. Arch Pathol Lab Med 132: 1723-1728, 2008.