The expression of embryonic liver development genes in hepatitis c induced cirrhosis and hepatocellular carcinoma

Cancers

Volumn 4, Issue 3, 2012, Pages 945-968

  Behnke, Martha ^a   Reimers, Mark ^b   Fisher, Robert ^c  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^b VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^c VIRGINIA COMMONWEALTH UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Hepatitis C; Hepatocellular carcinoma; Microarray analysis

Indexed keywords

FOLLISTATIN;

ARTICLE; CONTROLLED STUDY; DEVELOPMENTAL GENE; DEVELOPMENTAL STAGE; FOLLISTATIN GENE; FOLLISTATIN LIKE PROTEIN 3 GENE; GENE EXPRESSION; GENE IDENTIFICATION; GPC3 GENE; GREM1 GENE; HUMAN; HUMAN TISSUE; LIVER CARCINOGENESIS; LIVER CELL CARCINOMA; LIVER CIRRHOSIS; LIVER DEVELOPMENT; MAJOR CLINICAL STUDY; MALIGNANT TRANSFORMATION; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; UNINDEXED SEQUENCE;

EID: 84866892528     PISSN: None     EISSN: 20726694     Source Type: Journal    
DOI: 10.3390/cancers4030945     Document Type: Article

References (67)

1. McGivern, D.; Lemon, S. Virus-specific mechanisms of carcinogenesis in hepatitis C virus associated with liver cancer. Oncogene 2011, 30, 1969-1983.
2. Chen, X.; Cheung, S.; So, S.; Fan, S.; Barry, C.; Higgins, B.; Lai, K.; Ji, J.; Dudoit, S.; Ng, I.; et al. Gene expression patterns in human liver cancers. Mol. Biol. Cell 2002, 13, 1929-1939.
3. Iizuka, N.; Oka, M.; Yamada-Okabe, H.; Nishida, M.; Maeda, Y.; Mori, N.; Takao, T.; Tamesa, T.; Tangoku, A.; Tabuchi, H.; et al. Oligonucleotide microarray for predication of early intrahepatic recurrence of hepatocellular carcinoma after curative resection. Lancet 2003, 361, 923-929.
4. Kim, J.; Ye, Q.; Forgues, M.; Chen, Y.; Budhu, A.; Sime, J.; Hofseth, L.; Kaul, R.; Wang, X.-W. Cancer-associated molecular signature in the tissue samples of patients with cirrhosis. Hepatology 2004, 39, 518-527.
5. Llovet, J.; Chen, Y.; Wurmbach, E.; Roayaie, S.; Fiel, M.; Schwartz, M.; Thung, S.; Khitrov, G.; Zhang, W.; Villanueva, A.; et al. A molecular signature to discriminate dysplastic nodules from early hepatocellular carcinoma in HCV cirrhosis. Gastroenterology 2006, 131, 1758-1767.
6. Lee, J.; Chu, I.; Heo, J.; Calvisi, D.; Sun, Z.; Roskams, T.; Durnez, A.; Demetris, A.; Thorgeirsson, S. Classification and predication of survival in hepatocellular carcinoma by gene expression profiling. Hepatology 2004, 40, 667-676.
7. Budhu, A.; Forgues, M.; Ye, Q.; Jia, H.; He, P.; Zanetti, K.; Kammula, U.; Chen, Y.; Qin, L.; Tang, Z.; et al. Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment. Cancer Cell 2006, 10, 99-111.
8. Wang, S.; Ooi, L.; Hui, K. Identification and validation of a novel gene signature associated with the recurrence of human hepatocellular carcinoma. Clin. Cancer Res. 2007, 13, 6275-6283.
9. Jia, H.; Ye, Q.; Qin, L.; Budhu, A.; Forgues, M.; Chen, Y.; Liu, Y.; Sun, H.; Wang, L.; Lu, H.; et al. Gene expression profiling reveals potential biomarkers of human hepatocellular carcinoma. Clin. Cancer Res. 2007, 13, 1133-1139.
10. Wurmbach, E.; Chen, Y.; Khitrov, G.; Zhang, W.; Roayaie, S.; Schwartz, M.; Fiel, I.; Thung, S.; Mazzaferro, V.; Bruix, J.; et al. Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Hepatoloty 2007, 45, 42-52.
11. Hoshida, Y.; Villanueva, A.; Kobayashi, M.; Peix, J.; Chiang, D.; Camargo, A.; Bupta, S.; Moore, J.; Wrobel, M.; Lerner, J.; et al. Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N. Engl. J. Med. 2008, 359, 1995-2004.
12. Yamashita, T.; Ji, J.; Budhu, A.; Forgues, M.; Yang, W.; Wang, H.-Y.; Jia, H.; Ye, Q.; Qin, L.; Wauthier, E.; et al. EpCAM-positive hepatocellular carcinoma cells are tumor initiating cells with stem-progenitor cell features. Gastroenterology 2009, 69, 1012-1024.
13. Korn, E.; Troendle, J.; McShane, L.; Simon, R. Controlling the number of false discoveries: Application to high-dimensional genomic data. J. Stat. Plan. Inference 2004, 124, 379-398.
14. Owen, A. Variance of the number of false discoveries. J. R. Statist. Soc. B 2005, 67, 411-426.
15. Schwartzman, A.; Lin, X. The effect of correlation in false discovery rate estimation. Biometrika 2011, 98, 199-214.
16. Hu, Z.; Willsky, G. Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies. BMC Bioinformatics 2006, 7, 12.
17. Ochs, M.; Quackenbush, J.; Davulvuri, R.; Ressom, H. Knowledge-driven analysis and data integration for high-throughput biological data. Pac. Symp. Biocomput. 2008, 14, 353-355.
18. Turner, S.; Berg, R.; Linneman, G.; Peissig, P.; Crawford, D.; Denny, J.; Roden, D.; McCarty, C.; Ritchie, M.; Wilke, R. Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks. PLoS One 2011, 6, e19586.
19. Alterovitz, G.; Ramoni, M. Knowledge-Based Bioinformatics: From Analysis to Interpretation; John Wiley & Sons Ltd.: West Sussex, UK, 2010.
20. Merlo, L.; Pepper, J.; Reid, B.; Maley, C. Cancer as an evolutionary and ecological process. Nat. Rev. Cancer 2006, 6, 924.
21. Choe, S.; Boutros, M.; Michelson, A.; Church, G.; Halfon, M. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol. 2005, 6, R16.
22. Jung, K.; Friede, T.; Beissbarth, T. Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes. BMC Bioinformatics 2011, 12, 288.
23. Beilas, J.; Loeb, K.; Rubin, B.; True, L.; Loeb, L. Human cancers express a mutator phenotype. Proc. Natl. Acad. Sci. USA 2006, 103, 18238-18242.
24. Salk, J.; Fox, E.; Loeb, L. Mutational heterogeneity in human cancers: Origin and consequences. Annu. Rev. Pathol. Mech. Dis. 2010, 5, 51-75.
25. Peltomaki, P. Mutations and epimutations in the origin of cancer. Exp. Cell Res. 2011, 318, 299-310.
26. Lengauer, C.; Kinzler, K.; Vogelstein, B. Genetic instability in colorectal cancers. Nature 1997, 386, 623-627.
27. Reshmi, S.; Gollin, S. Chromosomal instability in oral cancer cells. J. Dent. Res. 2005, 84, 107-117.
28. Hsu, I.; Tokiwa, T.; Bennett, W.; Metcalf, R.; Welsh, J.; Sun, T.; Harris, C. p53 Gene mutation and integrated hepatitis B viral DNA sequences in human liver cancer cell lines. Carcinogenesis 1993, 14, 987-992.
29. Hussain, S.; Schwank, J.; Staib, F.; Wang, X.; Harris, C. TP53 mutations and Hepatocellular carcinoma: Insights into the etiology and pathogenesis of liver cancer. Oncogene 2007, 26, 2166-2176.
30. Kung, J.; Currie, I.; Forbes, S.; Ross, J. Liver development, regeneration, and carcinogenesis. J. Biomed. Biotechnol. 2010, 2010, 984248.
31. Naxerova, K.; Bult, C.; Peaston, A.; Fancher, K.; Knowles, B.; Kasif, S.; Kohane, I. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biol. 2008, 9, R108.
32. Si-Tayeb, K.; Lemaigre, F.; Duncan, S. Organogenesis and development of the liver. Dev. Cell 2010, 18, 175-188.
33. Loh, K.; Chia, J.; Greco, S.; Cozzi, S.; Buttenshaw, R.; Bond, C.; Simms, L.; Pike, T.; Young, J.; Jass, J.; et al. Bone Morphogenic protein 3 inactivation is an early and frequent event in colorectal cancer development. Genes Chromosomes Cancer 2008, 47, 449-460.
34. Chen, X.; Wang, J.; Li, X.; Zhang, H.; Ye, Z. Role of BMP3 in progression of gastric carcinoma in Chinese people. World J. Gastroenterol. 2010, 16, 1409-1413.
35. Kisial, J.; Tab, T.; Tablor, W.; Chari, S.; Petersen, G.; Mahoney, M.; Ahlquist, D. Stool DNA testing for the detection of pancreatic cancer. Cancer 2012, 118, 2623-2631.
36. Albergaria, A.; Riberio, A.; Pinho, S.; Milanezi, F.; Carneiro, V.; Sousa, B.; Sousa, S.; Oliveira, C.; Machado, J.; Seruca, R.; et al. ICI 182,780 induces P-cadherin overexpression in breast cancer cells through chromatin remodeling at the promoter level: A role for C/EBPbeta in CDH3 gene activation. Hum. Mol. Genet. 2010, 19, 2554-2566.
37. Taniuchi, K.; Nakagawa, H.; Hosokawa, M.; Nakamura, T.; Equchi, H.; Ohigashi, H.; Ishikawa, O.; Katagiri, T.; Nakamura, Y. Overexpressed P-cadherin/CDH3 promotes motility of pancreatic cancer cells by interacting with p120ctn and activating rho-family GTPases. Cancer Res. 2005, 65, 3092-3099.
38. Rosen, A.; Sevelda, P.; Klein, M.; Dobianer, K.; Hruza, C.; Czerwnda, K.; Hanak, H.; Vavra, N.; Salzer, H.; Leodolter, S. First experience with FGF-3 (INT-2) amplification in women with epithelial ovarian cancer. Br. J. Cancer 1993, 67, 1122-1125.
39. Champeme, M.; Bieche, I.; Hacene, K.; Lidereau, R. Int-2/FGF3 amplification is a better independent predictor of relapse than c-myc and c-erbB-2/neu amplifications in primary human breast cancer. Mod. Pathol. 1994, 7, 900-905.
40. Zaharieva, B.; Simon, R.; Diener, P.; Ackermann, D.; Maurer, R.; Alund, G.; Knonagel, H.; Rist, M.; Wilger, K.; Hering, F.; et al. High-throughput tissue microarray analysis of 11q13 gene amplification (CCND1, FGF3, FGF4, EMS1) in urinary bladder cancer. J. Pathol. 2003, 201, 603-608.
41. Chattopadhyay, I.; Singh, A.; Hukan, R.; Purkayashtha, J.; Kataki, A.; Mahanta, J.; Saxena, S.; Kapur, S. Genome-wide analysis of chromosomal alterations in patients with esophageal squamous cell carcinoma exposed to tobacco and betel quid from high-risk area in India. Mutat. Res. 2010, 696, 130-138.
42. Kang, J.; Koo, S.; Kwon, K.; Park, J.; Kim, J. Identification of novel candidate target genes, including EPHB3, MASP1 an SST at 3q26.2-q29 in squamous cell carcinoma of the lung. BMC Cancer 2009, 16, 237.
43. Hama, A.; Muramatsu, H.; Makishima, H.; Sugimoto, Y.; Szpurka, H.; Jasek, M.; O'Keefe, C.; Takahashi, Y.; Sakaguchi, H.; Doisaki, S.; et al. Molecular lesions in childhood and adult acute magakaryoblastic leukaemia. Br. J. Haematol. 2012, 156, 316-325.
44. Seo, M.; Liu, X.; Chang, M.; Park, J. GATA-binding protein 1 is a novel transcription regulator of peroxiredoxin 5 in human breast cancer cells. Int. J. Oncol. 2012, 40, 655-664.
45. Jiang, F.; Parsons, C.; Stefanovic, B. Gene expression profile of quiescent and activated rate hepatic stellate cells implicates Wnt signaling pathway in activation. J. Hepatol. 2006, 45, 401-409.
46. Li, D.; Friedman, S. Liver fibrogenesis and the role of hepatic stellate cells: New insights and prospects for therapy. J. Gastroenterol. Hepatol. 1999, 14, 618-633.
47. Wang, B.-B.; Cheng, J.-Y.; Gao, H.-H.; Zhang, Y.; Chen, Z.-N.; Bian, H. Hepatic stellate cells in inflammation-fibrosis-carcinoma axis. Anat. Rec. 2010, 293, 1492-1496.
48. Denecke, B.; Wickert, L.; Liu, Y.; Ciuclan, L.; Dooley, S.; Meindl-Beinker, N. Smad7 dependent expression signature highlights BMP2 and HK2 signaling in HSC transdifferentiation. World J. Gastroenterol. 2010, 16, 5211-5224.
49. Fan, J.; Shen, H.; Sun, Y.; Li, P.; Burczynski, F.; Namaka, M.; Gong, Y. Bone morphogenetic protein 4 mediates bile duct ligation induced liver fibrosis through activation of Smad1 and ERK1/2 in rat hepatic stellate cells. J. Cell. Physiol. 2006, 207, 499-505.
50. Tsai, S.; Wang, W. Expression and function of Fibroblast Growth Factor (FGF) 7 during liver regeneration. Cell Physiol. Biochem. 2011, 11, 641-652.
51. Ding, B.; Nolan, D.; Butler, J.; James, D.; Babazadeh, A.; Rosenwaks, Z.; Mittal, V.; Kobayashi, H.; Shido, K.; Lyden, D.; et al. Inductive angiocrine signals from sinusoidal endothelium are required for liver regeneration. Nature 2010, 468, 310-317.
52. Gilgenkrantz, H.; de l'Hortet, A. New insights into liver regeneration. Clin. Res. Hepatol. Gastroenterol. 2011, 35, 623-629.
53. Nejak-Bowen, K.; Monga, S. Beta-catenin signaling, liver regeneration and Hepatocellular cancer: Sorting the good from the bad. Semin. Cancer Biol. 2011, 21, 44-58.
54. Kosinki, C.; Li, V.; Chan, A.; Zhang, J.; Ho, C.; Tsui, W.; Chan, T.; Mifflin, R.; Powell, D.; Yuen, S.; et al. Gene expression patterns of human colon tops and basal crypts and BMP antagonists as intestinal stem cell niche factors. Proc. Natl. Acad. Sci. USA 2007, 104, 15418-15423.
55. Turner, R.; Lozoya, O.; Want, Y.; Cardinale, V.; Gaudio, E.; Alpini, G.; Mendel, G.; Wauthier, E.; Barbier, C.; Alvaro, D.; et al. Human hepatic stem cell and maturational liver lineage biology. Hepatology 2011, 53, 1035-1045.
56. Benhamouche, S.; Curto, M.; Saotome, I.; Gladden, A.; Liu, C.; Giovannini, M.; McClatchey, A. Nf2/Merlin controls progenitor homeostasis and tumorigenesis in the liver. Genes Dev. 2010, 24, 1718-1730.
57. Fisher, R.; Maroney, T.; Fulcher, A.; Maluf, D.; Clay, J.; Wolfe, L.; Dawson, S.; Cotterell, A.; Stravitz, R.; Luketic, V.; et al. Hepatocellular carcinoma: Strategy for optimizing surgical resection, transplantation and palliation. Clin. Transplant. 2001, 16, 52-58.
58. Wurmbach, E.; Chen, Y.; Khitrov, G.; Zhang, W.; Roayaie, S.; Schwartz, M.; Fiel, I.; Thung, S.; Mazzaferro, V.; Bruix, J.; et al. Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Hepatology 2007, 45, 938-947.
59. Kawamoto, S.; Yoshii, J.; Mizuno, K.; Ito, K.; Ohnishi, T.; Matoba, R.; Hori, N.; Matsumoto, Y.; Okumura, T.; Nakao, Y.; et al. BodyMap: A collection of 3' ESTs for analysis of human gene expression information. Genome Res. 2000, 10, 1817-1827.
60. Li, H.; Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25, 1754-1760.
61. Mas, V.; Maluf, D.; Stravitz, R.; Dumur, C.; Clark, B.; Rodgers, C.; Ferreira-Gonzalez, A.; Fisher, R.A. Hepatocellular carcinoma in HCV-infected patients awaiting liver transplantation: Genes involved in tumor progression. Liver Transpl. 2004, 10, 607-620.
62. Reimers, M.; Weinstein, J. Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases. BMC Bioinformatics 2005, 6, 166.
63. Sandberg, R.; Larsson, O. Improved precision and accuracy for microarrays using updated probe set definitions. BMC Bioinformatics 2007, 8, 48.
64. Guennel, T.; Reinhold, W.; Pommier, Y.; Selzer, R.; Weinstein, J.; Reimers, M. Noise reduction for aCGH data using technical covariates and probe level information. BMC Bioinformatics 2012, under review.
65. Venables, W.; Ripley, B. Modern Applied Statistics with S. Fourth Edition; Springer: New York, NY, USA, 2002; ISBN 0-387-95457-0.
66. Li, T.; Wan, B.; Huang, J.; Zhang, X. comparison of gene expression in Hepatocellular carcinoma, liver development, and liver regeneration. Mol. Genet. Genomics 2010, 283, 485-492.
67. Lu, J.; Hsia, Y.; Tu, H.-C.; Hsiao, Y.-C.; Yan, W.-Y.; Wang, H.-D.; Yuh, C.-H. Liver development and cancer formation in zebrafish. Birth Defects Res. C Embryo Today 2011, 93, 157-172.