Transcriptional modulation induced by ionizing radiation: P53 remains a central player

Molecular Oncology

Volumn 5, Issue 4, 2011, Pages 336-348

  Rashi Elkeles, Sharon ^a   Elkon, Ran ^a   Shavit, Seagull ^a   Lerenthal, Yaniv ^a   Linhart, Chaim ^a   Kupershtein, Ana ^a   Amariglio, Ninette ^b   Rechavi, Gideon ^b   Shamir, Ron ^a   Shiloh, Yosef ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b SHEBA MEDICAL CENTER   (Israel)

Author keywords

DNA damage response; Gene expression; Ionizing radiation; Meta analysis; P53; Transcriptional regulation

Indexed keywords

ALPHA LEVO FUCOSIDASE; EARLY GROWTH RESPONSE FACTOR 2; LAMIN A; MESSENGER RNA; PLACENTAL GROWTH FACTOR; PROTEIN P53; ZINC FINGER PROTEIN;

APOPTOSIS; BINDING SITE; CARCINOGENESIS; CELL COMMUNICATION; CELL CYCLE REGULATION; CELL DEATH; CELL SURVIVAL; CHROMATIN IMMUNOPRECIPITATION; DNA DAMAGE; DNA REPAIR; DOUBLE STRANDED DNA BREAK; DOWN REGULATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE INDUCTION; GENE REPRESSION; GENETIC VARIABILITY; GENOMIC INSTABILITY; HUMAN; INTRACELLULAR SIGNALING; IONIZING RADIATION; META ANALYSIS (TOPIC); MITOSIS; NUCLEAR DIVISION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; TRANSCRIPTION REGULATION; UPREGULATION;

EID: 80052139629     PISSN: 15747891     EISSN: 18780261     Source Type: Journal    
DOI: 10.1016/j.molonc.2011.06.004     Document Type: Review

References (95)

1. Adachi N., Nomoto M., et al. Cell-cycle regulation of the DNA topoisomerase IIalpha promoter is mediated by proximal CCAAT boxes: possible involvement of acetylation. Gene 2000, 245(1):49-57.
2. Akerman G.S., Rosenzweig B.A., et al. "Alterations in gene expression profiles and the DNA-damage response in ionizing radiation-exposed TK6 cells.". Environ. Mol. Mutagen. 2005, 45(2-3):188-205.
3. Al-Hakim A., Escribano-Diaz C., et al. The ubiquitous role of ubiquitin in the DNA damage response. DNA Repair (Amst) 2010, 9(12):1229-1240.
4. Alderson M.R., Smith C.A., et al. Molecular and biological characterization of human 4-1BB and its ligand. Eur. J. Immunol. 1994, 24(9):2219-2227.
5. Amundson S.A., Bittner M., et al. Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses. Oncogene 1999, 18(24):3666-3672.
6. Amundson S.A., Do K.T., et al. Identification of potential mRNA biomarkers in peripheral blood lymphocytes for human exposure to ionizing radiation. Radiat. Res. 2000, 154(3):342-346.
7. Amundson S.A., Lee R.A., et al. Differential responses of stress genes to low dose-rate gamma irradiation. Mol. Cancer Res. 2003, 1(6):445-452.
8. Amundson S.A., Do K.T., et al. Stress-specific signatures: expression profiling of p53 wild-type and -null human cells. Oncogene 2005, 24(28):4572-4579.
9. Andreassen C.N., Alsner J. Genetic variants and normal tissue toxicity after radiotherapy: a systematic review. Radiother. Oncol. 2009, 92(3):299-309.
10. Aoki Y., Niihori T., et al. Germline mutations in HRAS proto-oncogene cause Costello syndrome. Nat. Genet. 2005, 37(10):1038-1040.
11. Araki T., Milbrandt J. Ninjurin, a novel adhesion molecule, is induced by nerve injury and promotes axonal growth. Neuron 1996, 17(2):353-361.
12. Bandele O.J., Wang X., et al. Human single-nucleotide polymorphisms alter p53 sequence-specific binding at gene regulatory elements. Nucleic Acids Res. 2010, 39(1):178-189.
13. Bassing C.H., Alt F.W. The cellular response to general and programmed DNA double strand breaks. DNA Repair (Amst) 2004, 3(8-9):781-796.
14. Begley T.J., Samson L.D. Network responses to DNA damaging agents. DNA Repair (Amst) 2004, 3(8-9):1123-1132.
15. Bekker-Jensen S., Mailand N. Assembly and function of DNA double-strand break repair foci in mammalian cells. DNA Repair (Amst) 2010.
16. Bekker-Jensen S., Rendtlew Danielsen J., et al. HERC2 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Nat. Cell Biol. 2010, 12(1):80-86. sup pp. 81-12.
17. Bellone E., Di Maria E., et al. A novel mutation (D305V) in the early growth response 2 gene is associated with severe Charcot-Marie-Tooth type 1 disease. Hum. Mutat. 1999, 14(4):353-354.
18. Benatti P., Basile V., et al. A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response. Nucleic Acids Res 2008.
19. Bensimon A., Schmidt A., et al. ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage. Sci. Signal. 2010, 3(151):rs3.
20. Bentzen S.M. Preventing or reducing late side effects of radiation therapy: radiobiology meets molecular pathology. Nat. Rev. Cancer 2006, 6(9):702-713.
21. Bertheau P., Espie M., et al. TP53 status and response to chemotherapy in breast cancer. Pathobiology 2008, 75(2):132-139.
22. Bodnar A.G., Ouellette M., et al. Extension of life-span by introduction of telomerase into normal human cells. Science 1998, 279(5349):349-352.
23. Braithwaite A.W., Royds J.A., et al. The p53 story: layers of complexity. Carcinogenesis 2005, 26(7):1161-1169.
24. Ceribelli M., Alcalay M., et al. Repression of new p53 targets revealed by ChIP on chip experiments. Cell Cycle 2006, 5(10):1102-1110.
25. Chistiakov D.A., Voronova N.V., et al. Genetic variations in DNA repair genes, radiosensitivity to cancer and susceptibility to acute tissue reactions in radiotherapy-treated cancer patients. Acta Oncol. 2008, 47(5):809-824.
26. Chuang Y.Y., Chen Q., et al. Radiation-induced mutations at the autosomal thymidine kinase locus are not elevated in p53-null cells. Cancer Res. 1999, 59(13):3073-3076.
27. Chun H.H., Gatti R.A. Ataxia-telangiectasia, an evolving phenotype. DNA Repair (Amst) 2004, 3(8-9):1187-1196.
28. Ciccia A., Elledge S.J. The DNA damage response: making it safe to play with knives. Mol. Cell 2010, 40(2):179-204.
29. Criswell T., Leskov K., et al. Transcription factors activated in mammalian cells after clinically relevant doses of ionizing radiation. Oncogene 2003, 22(37):5813-5827.
30. Derheimer F.A., Kastan M.B. Multiple roles of ATM in monitoring and maintaining DNA integrity. FEBS Lett. 2010, 584(17):3675-3681.
31. el-Deiry W.S. Regulation of p53 downstream genes. Semin. Cancer Biol. 1998, 8(5):345-357.
32. Elkon R., Linhart C., et al. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res. 2003, 13(5):773-780.
33. Elkon R., Rashi-Elkeles S., et al. Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis. Genome Biol. 2005, 6(5):R43.
34. Elkon R., Vesterman R., et al. SPIKE-a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics 2008, 9:110.
35. Eyfjord J.E., Bodvarsdottir S.K. Genomic instability and cancer: networks involved in response to DNA damage. Mutat. Res. 2005, 592(1-2):18-28.
36. Fei P., El-Deiry W.S. P53 and radiation responses. Oncogene 2003, 22(37):5774-5783.
37. Fischer C., Jonckx B., et al. Anti-PlGF inhibits growth of VEGF(R)-inhibitor-resistant tumors without affecting healthy vessels. Cell 2007, 131(3):463-475.
38. Goodwin R.G., Din W.S., et al. Molecular cloning of a ligand for the inducible T cell gene 4-1BB: a member of an emerging family of cytokines with homology to tumor necrosis factor. Eur. J. Immunol. 1993, 23(10):2631-2641.
39. Gudkov A.V., Komarova E.A. The role of p53 in determining sensitivity to radiotherapy. Nat. Rev. Cancer 2003, 3(2):117-129.
40. Gudkov A.V., Komarova E.A. Prospective therapeutic applications of p53 inhibitors. Biochem. Biophys. Res. Commun. 2005, 331(3):726-736.
41. Halazonetis T.D., Gorgoulis V.G., et al. An oncogene-induced DNA damage model for cancer development. Science 2008, 319(5868):1352-1355.
42. Hartlerode A.J., Scully R. Mechanisms of double-strand break repair in somatic mammalian cells. Biochem. J. 2009, 423(2):157-168.
43. Heinloth A.N., Shackelford R.E., et al. ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiation. Radiat. Res. 2003, 160(3):273-290.
44. Heinloth A.N., Shackelford R.E., et al. Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation. Mol. Carcinog. 2003, 37(2):65-82.
45. Helton E.S., Chen X. p53 modulation of the DNA damage response. J. Cell Biochem. 2007, 100(4):883-896.
46. Hiom K. DNA repair: a riddle at a double-strand break. Curr. Biol. 2009, 19(8):R331-R333.
47. Hiom K. Coping with DNA double strand breaks. DNA Repair (Amst) 2010, 9(12):1256-1263.
48. Huebner K., Druck T., et al. Chromosomal localization of four human zinc finger cDNAs. Hum. Genet. 1993, 91(3):217-222.
49. Jackson S.P., Bartek J. The DNA-damage response in human biology and disease. Nature 2009, 461(7267):1071-1078.
50. Jackson J.G., Post S.M., et al. Regulation of tissue- and stimulus-specific cell fate decisions by p53 in vivo. J. Pathol. 2011, 223(2):127-136.
51. Jen K.Y., Cheung V.G. Transcriptional response of lymphoblastoid cells to ionizing radiation. Genome Res. 2003, 13(9):2092-2100.
52. Jen K.Y., Cheung V.G. Identification of novel p53 target genes in ionizing radiation response. Cancer Res. 2005, 65(17):7666-7673.
53. Joseph L.J., Le Beau M.M., et al. Molecular cloning, sequencing, and mapping of EGR2, a human early growth response gene encoding a protein with " zinc-binding finger" structure. Proc. Natl. Acad. Sci. U S A 1988, 85(19):7164-7168.
54. Jung M.S., Yun J., et al. p53 and its homologues, p63 and p73, induce a replicative senescence through inactivation of NF-Y transcription factor. Oncogene 2001, 20(41):5818-5825.
55. Kamat A.K., Rocchi M., et al. Lamin A/C gene and a related sequence map to human chromosomes 1q12.1-q23 and 10. Somat. Cell Mol. Genet. 1993, 19(2):203-208.
56. Knowles B.B., Howe C.C., et al. Human hepatocellular carcinoma cell lines secrete the major plasma proteins and hepatitis B surface antigen. Science 1980, 209(4455):497-499.
57. Ko L.J., Prives C. p53: puzzle and paradigm. Genes Dev. 1996, 10(9):1054-1072.
58. Komarova E.A., Kondratov R.V., et al. Dual effect of p53 on radiation sensitivity in vivo: p53 promotes hematopoietic injury, but protects from gastro-intestinal syndrome in mice. Oncogene 2004, 23(19):3265-3271.
59. Landmark H., Nahas S.A., et al. "Transcriptional response to ionizing radiation in human radiation sensitive cell lines. Radiother. Oncol. 2007, 83(3):256-260.
60. Laptenko O., Prives C. Transcriptional regulation by p53: one protein, many possibilities. Cell Death Differ. 2006, 13(6):951-961.
61. Lavin M.F. Ataxia-telangiectasia: from a rare disorder to a paradigm for cell signalling and cancer. Nat. Rev. Mol. Cell Biol. 2008, 9(10):759-769.
62. Lempiainen H., Halazonetis T.D. "Emerging common themes in regulation of PIKKs and PI3Ks. EMBO J. 2009, 28(20):3067-3073.
63. Linhart C., Elkon R., et al. "Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis. Cell Cycle 2005, 4(12):1788-1797.
64. Lopez-Contreras A.J., Fernandez-Capetillo O. The ATR barrier to replication-born DNA damage. DNA Repair (Amst) 2010, 9(12):1249-1255.
65. Maglione D., Guerriero V., et al. Two alternative mRNAs coding for the angiogenic factor, placenta growth factor (PlGF), are transcribed from a single gene of chromosome 14. Oncogene 1993, 8(4):925-931.
66. Manni I., Mazzaro G., et al. NF-Y mediates the transcriptional inhibition of the cyclin B1, cyclin B2, and cdc25C promoters upon induced G2 arrest. J. Biol. Chem. 2001, 276(8):5570-5576.
67. Mori M., Benotmane M.A., et al. Transcriptional response to ionizing radiation in lymphocyte subsets. Cell Mol. Life Sci. 2005, 62(13):1489-1501.
68. Neal J.A., Meek K. Choosing the right path: does DNA-PK help make the decision?. Mutat. Res 2011.
69. Negrini S., Gorgoulis V.G., et al. Genomic instability-an evolving hallmark of cancer. Nat. Rev. Mol. Cell Biol. 2010, 11(3):220-228.
70. Niu N., Qin Y., et al. Radiation pharmacogenomics: a genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines. Genome Res. 2010, 20(11):1482-1492.
71. Occhiodoro T., Beckmann K.R., et al. Human alpha-l-fucosidase: complete coding sequence from cDNA clones. Biochem. Biophys. Res. Commun. 1989, 164(1):439-445.
72. O'Driscoll M., Jeggo P.A. The role of double-strand break repair - insights from human genetics. Nat. Rev. Genet. 2006, 7(1):45-54.
73. Paz A., Brownstein Z., et al. SPIKE: a database of highly curated human signaling pathways. Nucleic Acids Res. 2011, 39(Database issue):D793-D799.
74. Peebles T.P.T.T., et al. Isolation of four unusual pediatric solid tumor cell lines. Pediatr. Res. 1978, 12(Suppl. 4).
75. Polo S.E., Jackson S.P. Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev. 2011, 25(5):409-433.
76. Ponten J., Saksela E. Two established in vitro cell lines from human mesenchymal tumours. Int. J. Cancer 1967, 2(5):434-447.
77. Popanda O., Marquardt J.U., et al. Genetic variation in normal tissue toxicity induced by ionizing radiation. Mutat. Res. 2009, 667(1-2):58-69.
78. Pugh T.J., Keyes M., et al. Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patients. Clin. Cancer Res. 2009, 15(15):5008-5016.
79. Rankin J., Ellard S. The laminopathies: a clinical review. Clin. Genet. 2006, 70(4):261-274.
80. Rashi-Elkeles S., Elkon R., et al. Parallel induction of ATM-dependent pro- and anti-apoptotic signals in response to ionizing radiation in murine lymphoid tissue. Oncogene 2006, 25(10):1584-1592.
81. Riley T., Sontag E., et al. Transcriptional control of human p53-regulated genes. Nat. Rev. Mol. Cell Biol. 2008, 9(5):402-412.
82. Skopek T.R., Liber H.L., et al. Isolation of a human lymphoblastoid line heterozygous at the thymidine kinase locus: possibility for a rapid human cell mutation assay. Biochem. Biophys. Res. Commun. 1978, 84(2):411-416.
83. Snyder A.R. Review of radiation-induced bystander effects. Hum. Exp. Toxicol. 2004, 23(2):87-89.
84. Tabach Y., Milyavsky M., et al. The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation. Mol. Syst. Biol. 2005, 1:0022.
85. Thony B., Auerbach G., et al. Tetrahydrobiopterin biosynthesis, regeneration and functions. Biochem. J. 2000, 347(Pt 1):1-16.
86. Turesson I. Individual variation and dose dependency in the progression rate of skin telangiectasia. Int. J. Radiat. Oncol. Biol. Phys. 1990, 19(6):1569-1574.
87. Ventura A., Kirsch D.G., et al. Restoration of p53 function leads to tumour regression in vivo. Nature 2007, 445(7128):661-665.
88. Warner L.E., Mancias P., et al. Mutations in the early growth response 2 (EGR2) gene are associated with hereditary myelinopathies. Nat. Genet. 1998, 18(4):382-384.
89. Wei C.L., Wu Q., et al. A global map of p53 transcription-factor binding sites in the human genome. Cell 2006, 124(1):207-219.
90. Willems P.J., Gatti R., et al. Fucosidosis revisited: a review of 77 patients. Am. J. Med. Genet. 1991, 38(1):111-131.
91. Wong-Staal F., Dalla-Favera R., et al. Three distinct genes in human DNA related to the transforming genes of mammalian sarcoma retroviruses. Science 1981, 213(4504):226-228.
92. Yun J., Chae H.D., et al. p53 negatively regulates cdc2 transcription via the CCAAT-binding NF-Y transcription factor. J. Biol. Chem. 1999, 274(42):29677-29682.
93. Zamzami N., Kroemer G. p53 in apoptosis control: an introduction. Biochem. Biophys. Res. Commun. 2005, 331(3):685-687.
94. Zhu Z., Shendure J., et al. Discovering functional transcription-factor combinations in the human cell cycle. Genome Res. 2006, 15:848-855.
95. Zschenker O., Borgmann K., et al. Lymphoblastoid cell lines differing in p53 status show clear differences in basal gene expression with minor changes after irradiation. Radiother. Oncol. 2006, 80(2):236-249.