Integrative transcriptional analysis between human and mouse cancer cells provides a common set of transformation associated genes

Biotechnology Advances

Volumn 30, Issue 1, 2012, Pages 16-29

  Balestrieri, C ^a   Vanoni, M ^a   Hautaniemi, S ^b   Alberghina, L ^a   Chiaradonna, F ^a  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Bioinformatics; Cancer genes; Cross species comparison; K ras oncogene; NIH3T3; Transcriptome; Transformation

Indexed keywords

CANCER GENES; CROSS-SPECIES; K-RAS ONCOGENE; NIH3T3; TRANSCRIPTOMES; TRANSFORMATION;

ACTIVATION ANALYSIS; BIOINFORMATICS; CELL CULTURE; DISEASES; GENES; HISTOLOGY; MAMMALS; TISSUE; TRANSCRIPTION;

CELLS;

TRANSCRIPTOME;

BIOINFORMATICS; CANCER; CYTOLOGY; GENE EXPRESSION; PATHOLOGY; PHYSIOLOGY; RODENT;

ANALYSIS OF VARIANCE; ANIMAL; ARTICLE; BIOLOGY; CELL STRAIN 3T3; CELL TRANSFORMATION; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HUMAN; METHODOLOGY; MOUSE; NEOPLASM; ONCOGENE; PATHOLOGY; REPRODUCIBILITY; SPECIES DIFFERENCE; TUMOR CELL LINE;

ANALYSIS OF VARIANCE; ANIMALS; CELL LINE, TUMOR; CELL TRANSFORMATION, NEOPLASTIC; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MICE; NEOPLASMS; NIH 3T3 CELLS; ONCOGENES; REPRODUCIBILITY OF RESULTS; SPECIES SPECIFICITY; TRANSCRIPTOME;

MAMMALIA;

EID: 84855744381     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2011.06.013     Document Type: Article

References (108)

1. Aitman T.J., Critser J.K., Cuppen E., Dominiczak A., Fernandez-Suarez X.M., Flint J., et al. Progress and prospects in rat genetics: a community view. Nat Genet 2008, 40:516-522.
2. Alon U., Barkai N., Notterman D.A., Gish K., Ybarra S., Mack D., et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 1999, 96:6745-6750.
3. Amstad P., Reddel R.R., Pfeifer A., Malan-Shibley L., Mark G.E., Harris C.C. Neoplastic transformation of a human bronchial epithelial cell line by a recombinant retrovirus encoding viral Harvey ras. Mol Carcinog 1988, 1:151-160.
4. Balestrieri C., Alberghina L., Vanoni M., Chiaradonna F. Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes. BMC Bioinformatics 2009, 10(Suppl. 12):S1.
5. Baracca A., Chiaradonna F., Sgarbi G., Solaini G., Alberghina L., Lenaz G. Mitochondrial Complex I decrease is responsible for bioenergetic dysfunction in K-ras transformed cells. Biochim Biophys Acta 2010, 1797:314-323.
6. Barrett T., Suzek T.O., Troup D.B., Wilhite S.E., Ngau W.C., Ledoux P., et al. NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Res 2005, 33:D562-D566.
7. Bedell M.A., Jenkins N.A., Copeland N.G. Mouse models of human disease. Part I: techniques and resources for genetic analysis in mice. Genes Dev 1997, 11:1-10.
8. Bedell M.A., Largaespada D.A., Jenkins N.A., Copeland N.G. Mouse models of human disease. Part II: recent progress and future directions. Genes Dev 1997, 11:11-43.
9. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995, 57:289-300.
10. Bergmann S., Ihmels J., Barkai N. Similarities and differences in genome-wide expression data of six organisms. PLoS Biol 2004, 2:E9.
11. Blaxall B.C., Dwyer-Nield L.D., Bauer A.K., Bohlmeyer T.J., Malkinson A.M., Port J.D. Differential expression and localization of the mRNA binding proteins, AU-rich element mRNA binding protein (AUF1) and Hu antigen R (HuR), in neoplastic lung tissue. Mol Carcinog 2000, 28:76-83.
12. Bossu P., Vanoni M., Wanke V., Cesaroni M.P., Tropea F., Melillo G., et al. A dominant negative RAS-specific guanine nucleotide exchange factor reverses neoplastic phenotype in K-ras transformed mouse fibroblasts. Oncogene 2000, 19:2147-2154.
13. Briand P., Petersen O.W., Van Deurs B. A new diploid nontumorigenic human breast epithelial cell line isolated and propagated in chemically defined medium. In Vitro Cell Dev Biol 1987, 23:181-188.
14. Cheon D.J., Orsulic S. Mouse models of cancer. Annu Rev Pathol 2010, 6:95-119.
15. Chiaradonna F., Gaglio D., Vanoni M., Alberghina L. Expression of transforming K-Ras oncogene affects mitochondrial function and morphology in mouse fibroblasts. Biochim Biophys Acta 2006, 1757:1338-1356.
16. Chiaradonna F., Magnani C., Sacco E., Manzoni R., Alberghina L., Vanoni M. Acquired glucose sensitivity of k-ras transformed fibroblasts. Biochem Soc Trans 2005, 33:297-299.
17. Chiaradonna F., Sacco E., Manzoni R., Giorgio M., Vanoni M., Alberghina L. Ras-dependent carbon metabolism and transformation in mouse fibroblasts. Oncogene 2006, 25:5391-5404.
18. Cho S.Y., Klemke R.L. Extracellular-regulated kinase activation and CAS/Crk coupling regulate cell migration and suppress apoptosis during invasion of the extracellular matrix. J Cell Biol 2000, 149:223-236.
19. Clark E.S., Whigham A.S., Yarbrough W.G., Weaver A.M. Cortactin is an essential regulator of matrix metalloproteinase secretion and extracellular matrix degradation in invadopodia. Cancer Res 2007, 67:4227-4235.
20. Coombes K.R., Highsmith W.E., Krogmann T.A., Baggerly K.A., Stivers D.N., Abruzzo L.V. Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays. J Comput Biol 2002, 9:655-669.
21. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868.
22. Fang Y., Fu D., Shen X.Z. The potential role of ubiquitin c-terminal hydrolases in oncogenesis. Biochim Biophys Acta 2010, 1806:1-6.
23. Fernandez-Vizarra E., Tiranti V., Zeviani M. Assembly of the oxidative phosphorylation system in humans: what we have learned by studying its defects. Biochim Biophys Acta 2009, 1793:200-211.
24. Fisher L. Biostatistics: a methodology for the health sciences 1993, John Wiley & Sons Inc, New York.
25. Fisher R.A. Statistical Methods for Research Workers 1925, Oliver and Boyd, Edinburg.
26. Fraser H.B. Modularity and evolutionary constraint on proteins. Nat Genet 2005, 37:351-352.
27. Friedl P., Wolf K. Tumour-cell invasion and migration: diversity and escape mechanisms. Nat Rev Cancer 2003, 3:362-374.
28. Gaglio D., Soldati C., Vanoni M., Alberghina L., Chiaradonna F. Glutamine deprivation induces abortive s-phase rescued by deoxyribonucleotides in k-ras transformed fibroblasts. PLoS One 2009, 4:e4715.
29. Galluzzi L., Morselli E., Kepp O., Vitale I., Rigoni A., Vacchelli E., et al. Mitochondrial gateways to cancer. Mol Aspects Med 2010, 31:1-20.
30. Geho D.H., Bandle R.W., Clair T., Liotta L.A. Physiological mechanisms of tumor-cell invasion and migration. Physiology (Bethesda) 2005, 20:194-200.
31. Ghigna C., Valacca C., Biamonti G. Alternative splicing and tumor progression. Curr Genomics 2008, 9:556-570.
32. Gogvadze V., Orrenius S., Zhivotovsky B. Mitochondria in cancer cells: what is so special about them?. Trends Cell Biol 2008, 18:165-173.
33. Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (New York NY) 1999, 286:531-537.
34. Gouble A., Grazide S., Meggetto F., Mercier P., Delsol G., Morello D. A new player in oncogenesis: AUF1/hnRNPD overexpression leads to tumorigenesis in transgenic mice. Cancer Res 2002, 62:1489-1495.
35. Grizzi F., Chiriva-Internati M. Cancer: looking for simplicity and finding complexity. Cancer Cell Int 2006, 6:1475-2867.
36. Hanahan D., Weinberg R.A. The hallmarks of cancer. Cell 2000, 100:57-70.
37. Hanahan D., Weinberg R.A. Hallmarks of cancer: the next generation. Cell 2011, 144:646-674.
38. Hanash S. Integrated global profiling of cancer. Nat Rev Cancer 2004, 4:638-644.
39. Hayflick L., Moorhead P.S. The serial cultivation of human diploid cell strains. Exp Cell Res 1961, 25:585-621.
40. Herzig M., Christofori G. Recent advances in cancer research: mouse models of tumorigenesis. Biochim Biophys Acta 2002, 1602:97-113.
41. Hinds P.W., Dowdy S.F., Eaton E.N., Arnold A., Weinberg R.A. Function of a human cyclin gene as an oncogene. Proc Natl Acad Sci USA 1994, 91:709-713.
42. http://csbi.ltdk.helsinki.fi/pina/.
43. http://discover.nci.nih.gov/cellminer/home.do.
44. http://genecodis.dacya.ucm.es/.
45. http://www.ebi.ac.uk/arrayexpress/.
46. http://www.genome.jp/kegg/pathway.html.
47. http://www.ncbi.nlm.nih.gov/geo/.
48. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264.
49. Jackson S.E., Queitsch C., Toft D. Hsp90: from structure to phenotype. Nat Struct Mol Biol 2004, 11:1152-1155.
50. Jacobs J.P. A simple medium for the propagation and maintenance of human diploid cell strains. Nature 1966, 210:100-101.
51. Jezek P., Plecita-Hlavata L., Smolkova K., Rossignol R. Distinctions and similarities of cell bioenergetics and the role of mitochondria in hypoxia, cancer, and embryonic development. Int J Biochem Cell Biol 2010, 42:604-622.
52. Johnson S.C. Hierarchical clustering schemes. Psychometrika 1967, 32:241-254.
53. Kerr M.K., Martin M., Churchill G.A. Analysis of variance for gene expression microarray data. J Comput Biol 2000, 7:819-837.
54. Klein A., Wessel R., Graessmann M., Jurgens M., Petersen I., Schmutzler R., et al. Comparison of gene expression data from human and mouse breast cancers: identification of a conserved breast tumor gene set. Int J Cancer 2007, 121:683-688.
55. Knudson A.G. Two genetic hits (more or less) to cancer. Nat Rev Cancer 2001, 1:157-162.
56. Kohonen T. Self Organizing Maps 1995, Springer, Berlin.
57. Lafferty-Whyte K., Bilsland A., Cairney C.J., Hanley L., Jamieson N.B., Zaffaroni N., et al. Scoring of senescence signalling in multiple human tumour gene expression datasets, identification of a correlation between senescence score and drug toxicity in the NCI60 panel and a pro-inflammatory signature correlating with survival advantage in peritoneal mesothelioma. BMC Genomics 2010, 11:532.
58. Lazarou M., Thorburn D.R., Ryan M.T., McKenzie M. Assembly of mitochondrial complex I and defects in disease. Biochim Biophys Acta 2009, 1793:78-88.
59. Le Devedec S.E., Yan K., de Bont H., Ghotra V., Truong H., Danen E.H., et al. Systems microscopy approaches to understand cancer cell migration and metastasis. Cell Mol Life Sci 2010, 67:3219-3240.
60. Lelandais G., Vincens P., Badel-Chagnon A., Vialette S., Jacq C., Hazout S. Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms. Bioinformatics (Oxford, England) 2006, 22:1359-1366.
61. Lenaz G., Baracca A., Barbero G., Bergamini C., Dalmonte M.E., Del Sole M., et al. Mitochondrial respiratory chain super-complex I-III in physiology and pathology. Biochim Biophys Acta 2010, 1797:633-640.
62. Levine A.J., Puzio-Kuter A.M. The control of the metabolic switch in cancers by oncogenes and tumor suppressor genes. Science 2010, 330:1340-1344.
63. Liao B.Y., Zhang J. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 2006, 23:530-540.
64. Liao B.Y., Zhang J. Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol 2006, 23:1119-1128.
65. Licatalosi D.D., Darnell R.B. RNA processing and its regulation: global insights into biological networks. Nat Rev 2010, 11:75-87.
66. Meuwissen R., Berns A. Mouse models for human lung cancer. Genes Dev 2005, 19:643-664.
67. Nagaraju G., Scully R. Minding the gap: the underground functions of BRCA1 and BRCA2 at stalled replication forks. DNA Repair 2007, 6:1018-1031.
68. Neckers L. Heat shock protein 90: the cancer chaperone. J Biosci 2007, 32:517-530.
69. Nogales-Cadenas R., Carmona-Saez P., Vazquez M., Vicente C., Yang X., Tirado F., et al. GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Res 2009, 37:W317-W322.
70. Ovaska K., Laakso M., Haapa-Paananen S., Louhimo R., Chen P., Aittomaki V., et al. Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Med 2010, 2:65.
71. Panaretou B., Piper P. Isolation of yeast plasma membranes. Methods Mole Biol (Clifton NJ) 1996, 53:117-121.
72. Pantel K., Brakenhoff R.H. Dissecting the metastatic cascade. Nat Rev Cancer 2004, 4:448-456.
73. Pavlidis P., Noble W.S. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol 2001, 2. (RESEARCH0042).
74. Potter C.J., Turenchalk G.S., Xu T. Drosophila in cancer research. An expanding role. Trends Genet 2000, 16:33-39.
75. Poulin G., Nandakumar R., Ahringer J. Genome-wide RNAi screens in Caenorhabditis elegans: impact on cancer research. Oncogene 2004, 23:8340-8345.
76. Quelle D.E., Ashmun R.A., Shurtleff S.A., Kato J.Y., Bar-Sagi D., Roussel M.F., et al. Overexpression of mouse D-type cyclins accelerates G1 phase in rodent fibroblasts. Genes Dev 1993, 7:1559-1571.
77. Rhodes D.R., Chinnaiyan A.M. Integrative analysis of the cancer transcriptome. Nat Genet 2005, 37(Suppl.):S31-S37.
78. Rosenow C, Vailaya A, Kuchinsky AJ, Middleton FA. Combining expression and genotyping analysis in neuropsychiatric research. Agilent GeneSpring Platform Application Note; 2005;p. 1-4.
79. Ross D.T., Scherf U., Eisen M.B., Perou C.M., Rees C., Spellman P., et al. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 2000, 24:227-235.
80. Sacco J.J., Coulson J.M., Clague M.J., Urbe S. Emerging roles of deubiquitinases in cancer-associated pathways. IUBMB Life 2010, 62:140-157.
81. Saito R.M., van den Heuvel S. Malignant worms: what cancer research can learn from C. elegans. Cancer Invest 2002, 20:264-275.
82. Scheffzek K., Ahmadian M.R. GTPase activating proteins: structural and functional insights 18years after discovery. Cell Mol Life Sci 2005, 62:3014-3038.
83. Scherf U., Ross D.T., Waltham M., Smith L.H., Lee J.K., Tanabe L., et al. A gene expression database for the molecular pharmacology of cancer. Nat Genet 2000, 24:236-244.
84. Schiller J., Sabatini L., Bittner G. Phenotypic, molecular, and genetic characterization of transformed hmnan bronchial epithelial cell strains. Int J Oncol 1993, 4:461-470.
85. Segal E., Friedman N., Kaminski N., Regev A., Koller D. From signatures to models: understanding cancer using microarrays. Nat Genet 2005, 37:S38-S45. Suppl.
86. Sell S. Mouse models to study the interaction of risk factors for human liver cancer. Cancer Res 2003, 63:7553-7562.
87. Smits B.M., Cotroneo M.S., Haag J.D., Gould M.N. Genetically engineered rat models for breast cancer. Breast Dis 2007, 28:53-61.
88. Solaini G., Sgarbi G., Baracca A. Oxidative phosphorylation in cancer cells. Biochim Biophys Acta 2010, 27(1-3):11-21.
89. Somyajit K., Subramanya S., Nagaraju G. RAD51C: a novel cancer susceptibility gene is linked to Fanconi anemia and breast cancer. Carcinogenesis 2010, 31:2031-2038.
90. Strand A.D., Aragaki A.K., Baquet Z.C., Hodges A., Cunningham P., Holmans P., et al. Conservation of regional gene expression in mouse and human brain. PLoS Genet 2007, 3:e59.
91. Su A.I., Cooke M.P., Ching K.A., Hakak Y., Walker J.R., Wiltshire T., et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 2002, 99:4465-4470.
92. van 't Veer L.J., Dai H., van de Vijver M.J., He Y.D., Hart A.A., Mao M., et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536.
93. van Alphen R.J., Wiemer E.A., Burger H., Eskens F.A. The spliceosome as target for anticancer treatment. Br J Cancer 2009, 100:228-232.
94. Vander Heiden M.G., Cantley L.C., Thompson C.B. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 2009, 324:1029-1033.
95. Vesanto J. SOM-Based data visualization methods. Int Data Anal J 1999, 3(2):111-126.
96. Vesanto J., Alhoniemi E. Clustering of the self-organizing map. IEEE Trans Neural Netw 2000, 11(3):586-600.
97. Vidal M., Cagan R.L. Drosophila models for cancer research. Curr Opin Genet Dev 2006, 16:10-16.
98. Vogelstein B., Kinzler K.W. The multistep nature of cancer. Trends Genet 1993, 9:138-141.
99. Wandinger S.K., Richter K., Buchner J. The Hsp90 chaperone machinery. J Biol Chem 2008, 283:18473-18477.
100. Wang H., Huang S., Shou J., Su E.W., Onyia J.E., Liao B., et al. Comparative analysis and integrative classification of NCI60 cell lines and primary tumors using gene expression profiling data. BMC Genomics 2006, 7:166.
101. Wang Y., Rekaya R. A comprehensive analysis of gene expression evolution between humans and mice. Evol Bioinf Online 2009, 5:81-90.
102. Wang Z., Burge C.B. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA (New York, NY) 2008, 14:802-813.
103. Welsh M., Mangravite L., Medina M.W., Tantisira K., Zhang W., Huang R.S., et al. Pharmacogenomic discovery using cell-based models. Pharmacol Rev 2009, 61:413-429.
104. Whitesell L., Lindquist S.L. HSP90 and the chaperoning of cancer. Nat Rev Cancer 2005, 5:761-772.
105. Workman P., de Billy E. Putting the heat on cancer. Nat Med 2007, 13:1415-1417.
106. Wu J., Vallenius T., Ovaska K., Westermarck J., Makela T.P., Hautaniemi S. Integrated network analysis platform for protein-protein interactions. Nat Methods 2009, 6:75-77.
107. Yamada T., Bork P. Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev 2009, 10:791-803.
108. Zhou X.J., Gibson G. Cross-species comparison of genome-wide expression patterns. Genome Biol 2004, 5:232.