The complexity of radiation stress responses: Analysis by informatics and functional genomics approaches

Gene Expression

Volumn 7, Issue 4-6, 1999, Pages 387-400

  Fornace Jr , Albert J ^a,b   Amundson, Sally A ^a   Bittner, Michael ^c   Myers, Timothy G ^b   Meltzer, Paul ^c   Weinsten, John N ^a   Trent, Jeffrey ^c  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

Genotoxic stress; Ionizing radiation; Microarray; p53

Indexed keywords

CELL DNA; COMPLEMENTARY DNA; PROTEIN P53;

ANALYTIC METHOD; APOPTOSIS; CANCER CELL CULTURE; CONFERENCE PAPER; DNA DAMAGE; DNA DETERMINATION; GENE FUNCTION; GENOTYPE; HUMAN; IONIZING RADIATION; RADIATION RESPONSE; STRAIN DIFFERENCE; TECHNIQUE; TRANSCRIPTION REGULATION; TUMOR SUPPRESSOR GENE; VALIDATION PROCESS;

ANIMALS; APOPTOSIS; BIOLOGICAL MARKERS; GENE EXPRESSION REGULATION; GENES, P53; GENETIC TECHNIQUES; HEAT-SHOCK RESPONSE; HUMANS;

EID: 0032773409     PISSN: 10522166     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (74)

1. Amundson, S. A.; Bittner, M.; Chen, Y. D.; Trent, J.; Meltzer, P.; Fornace, A. J., Jr. cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses. Oncogene (in press).
2. Amundson, S. A.; Myers, T. G.; Fornace, A. J., Jr. Roles for p53 in growth arrest and apoptosis: Putting on the brakes after genotoxic stress. Oncogene 17: 3287-3300; 1999.
3. Angel, P.; Poting, A.; Mallick, U.; Rahmsdorf, H. J.; Schorpp, M.; Herrlich, P. Induction of metallothionein and other mRNA species by carcinogens and tumor promoters in primary human skin fibroblasts. Mol. Cell. Biol. 6:1 760-1766; 1986.
4. Bae, I.; Smith, M. L.; Sheikh, M. S.; Zhan, Q.; Scudiero, D. A.; Friend, S. H.; O'Connor, P. M.; Fornace, A. J., Jr. An abnormality in the p53 pathway following γ-irradiation in many wild-type p53 human melanoma lines. Cancer Res. 56:8 40-847; 1996.
5. Barak, Y.; Juven, T.; Haffner, R.; Oren, M. mdm2 expression is induced by wild type p53 activity. EMBO J. 12:4 61-468; 1993.
6. Bennett, C. B.; Westmoreland, T. J.; Snipe, J. R.; Resnick, M. A. A double-strand break within a yeast artificial chromosome (YAC) containing human DNA can result in YAC loss, deletion or cell lethality. Mol. Cell. Biol. 16:4 414-4425; 1996.
7. Boothman, D. A.; Burrows, H. L.; Yang, C. R.; Davis, T. W.; Wuerzberger, S. M.; Planchon, S. M.; Odegaard, E.; Lewis, J. E.; Pink, J.; Meyers, M.; Patten, C. W.; Sharda, N.; Kinsella, T. J. Damage-sensing mechanisms in human cells after ionizing radiation. Stem Cells 15(Suppl. 2):2 7-42; 1997.
8. Carrier, F.; Georgel, P. T.; Pourquier, P.; Blake, M.; Kontny, H. U.; Antinore, M. J.; Gariboldi, M.; Myers, T. G.; Weinstein, J.; Pommier, Y.; Fornace, A. J., Jr. Gadd45, a p53-responsive stress protein, modifies DNA accessibility on damaged chromatin. Mol. Cell. Biol. (in press).
9. Chen, B. P.; Liang, G.; Whelan, J.; Hai, T. ATF3 and ATF3 delta Zip. Transcriptional repression versus activation by alternatively spliced isoforms. J. Biol. Chem. 269:1 5819-15826; 1994.
10. Chen, B. P.; Wolfgang, C. D.; Hai, T. Analysis of ATF3, a transcription factor induced by physiological stresses and modulated by gadd153/Chop10. Mol. Cell. Biol. 16:1 157-1168; 1996.
11. Chen, C. Y.; Oliner, J. D.; Zhan, Q.; Fornace, A. J., Jr.; Vogelstein, B.; Kastan, M. B. Interactions between p53 and MDM2 in a mammalian cell cycle checkpoint pathway. Proc. Natl. Acad. Sci. USA 91:2 684-2688; 1994.
12. Chen, Y.; Dougherty, E. R.; Bittner, M. L. Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Opt. 2:3 64-374; 1997.
13. Deb, S. P.; Munoz, R. M.; Brown, D. R.; Subler, M. A.; Deb, S. Wild-type human p53 activates the human epidermal growth factor receptor promoter. Oncogene 9:1 341-1349; 1994.
14. DeRisi, J.; Penland, L.; Brown, P. O.; Bittner, M. L.; Meltzer, P. S.; Ray, M.; Chen, Y.; Su, Y. A.; Trent, J. M. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14:4 57-460; 1996.
15. Dewey, W. C.; Ling, C. C.; Meyn, R. E. Radiation-induced apoptosis: Relevance to radiotherapy. Int. J. Radiat. Oncol. Biol. Phys. 33:7 81-796; 1995.
16. Duggan, D. J.; Bittner, M.; Chen, Y.; Meltzer, P.; Trent, J. M. Expression profiling using cDNA microarrays. Nat. Genet. 21:1 0-14; 1999.
17. El-Deiry, W. S.; Tokino, T.; Velculescu, V. E.; Levy, D. B.; Parsons, R.; Trent, J. M.; Lin, D.; Mercer, W. E.; Kinzler, K. W.; Vogelstein, B. WAF1, a potential mediator of p53 tumor suppression. Cell 75:8 17-825; 1993.
18. Ermolaeva, O.; Rastogi, M.; Pruitt, K. D.; Schuler, G. D.; Bittner, M. L.; Chen, Y.; Simon, R.; Meltzer, P.; Trent, J. M.; Boguski, M. S. Data management and analysis for gene expression arrays. Nat. Genet. 20:1 9-23; 1998.
19. Fornace, A. J., Jr. Mammalian genes induced by radiation; activation of genes associated with growth control. Annu. Rev. Genet. 26:5 07-526; 1992.
20. Fornace, A. J., Jr.; Alamo, I. J.; Hollander, M. C. DNA damage-inducible transcripts in mammalian cells. Proc. Natl. Acad. Sci. USA 85:8 800-8804; 1988.
21. Friedberg, E. C.; Walker, G. C.; Siede, W. DNA repair and mutagenesis. Washington, DC: ASM Press; 1995.
22. CIP1/WAF1 expression by cellular stress: p53-dependent and p53-independent mechanisms. Mol. Cell. Differ. 4:4 7-65; 1996.
23. Grever, M. R.; Schepartz, S. A.; Chabner, B. A. The National Cancer Institute: Cancer drug discovery and development program. Semin. Oncol. 19:6 22-638; 1992.
24. Gu, W.; Roeder, R. G. Activation of p53 sequencespecific DNA binding by acetylation of the p53 C-terminal domain. Cell 90:5 95-606; 1997.
25. Hall, E. J. Radiobiology for the radiobiologist, 3rd ed. Philadelphia: J. P. Lippincott; 1988.
26. Herrlich, P.; Ponta, H.; Rahmsdorf, H. J. DNA damage induced gene expression: Signal transduction and relation to growth factor signaling. Rev. Physiol. Biochem. Pharmacol. 119:1 87-223; 1992.
27. Holbrook, N. J.; Liu, Y.; Fornace, A. J., Jr. Signaling events controlling the molecular response to genotoxic stress. In: Feige, U.; Morimoto, R. I.; Yahara, I.; Polla, B. S., eds. Stress-inducible cellular responses. Basel: Birkhauser Verlag; 1996:2 73-288.
28. Kastan, M. B.; Zhan, Q.; El-Deiry, W. S.; Carrier, F.; Jacks, T.; Walsh, W. V.; Plunkett, B. S.; Vogelstein, B.; Fornace, A. J., Jr. A mammalian cell cycle checkpoint utilizing p53 and GADD45 is defective in ataxia telangiectasia. Cell 71:5 87-597; 1992.
29. Ko, L. J.; Prives, C. p53: Puzzle and paradigm. Genes Dev. 10:1 054-1072; 1996.
30. Kozopas, K. M.; Yang, T.; Buchan, H. L.; Zhou, P.; Craig, R. W. MCL1, a gene expressed in programmed myeloid cell differentiation, has sequence similarity to BCL2. Proc. Natl. Acad. Sci. USA 90:3 516-3520; 1993.
31. Liang, G.; Wolfgang, C. D.; Chen, B. P.; Chen, T. H.; Hai, T. ATF3 gene. Genomic organization, promoter, and regulation. J. Biol. Chem. 271:1 695-1701; 1996.
32. Liu, Z. G.; Baskaran, R.; Lea-Chou, E. T.; Wood, L. D.; Chen, Y.; Karin, M.; Wang, J. Y. Three distinct signalling responses by murine fibroblasts to genotoxic stress. Nature 384:2 73-276; 1996.
33. Madden, S. L.; Galella, E. A.; Zhu, J.; Bertelsen, A. H.; Beaudry, G. A. SAGE transcript profiles for p53-dependent growth regulation. Oncogene 15:1 079-1085; 1997.
34. Monks, A.; Seudiero, D.; Skehan, P.; Shoemaker, R.; Paull, K.; Vistica, D.; Hose, C.; Langley, J.; Cronise, P.; Vaigro-Wolff, A.; et al. Feasibility of a high-flux anticancer drug screen using a diverse panel of cultured human tumor cell lines. J. Natl. Cancer Inst. 83: 757-766; 1991.
35. Myers, T. G.; Anderson, N. L.; Waltham, M.; Li, G.; Buolamwini, J. K.; Seudiero, D. A.; Paull, K. D.; Sausville, E. A.; Weinstein, J. N. A protein expression database for the molecular pharmacology of cancer. Electrophoresis 18:6 47-653; 1997.
36. Oberhammer, F.; Wilson, J. W.; Dive, C.; Morris, I. D.; Hickman, J. A.; Wakeling, A. E.; Walker, P. R.; Sikorska, M. Apoptotic death in epithelial cells: Cleavage of DNA to 300 and/or 50 kb fragments prior to or in the absence of internucleosomal fragmentation. EMBO J. 12:3 679-3684; 1993.
37. O'Connor, P. M.; Jackman, J.; Bae, I.; Myers, T. G.; Fan, S.; Mutoh, M.; Scudiero, D.; Monks, A.; Sausville, E. A.; Weinstein, J. N.; Friend, S.; Fornace, A. J., Jr.; Kohn, K. W. 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. 57:4 285-4300; 1997.
38. Oliner, J. D.; Pietenpol, J. A.; Thiagalingam, S.; Gyuris, J.; Kinzler, K. W.; Vogelstein, B. Oncoprotein MDM2 conceals the activation domain of tumor suppressor p53. Nature 362:8 57-860; 1993.
39. Owen-Schaub, L. B.; Zhang, W.; Cusack, J. C.; Angelo, L. S.; Santee, S. M.; Fujiwara, T.; Roth, J. A.; Deisseroth, A. B.; Zhang, W. W.; Kruzel, E.; et al. Wild-type human p53 and a temperature-sensitive mutant induce Fas/APO-1 expression. Mol. Cell. Biol. 15: 3032-3040; 1995.
40. Paull, K. D.; Hamel, E.; Malspeis, L. Prediction of biochemical mechanism of action from the in vitro antitumor screen of the National Cancer Institute. In: Foye, W. O., ed. Cancer chemotherapeutic agents. Washington, DC: American Cancer Society; 1995.
41. Paull, K. D.; Shoemaker, R. H.; Hodes, L.; Monks, A.; Seudiero, D. A.; Rubinstein, L.; Plowman, J.; Boyd, M. R. Display and analysis of patterns of differential activity of drugs against human tumor cell lines: De-velopment of mean graph and COMPARE algorithm. J. Natl. Cancer Inst. 81:1 088-1092; 1989.
42. Perry, M. E.; Piette, J.; Zawadzki, J. A.; Harvey, D.; Levine, A. J. The mdm-2 gene is induced in response to UV light in a p53-dependent manner. Proc. Natl. Acad. Sci. USA 90:1 1623-11627; 1993.
43. Polyak, K.; Xia, Y.; Zweier, J. L.; Kinzler, K. W.; Vogelstein, B. A model for p53-induced apoptosis. Nature 389:3 00-306; 1997.
44. Rubinstein, L. V.; Shoemaker, R. H.; Paull, K. D.; Simon, R. M.; Tosini, S.; Skehan, P.; Scudiero, D. A.; Monks, A.; Boyd, M. R. Comparison of in vitro anticancer-drug-screening data generated with a tetrazolium assay versus a protein assay against a diverse panel of human tumor cell lines. J. Natl. Cancer Inst. 82:1 113-1118; 1990.
45. Ruby, S. W.; Szostak, J. W. Specific Saccharomyces cerevisiae genes are expressed in response to DNA-damaging agents. Mol. Cell. Biol. 5:7 5-84; 1985.
46. Schena, M.; Shalon, D.; Davis, R. W.; Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470; 1995.
47. Schena, M.; Shalon, D.; Heller, R.; Chai, A.; Brown, P. O.; Davis, R. W. Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA 93:1 0614-10619; 1996.
48. Shieh, S. Y.; Ikeda, M.; Taya, Y.; Prives, C. DNA damage-induced phosphorylation of p53 alleviates inhibition by MDM2. Cell 91:3 25-334; 1997.
49. Siliciano, J. D.; Canman, C. E.; Taya, Y.; Sakaguchi, K.; Appella, E.; Kastan, M. B. DNA damage induces phosphorylation of the amino terminus of p53. Genes Dev. 11:3 471-3481; 1997.
50. Smith, M. L.; Fornace, A. J., Jr. Mammalian DNA damage-inducible genes associated with growth arrest and apoptosis. Mutat. Res. 340:1 09-124; 1996.
51. Stinson, S. F.; Alley, M. C.; Kopp, W. C.; Fiebig, H. H.; Mullendore, L. A.; Pittman, A. F.; Kenney, S.; Keller, J.; Boyd, M. R. Morphological and immunocytochemical characteristics of human tumor cell lines for use in a disease-oriented anticancer drug screen. Anticancer Res. 12:1 035-1053; 1992.
52. Testolin, L.; Carson, C.; Wang, Y.; Walker, P. R.; Armato, U.; Sikorska, M. Jun and JNK kinase are activated in thymocytes in response to VM26 and radiation but not glucocorticoids. Exp. Cell Res. 230:2 20-232; 1997.
53. Tokino, T.; Thiagalingam, S.; el-Deiry, W. S.; Waldman, T.; Kinzler, K. W.; Vogelstein, B. p53 tagged sites from human genomic DNA. Hum. Mol. Genet. 3: 1537-1542; 1994.
54. Uckun, F. M.; Tuel-Ahlgren, L.; Song, C. W.; Waddick, K.; Myers, D. E.; Kirihara, J.; Ledbetter, J. A.; Schieven, G. L. Ionizing radiation stimulates unidentified tyrosine-specific protein kinases in human B-lymphocyte precursors, triggering apoptosis and clonogenic cell death. Proc. Natl. Acad. Sci. USA 89: 9005-9009; 1992.
55. Uckun, F. M.; Waddick, K. G.; Mahajan, S.; Jun, X.; Takata, M.; Bolen, J.; Kurosaki, T. BTK as a mediator of radiation-induced apoptosis in DT-40 lymphoma B cells. Science 273:1 096-1100; 1996.
56. van Osdol, W. W.; Myers, T. G.; Paull, K. D.; Kohn, K. W.; Weinstein, J. N. Use of the Kohonen self-organizing map to study the mechanisms of action of chemotherapeutic agents. J. Natl. Cancer Inst. 86:1 853-1859; 1994.
57. Velculescu, V. E.; Zhang, L.; Vogelstein, B.; Kinzler, K. W. Serial analysis of gene expression. Science 270: 484-487; 1995.
58. Verheij, M.; Bose, R.; Lin, X. H.; Yao, B.; Jarvis, W. D.; Grant, S.; Birrer, M. J.; Szabo, E.; Zon, L. I.; Kyriakis, J. M.; Haimovitz-Friedman, A.; Fuks, Z.; Kolesnick, R. N. Requirement for ceramide-initiated SAPK/ JNK signalling in stress-induced apoptosis. Nature 380:7 5-79; 1996.
59. Vidair, C. A.; Chen, C. H.; Ling, C. C.; Dewey, W. C. Apoptosis induced by X-irradiation of rec-myc cells is postmitotic and not predicted by the time after irradiation or behavior of sister cells. Cancer Res. 56:4 116-4118; 1996.
60. Weinstein, J. N. Fishing expeditions. Science 282:6 28-629; 1998.
61. Weinstein, J. N.; Kohn, K. W.; Grever, M. R.; Viswanadhan, V. N.; Rubinstein, L. V.; Monks, A. P.; Scudiero, D. A.; Welch, L.; Koutsoukos, A. D.; Chiausa, A. J.; Paull, K. D. Neural computing in cancer drug development: Predicting mechanism of action. Science 258:4 47-451; 1992.
62. Weinstein, J. N.; Myers, T. G.; O'Connor, P. M.; Friend, S. H.; Fornace, A. J., Jr.; Kohn, K. W.; Fojo, T.; Bates, S. E.; Rubinstein, L. V.; Anderson, N. L.; Buolamwini, J. K.; Osdol, W. W.; Monks, A. P.; Scudiero, D. A.; Sausville, E. A.; Zaharevitz, D. W.; Bunow, B.; Johnson, G. S.; Wittes, R. E.; Paull, K. D. An information intensive approach to the molecular pharmacology of cancer. Science 275:3 43-349; 1997.
63. White, E. Life, death, and the pursuit of apoptosis. Genes Dev. 10:1 -15; 1996.
64. Woloschak, G. E. Radiation-induced responses in mammalian cells. In: Koval, T., ed. Stress-inducible processes in higher eukaryotic cells. New York: Plenum Press; 1997:1 85-219.
65. Wu, G. S.; Burns, T. F.; McDonald, E. R., III; Jiang, W.; Meng, R.; Krantz, I. D.; Kao, G.; Gan, D. D.; Zhou, J. Y.; Muschel, R.; Hamilton, S. R.; Spinner, N. B.; Markowitz, S.; Wu, G.; El-Deiry, W. S. KILLER/ DR5 is a DNA damage-inducible p53-regulated death receptor gene. Nat. Genet. 17:1 41-143; 1997.
66. Yang, E.; Korsmeyer, S. J. Molecular thanatopsis: A discourse on the BCL2 family and cell death. Blood 88:3 86-401; 1996.
67. L depends on normal p53 function. Oncogene 13:2 287-2293; 1996.
68. Zhan, Q.; Bae, I.; Fornace, A. J., Jr.; Craig, R. W. Induction of Bcl-2 family member Mcl-1 as an early re-sponse to DNA damage. Oncogene 14:1 031-1039; 1997.
69. Zhan, Q.; Bae, I.; Kastan, M. B.; Fornace, A. J., Jr. The p53-dependent γ-ray response of GADD45. Cancer Res. 54:2 755-2760; 1994.
70. Zhan, Q.; Carrier, F.; Fornace, A. J., Jr. Induction of cellular p53 activity by DNA-damaging agents and growth arrest. Mol. Cell. Biol. 13:4 242-4250; 1993.
71. Zhan, Q.; Chen, I. T.; Antinore, M. J.; Fornace, A. J., Jr. Tumor suppressor p53 can participate in transcriptional induction of the GADD45 promoter in the absence of direct DNA binding. Mol. Cell. Biol. 18: 2768-2778; 1998.
72. Zhan, Q.; El-Deiry, W.; Bae, I.; Alamo, I., Jr.; Kastan, M. B.; Vogelstein, B.; Fornace, A. J., Jr. Similarity of the DNA-damage responsiveness and growth-suppressive properties of WAF1 to GADD45. Int. J. Oncol. 6: 937-946; 1995.
73. Zhan, Q.; Fan, S.; Bae, I.; Guillouf, C.; Liebermann, D. A.; O'Connor, P. M.; Fornace, A. J., Jr. Induction of BAX by genotoxic stress in human cells correlates with normal p53 status and apoptosis. Oncogene 9: 3743-3751; 1994.
74. Zhan, Q.; Kontny, U.; Iglesias, M.; Alamo, I.; Yu, K.; Hollander, M. C.; Woodworth, C. D.; Fornace, A. J., Jr. Inhibitory effect of Bcl-2 on p53-mediated transactivation following genotoxic stress. Oncogene (in press).