Identification of genes involved in radiation-induced G1 arrest

Journal of Chemometrics

Volumn 21, Issue 10-11, 2007, Pages 398-405

  Musumarra, Giuseppe ^a   Trovato Salinaro, Angela ^a   Scirè, Salvatore ^a   Foti, Anna ^b   Barresi, Vincenza ^a   Fortuna, Cosimo Gianluca ^a   Strazzulla, Giovanni ^c   Condorelli, Daniele Filippo ^a  

^a UNIVERSITY OF CATANIA   (Italy)

^b Rem Radioterapia Srl   (Italy)

^c INAF OSSERVATORIO ASTROFISICO DI CATANIA   (Italy)

Author keywords

cDNA microarray; Cell cycles; Gene transcripts; PLS; Radiation

Indexed keywords

CELL CULTURE; GAMMA RAYS; IRRADIATION; LEAST SQUARES APPROXIMATIONS; MULTIVARIANT ANALYSIS; RADIOTHERAPY; TUMORS;

CDNA MICROARRAY; CELL CYCLE; GENE TRANSCRIPTS; LARGE DATASETS; MICROARRAY GENE EXPRESSION; PARTIAL LEAST-SQUARES; RADIATION-INDUCED; SIMULTANEOUS ANALYSIS; TUMOR CELL LINES;

GENE EXPRESSION;

EID: 36148973949     PISSN: 08869383     EISSN: 1099128X     Source Type: Journal    
DOI: 10.1002/cem.1080     Document Type: Article

References (46)

1. Wold S, Sjostrom M. Chemometrics, present and future success. Chemom. Intell. Lab. Syst. 1998; 44: 3-14.
2. Musumarra G, Condorelli DF, Costa AS, Fichera M. A multivariate insight into the in vitro antitumor screen database of the National Cancer Institute: classification of compounds, similarities among cell lines and influence of molecular targets. J. Comput. Aid Mol. Des. 2001; 15: 219-234.
3. Musumarra G, Condorelli DF, Scire S, Costa AS. Shortcuts in genome-scale cancer pharmacology research from multivariate analysis of the National Cancer Institute gene expression database. Biochem. Pharmacol. 2001; 62: 547-553.
4. Nguyen DV, Rocke DM. Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 2002; 18: 39-50.
5. Nguyen DV, Rocke DM. Multi-class cancer classification via partial least squares with gene expression profiles. Bioinformatics 2002; 18: 1216-1226.
6. Nguyen DV, Rocke DM. On partial least squares dimension reduction for microarray-based classification: a simulation study. Comput. Stat. Data Anal. 2004; 46: 407-425.
7. Musumarra G, Barresi V, Condorelli DF, Scirè S. A Bioinformatic approach to the identification of candidate genes for the development of new cancer diagnostics. Biol. Chem. 2003; 384: 321-327.
8. Wold S, Sjöström M, Eriksson L. PLS in Chemistry. In: The Encyclopedia of Computational Chemistry, Schleyer PvR (ed.). John Wiley & Sons: Chichester, 1998; 2006-2020.
9. Pérez-Enciso M, Tenenhaus M. Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach. Hum. Genet. 2003; 112: 581-592.
10. Musumarra G, Barresi V, Condorelli DF, Fortuna CG, Scirè S. Potentialites of multaviariate approaches in genome based cancer research: identification of candidate genes for new diagnostics by PLS-discriminant analysis. J. Chemometrics 2004; 18: 125-132.
11. Musumarra G, Barresi V, Condorelli DF, Fortuna CG, Scirè S. Genome-based identification of diagnostic mol-ecular markers for human lung carcinomas by PLS-DA. Comput. Biol. Chem. 2005; 29: 183-195.
12. Barresi V, Fortuna CG, Garozzo R, Musumarra G, Scirè S, Condorelli DF. Identification of genes involved in the sensitivity to antitumour drug 17-allylamino,17-demethoxygeldanamycin (17AAG). MoL. Biosyst. 2006; 2: 231-239.
13. Alsbeih G, Malone S, Lochrin C, Girard A, Fertil B, Raaphorst GP. Correlation between normal tissue complications and in vitro radiosensitivity of skin fibroblasts derived from radiotherapy patients treated for variety of tumors. Int. J. Radiat. Oncol. Biol. Phys. 2000; 46: 143-152.
14. 1 arrest in established human tumor cell lines. Oncogene 1995; 11: 1885-1892.
15. Dikomey E, Borgmann K, Brammer I, Kasten-Pisula U. Molecular mechanisms of individual radiosensitivity studied in normal diploid human fiobroplasts. Toxicology 2003; 193: 125-135.
16. O'Connor PM, Jackman J, Bae I, Myers TG, Fan S, Mutoh M, Scudiero DA, Monks A, Sausville EA, Weinstein JN, Friend S, Fornace AJ, Jr., Kohn KW. Characterization of the p53 tumor suppressor pathway in cell lines of the National Cancer Institute anticancer drug screen and correlations with the growth-inhibitory potency of 123 anticancer agents. Cancer Res. 1997; 57: 4285-4300.
17. Database resources currently available on the World Wide Web: http://www.dtp.nci.nih.gov/webdata.html
18. Shao J. Linear Model selection by cross-validation. J. Am. Stat. Assoc. 1993; 88: 486-494.
19. SIMCA-P 8.0. User Guide and Tutorial. Umetrics AB: Umeå, Sweden, 1999.
20. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001; 411: 494-498.
21. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J. Mol. Biol. 1990; 215: 403-410.
22. White TW, Srinivas M, Ripps H, Trovato-Salinaro A, Condorelli DF, Bruzzone R. Virtual cloning, functional expression, and gating analysis of human connexin 31.9. Am. J. Physiol. Cell. Physiol. 2002; 283: C960-C970.
23. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001; 25: 402-408.
24. Lane DP. Cancer, p53, guardian of the genome. Nature (London) 1992; 358: 15-16.
25. Harris CC. Structure and function of the p53 tumor suppressor gene: clues for rational cancer therapeutic strategies. J. Nat. Cancer Inst. 1996; 88: 1442-1455.
26. Hollstein M, Sidransky D, Vogelstein B, Harris CC. p53 mutations in human cancers. Science 1991; 253: 49-53.
27. Sidransky D, Hollstein M. Clinical implications of the p53 gene. Annu. Rev. Med. 1996; 47: 285-301.
28. Hofseth LJ, Hussain SP, Harris CC. p53:25 years after its discovery. Trends Pharmacol. Sci. 2004; 25: 177-181.
29. Robinson M, Jiang P, Cui J, Li J, Wang Y, Swaroop M, Madore S, Lawrence TS, Sun Y. Global genechip profiling to identify genes responsive to p53-induced growth arrest and apoptosis in human lung carcinoma cells. Cancer Biol. Ther. 2003; 2: 406-415.
30. Amundson SA, Myers TG, Scudiero D, Kitada S, Reed JC, Fornace AJ, Jr. An informatics approach identifying markers of chemosensitivity in human cancer cell lines. Cancer Res. 2000; 60: 6101-6110.
31. Wang L, Wu Q, Qiu P, Mirza A, McGuirk M, Kirschmeier P, Greene JR, Wang Y, Pickett CB, Liu S. Analyses of p53 target genes in the human genome by bioinformatic and microarray approaches. J Biol. Chem. 2001; 276: 43604-43610.
32. Kaufmann WK, Paules RS. DNA damage and cell cycle checkpoints. FASEB J. 1996; 10: 238-247.
33. Kastan MB, Zhan Q, El-Deiry WS, Carrier F, Jacks T, Walsh WV, Plunkett BS, Vogelstein B, Fornace AJ, Jr. A mammalian cell cycle checkpoint utilizing p53 and GADD45 is defective in ataxia telangiectasia. Cell 1992; 71: 587-597.
34. Hollander MC, Alamo I, Jackman J, McBride OW, Fornace AJ, Jr. Sequence conservation and DNA damage-responsiveness of the mammalian gadd45 gene. J. Biol. Chem. 1193; 268: 24385-24393.
35. Durant ST, Morris MM, Illand M, McKay HJ, McCormick C, Hirst GL, Boris RH, Brown R. Dependence on RAD52 and RADl for anticancer drug resistance mediated by inactivation of mismatch repair genes. Curr. Biol. 1999; 9: 51-54.
36. Lin X, Ramamurthi K, Mishima M, Kondo A, Howell SB. p53 interacts with the DNA mismatch repair system to modulate the cytotoxicity and mutagenicity of hydrogen peroxide. Mol. Pharmacol. 2000; 58: 1222-1229.
37. Nehmé A, Baskaran R, Aebi S, Fink D, Nebel S, Cenni B, Wang JY, Howell SB, Christen RD. Differential induction of c-Jun NH2-terminal kinase and c-Abl kinase in DNA mismatch repair-proficient and -deficient cells exposed to cisplatin. Cancer Res. 1997; 57: 3253-3257.
38. Davis TW, Wilson-Van Patten C, Meyers M, Kunugi KA, Cuthill S, Reznikoff C, Garces C, Boland CR, Kinsella TJ, Fishel R, Boothman DA. Defective expression of the DNA mismatch repair protein, MLHl, alters G2-M cell cycle checkpoint arrest following ionizing radiation. Cancer Res. 1998; 58: 767-778.
39. Lin X, Ramamurthi K, Mishima M, Kondo A, Christen RD, Howell SB. P53 modulates the effect of loss of DNA mismatch repair on the sensitivity of human colon cancer cells to the cytotoxic and mutagenic effects of cisplatin. Cancer Res. 2001; 61: 1508-1516.
40. Lin X, Howell SB. DNA mismatch repair and p53 function are major determinants of the rate of development of cisplatin resistance. Mol. Cancer Ther. 2006; 5: 1239-1247.
41. Wang Z, Castano IB, Adams C, Vu C, Fitzhugh D, Christman MF. Structure/function analysis of the Saccharomyces cerevisiae Trf4/Pol sigma DNA polymerase. Genetics 2002; 160: 381-391.
42. Read RL, Martinho RG, Wang SW, Carr AM, Norbury CJ. Cytoplasmic poly(A) polymerases mediate cellular responses to S phase arrest. Proc. Natl. Acad. Sci. USA 2002; 99: 12079-12084.
43. Walowsky C, Fitzhugh DJ, Castano IB, Ju JY, Levin NA, Christman MF. The topoisomerase-related function gene TRF4 affects cellular sensitivity to the antitumor agent camptothecin. J. Biol. Chem. 1999; 274: 7302-7308.
44. Haracska L, Johnson RE, Prakash L, Prakash S. Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit poly(A) RNApolymerase activity but no DNA polymerase activity. Mol. Cell. Biol. 2005; 25: 10183-10189.
45. Win TZ, Draper S, Read RL, Pearce J, Norbury CJ, Wang SW. Requirement of fission yeast Cid14 in polyadenylation of rRNAs. Mol. Cell. Biol. 2006; 26: 1710-1721.
46. Pal R, Datta A, Fornace AJ, Jr., Bittner ML, Dougherty ER. Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS. Bioinformatics 2005; 21: 1542-1549.