Gene network analysis leads to functional validation of pathways linked to cancer cell growth and survival

Biotechnology Journal

Volumn 7, Issue 11, 2012, Pages 1395-1404

  Berger, Emmanuelle ^a   Vega, Nathalie ^a   Vidal, Hubert ^a   Geloën, Alain ^a  

^a UNIVERSITÉ DE LYON   (France)

Author keywords

HCC; Human hepatocellular carcinoma; Real time proliferation assay; Signal transduction

Indexed keywords

BIOINFORMATIC ANALYSIS; BIOLOGICAL FUNCTIONS; CANCER CELL GROWTH; CELL DIFFERENTIATION; CELL LINES; FUNCTIONAL VALIDATION; G PROTEIN; HCC; HEPATOCELLULAR CARCINOMA; HEPG2 CELLS; HUMAN CANCER; IN-SILICO; POTENTIAL TARGETS; PROTEIN KINASE C; SIGNALING INHIBITORS; SIGNALING MOLECULES; SIGNALING PATHWAYS; SURGICAL RESECTION; TUMORIGENICITY;

ASSAYS; CELL CULTURE; DRUG THERAPY; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

BIOINFORMATICS;

CCAAT ENHANCER BINDING PROTEIN ALPHA; GUANINE NUCLEOTIDE BINDING PROTEIN; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; JANUS KINASE 1; LOW DENSITY LIPOPROTEIN RECEPTOR; MITOGEN ACTIVATED PROTEIN KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE 3; MITOGEN ACTIVATED PROTEIN KINASE KINASE 1; MITOGEN ACTIVATED PROTEIN KINASE KINASE 2; OCTAMER TRANSCRIPTION FACTOR 1; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA COACTIVATOR 1ALPHA; TRANSCRIPTION FACTOR EGR 1; TRANSCRIPTION FACTOR ELK 1; TRANSCRIPTION FACTOR FKHR; TRANSCRIPTION FACTOR RELA;

ARTICLE; BIOINFORMATICS; CELL DIFFERENTIATION; CELL PROLIFERATION; CELL STRAIN HEPG2; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC ASSOCIATION; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HUMAN CELL; IN VITRO STUDY; LIVER CELL CARCINOMA; METHYLATION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

CARCINOMA, HEPATOCELLULAR; CELL GROWTH PROCESSES; CELL LINE, TUMOR; CELL SURVIVAL; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HEP G2 CELLS; HUMANS; LIVER; LIVER NEOPLASMS; MAP KINASE SIGNALING SYSTEM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REAL-TIME POLYMERASE CHAIN REACTION; RNA, MESSENGER; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84868651896     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201200188     Document Type: Article

References (52)

1. Tanaka, S., Arii, S., Molecular targeted therapy for hepatocellular carcinoma in the current and potential next strategies. J. Gastroenterol. 2010, 46, 289-296.
2. Patil, M. A., Gutgemann, I., Zhang, J., Ho, C. et al., Array-based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for 8q gain in hepatocellular carcinoma. Carcinogenesis 2005, 26, 2050-2057.
3. Aburatani, S., Sun, F., Saito, S., Honda, M. et al., Gene systems network inferred from expression profiles in hepatocellular carcinogenesis by graphical Gaussian model. EURASIP J. Bioinform. Syst. Biol. 2007, XX 47214.
4. Teufel, A., Staib, F., Kanzler, S., Weinmann, A. et al., Genetics of hepatocellular carcinoma. World J. Gastroenterol. 2007, 13, 2271-2282.
5. Hoshida, Y., Toffanin, S., Lachenmayer, A., Villanueva, A. et al., Molecular classification and novel targets in hepatocellular carcinoma: recent advancements. Semin. Liver Dis. 2010, 30, 35-51.
6. Whittaker, S., Marais, R., Zhu, A. X., The role of signaling pathways in the development and treatment of hepatocellular carcinoma. Oncogene 29, 4989-5005.
7. Ito, Y., Sasaki, Y., Horimoto, M., Wada, S. et al., Activation of mitogen-activated protein kinases/extracellular signal-regulated kinases in human hepatocellular carcinoma. Hepatology 1998, 27, 951-958.
8. Zender, L., Villanueva, A., Tovar, V., Sia, D. et al., Cancer gene discovery in hepatocellular carcinoma. J. Hepatol. 2010, 52, 921-929.
9. Schmidt, C. M., McKillop, I. H., Cahill, P. A., Sitzmann, J. V., The role of cAMP-MAPK signalling in the regulation of human hepatocellular carcinoma growth in vitro. Eur. J. Gastroenterol. Hepatol. 1999, 11, 1393-1399.
10. Iyoda, K., Sasaki, Y., Horimoto, M., Toyama, T. et al., Involvement of the p38 mitogen-activated protein kinase cascade in hepatocellular carcinoma. Cancer 2003, 97, 3017-3026.
11. Adachi, M., Brenner, D. A., High molecular weight adiponectin inhibits proliferation of hepatic stellate cells via activation of adenosine monophosphate-activated protein kinase. Hepatology 2008, 47, 677-685.
12. Ng, S. K., Neo, S. Y., Yap, Y. W., Karuturi, R. K. et al., Ablation of phosphoinositide-3-kinase class II alpha suppresses hepatoma cell proliferation. Biochem. Biophys. Res. Commun. 2009, 387, 310-315.
13. Calvisi, D. F., Ladu, S., Pinna, F., Frau, M. et al., SKP2 and CKS1 promote degradation of cell cycle regulators and are associated with hepatocellular carcinoma prognosis. Gastroenterology 2009, 137, 1816-1826.
14. Xu, L., Hui, L., Wang, S., Gong, J. et al., Expression profiling suggested a regulatory role of liver-enriched transcription factors in human hepatocellular carcinoma. Cancer Res. 2001, 61, 3176-3181.
15. Tomizawa, M., Horie, H., Yamamoto, H., Matsunaga, T. et al., Reciprocal expression of CCAAT/enhancer binding proteins alpha and beta in hepatoblastomas and its prognostic significance. Oncol. Rep. 2007, 17, 341-344.
16. Berger, E., Rome, S., Vega, N., Ciancia, C., Vidal, H., Transcriptome profiling in response to adiponectin in human cancer-derived cells. Physiol. Genomics 2010, 42, 61-70.
17. Chang, K. J., Lin, J. K., Lee, P. H., Hsieh, Y. S. et al., The altered activity of membrane-bound protein kinase C in human liver cancer. Cancer Lett. 1996, 105, 211-215.
18. Schmidt, C. M., McKillop, I. H., Cahill, P. A., Sitzmann, J. V., Alterations in guanine nucleotide regulatory protein expression and activity in human hepatocellular carcinoma. Hepatology 1997b, 26, 1189-1194.
19. Tsai, J. H., Hsieh, Y. S., Kuo, S. J., Chen, S. T. et al., Alteration in the expression of protein kinase C isoforms in human hepatocellular carcinoma. Cancer Lett. 2000, 161, 171-175.
20. Fuke, H., Shiraki, K., Sugimoto, K., Tanaka, J. et al., Jak inhibitor induces S phase cell-cycle arrest and augments TRAIL-induced apoptosis in human hepatocellular carcinoma cells. Biochem. Biophys. Res. Commun. 2007, 363, 738-744.
21. Kusaba, M., Nakao, K., Goto, T., Nishimura, D. et al., Abrogation of constitutive STAT3 activity sensitizes human hepatoma cells to TRAIL-mediated apoptosis. J. Hepatol. 2007, 47, 546-555.
22. Moon, D. O., Kim, M. O., Choi, Y. H., Hyun, J. W. et al., Butein induces G(2)/M phase arrest and apoptosis in human hepatoma cancer cells through ROS generation. Cancer Lett. 2010, 288, 204-213.
23. Sasse, J., Hemmann, U., Schwartz, C., Schniertshauer, U. et al., Mutational analysis of acute-phase response factor/Stat3 activation and dimerization. Mol. Cell. Biol. 1997, 17, 4677-4686.
24. Hah, N., Lee, S. T., An absolute role of the PKC-dependent NF-kappaB activation for induction of MMP-9 in hepatocellular carcinoma cells. Biochem. Biophys. Res. Commun. 2003, 305, 428-433.
25. Chiao, P. J., Na, R., Niu, J., Sclabas, G. M. et al., Role of Rel/NF-kappaB transcription factors in apoptosis of human hepatocellular carcinoma cells. Cancer 2002, 95, 1696-1705.
26. Alisi, A., Piemonte, F., Pastore, A., Panera, N. et al., Glutathionylation of p65NF-kappaB correlates with proliferating/apoptotic hepatoma cells exposed to pro- and anti-oxidants. Int. J. Mol. Med. 2009, 24, 319-326.
27. Wu, L. F., Li, G. P., Su, J. D., Pu, Z. J. et al., Involvement of NF-kappaB activation in the apoptosis induced by extracellular adenosine in human hepatocellular carcinoma HepG2 cells. Biochem. Cell. Biol. 2010, 88, 705-714.
28. Feo, F., Frau, M., Tomasi, M. L., Brozzetti, S., Pascale, R. M., Genetic and epigenetic control of molecular alterations in hepatocellular carcinoma. Exp. Biol. Med. 2009, 234, 726-736.
29. Pilarsky, C., Wenzig, M., Specht, T., Saeger, H. D., Grutzmann, R., Identification and validation of commonly overexpressed genes in solid tumors by comparison of microarray data. Neoplasia 2004, 6, 744-750.
30. Sun, H. C., Li, M., Lu, J. L., Yan, D. W. et al., Overexpression of Forkhead box M1 protein associates with aggressive tumor features and poor prognosis of hepatocellular carcinoma. Oncol. Rep. 2011, 25, 1533-1539.
31. Yuen, M. F., Wu, P. C., Lai, V. C., Lau, J. Y., Lai, C. L., Expression of c-Myc, c-Fos, and c-jun in hepatocellular carcinoma. Cancer 2001, 91, 106-112.
32. Hao, M. W., Liang, Y. R., Liu, Y. F., Liu, L. et al., Transcription factor EGR-1 inhibits growth of hepatocellular carcinoma and esophageal carcinoma cell lines. World J. Gastroenterol. 2002, 8, 203-207.
33. Burns, K. A., Vanden Heuvel, J. P., Modulation of PPAR activity via phosphorylation. Biochim. Biophys. Acta 2007, 1771, 952-960.
34. Okano, H., Shiraki, K., Inoue, H., Yamanaka, T. et al., Peroxisome proliferator-activated receptor gamma augments tumor necrosis factor family-induced apoptosis in hepatocellular carcinoma. Anticancer Drugs 2002, 13, 59-65.
35. Toyoda, M., Takagi, H., Horiguchi, N., Kakizaki, S. et al., A ligand for peroxisome proliferator activated receptor gamma inhibits cell growth and induces apoptosis in human liver cancer cells. Gut 2002, 50, 563-567.
36. Li, M. Y., Deng, H., Zhao, J. M., Dai, D., Tan, X. Y., PPARgamma pathway activation results in apoptosis and COX-2 inhibition in HepG2 cells. World J. Gastroenterol. 2003, 9, 1220-1226.
37. Zhou, Y. M., Wen, Y. H., Kang, X. Y., Qian, H. H. et al., Troglitazone, a peroxisome proliferator-activated receptor gamma ligand, induces growth inhibition and apoptosis of HepG2 human liver cancer cells. World J. Gastroenterol. 2008, 14, 2168-2173.
38. Koga, H., Harada, M., Ohtsubo, M., Shishido, S. et al., Troglitazone induces p27Kip1-associated cell-cycle arrest through down-regulating Skp2 in human hepatoma cells. Hepatology 2003, 37, 1086-1096.
39. Yu, J., Qiao, L., Zimmermann, L., Ebert, M. P. et al., Troglitazone inhibits tumor growth in hepatocellular carcinoma in vitro and in vivo. Hepatology 2006, 43, 134-143.
40. Tachibana, K., [Application of the human hepatoblastoma cell lines inducibly expressing peroxisome proliferator-activated receptors (PPARs)]. Yakugaku Zasshi 2007, 127, 1223-1229.
41. Watkins, P. A., Ferrell, E. V. Jr., Pedersen, J. I., Hoefler, G., Peroxisomal fatty acid beta-oxidation in HepG2 cells. Arch. Biochem. Biophys. 1991, 289, 329-336.
42. Gulick, T., Cresci, S., Caira, T., Moore, D. D., Kelly, D. P., The peroxisome proliferator-activated receptor regulates mitochondrial fatty acid oxidative enzyme gene expression. Proc. Natl. Acad. Sci. USA 1994, 91, 11012-11016.
43. Lee, W. N., Lim, S., Bassilian, S., Bergner, E. A., Edmond, J., Fatty acid cycling in human hepatoma cells and the effects of troglitazone. J. Biol. Chem. 1998, 273, 20929-20934.
44. Maggiora, M., Oraldi, M., Muzio, G., Canuto, R. A., Involvement of PPARalpha and PPARgamma in apoptosis and proliferation of human hepatocarcinoma HepG2 cells. Cell Biochem. Funct. 2011, 28, 571-577.
45. Cosulich, S., James, N., Roberts, R., Role of MAP kinase signalling pathways in the mode of action of peroxisome proliferators. Carcinogenesis 2000, 21, 579-584.
46. Glauert, H. P., Calfee-Mason, K., Li, Y., Nilakantan, V. et al., The Role of NF-kappaB in PPARalpha-mediated hepatocarcinogenesis. PPAR. Res. 2008, 2008, 286-249.
47. Shyamsundar, R., Kim, Y. H., Higgins, J. P., Montgomery, K. et al., A DNA microarray survey of gene expression in normal human tissues. Genome Biol. 2005, 6, R22.
48. Diehl, A. M., Johns, D. C., Yang, S., Lin, H. et al., Adenovirus-mediated transfer of CCAAT/enhancer-binding protein-alpha identifies a dominant antiproliferative role for this isoform in hepatocytes. J. Biol. Chem. 1996, 271, 7343-7350.
49. Harris, T. E., Albrecht, J. H., Nakanishi, M., Darlington, G. J., CCAAT/enhancer-binding protein-alpha cooperates with p21 to inhibit cyclin-dependent kinase-2 activity and induces growth arrest independent of DNA binding. J. Biol. Chem. 2001, 276, 29200-29209.
50. Lu, G. D., Leung, C. H., Yan, B., Tan, C. M. et al., C/EBPalpha is up-regulated in a subset of hepatocellular carcinomas and plays a role in cell growth and proliferation. Gastroenterology 2010, 139, 632-643.
51. Dannenberg, L. O., Edenberg, H. J., Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation. BMC Genomics 2006, 7, 181.
52. 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.