Characterization of gene expression profiles at low and very low doses of ionizing radiation

DNA Repair

Volumn 12, Issue 7, 2013, Pages 508-517

  Nosel, Ingrid ^a   Vaurijoux, Aurélie ^a   Barquinero, Joan Francesc ^a   Gruel, Gaetan ^a  

^a INSTITUT DE RADIOPROTECTION ET DE SÛRETÉ NUCLÉAIRE IRSN   (France)

Author keywords

Gene expression; Ionizing radiation; Low dose; Microarray; TCD4+ lymphocytes

Indexed keywords

ARTICLE; BLOOD SAMPLING; CD4+ T LYMPHOCYTE; CELL RESPIRATION; DNA DAMAGE; DNA MICROARRAY; DOWN REGULATION; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; HUMAN; IONIZING RADIATION; MALE; MOLECULAR MECHANICS; NORMAL HUMAN; PRIORITY JOURNAL; RADIATION DOSE; REGULATORY MECHANISM; UPREGULATION;

CD4-POSITIVE T-LYMPHOCYTES; CELL RESPIRATION; DNA DAMAGE; DOSE-RESPONSE RELATIONSHIP, RADIATION; GAMMA RAYS; GENE EXPRESSION PROFILING; HUMANS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; TRANSCRIPTION, GENETIC; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84878664063     PISSN: 15687864     EISSN: 15687856     Source Type: Journal    
DOI: 10.1016/j.dnarep.2013.04.021     Document Type: Article

References (40)

1. UNSCEAR Sources and Effects of Ionizing Radiation 2008, United Nations, Vienna, Austria.
2. Amundson S.A., Bittner M., Fornace A.J. Functional genomics as a window on radiation stress signaling. Oncogene 2003, 22:5828-5833.
3. Dent P., Yacoub A., Contessa J., Caron R., Amorino G., Valerie K., et al. Stress and radiation-induced activation of multiple intracellular signaling pathways. Radiat. Res. 2003, 159:283-300.
4. Coates P.J., Lorimore S.A., Wright E.G. Cell and tissue responses to genotoxic stress. J. Pathol. 2005, 205:221-235.
5. Ohnishi T., Mori E., Takahashi A. DNA double-strand breaks: their production, recognition, and repair in eukaryotes. Mutat. Res. 2009, 669:8-12.
6. Mladenov E., Iliakis G. Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways. Mutat. Res. 2011, 711:61-72.
7. Huang L.C., Clarkin K.C., Wahl G.M. Sensitivity and selectivity of the DNA damage sensor responsible for activating p53-dependent G1 arrest. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:4827-4832.
8. Nelson W.G., Kastan M.B. DNA strand breaks: the DNA template alterations that trigger p53-dependent DNA damage response pathways. Mol. Cell. Biol. 1994, 14:1815-1823.
9. Criswell T., Leskov K., Miyamoto S., Luo G., Boothman D.A. Transcription factors activated in mammalian cells after clinically relevant doses of ionizing radiation. Oncogene 2003, 22:5813-5827.
10. Rothkamm K., Löbrich M. Evidence for a lack of DNA double-strand break repair in human cells exposed to very low X-ray doses. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:5057-5062.
11. Suzuki K., Kodama S., Watanabe M. Extremely low-dose ionizing radiation causes activation of mitogen-activated protein kinase pathway and enhances proliferation of normal human diploid cells. Cancer Res. 2001, 61:5396-5401.
12. Azzam E.I., Little J.B. The radiation-induced bystander effect: evidence and significance. Hum. Exp. Toxicol. 2004, 23:61-65.
13. Chaudhry M.A. Bystander effect: biological endpoints and microarray analysis. Mutat. Res. 2006, 597:98-112.
14. Zhou H., Ivanov V.N., Gillespie J., Geard C.R., Amundson S.A., Brenner D.J., et al. Mechanism of radiation-induced bystander effect: role of the cyclooxygenase-2 signaling pathway. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:14641-14646.
15. Lyng F.M., Maguire P., McClean B., Seymour C., Mothersill C. The involvement of calcium and MAP kinase signaling pathways in the production of radiation-induced bystander effects. Radiat. Res. 2006, 165:400-409.
16. Amundson S.A., Bittner M., Chen Y., Trent J., Meltzer P., Fornace A.J. Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses. Oncogene 1999, 18:3666-3672.
17. Franco N., Lamartine J., Frouin V., Le Minter P., Petat C., Leplat J.-J., et al. Low-dose exposure to gamma rays induces specific gene regulations in normal human keratinocytes. Radiat. Res. 2005, 163:623-635.
18. + lymphocyte subpopulations in response to low doses of ionizing radiation. Radiat. Res. 2008, 170:335-344.
19. R Development Core Team R: A Language and Environment for Statistical Computing 2009, R Foundation for Statistical Computing, Vienna, Austria.
20. Smyth G.K., Speed T. Normalization of cDNA microarray data. Methods 2003, 31:265-273.
21. Edgar R., Domrachev M., Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30:207-210.
22. Barrett T., Troup D.B., Wilhite S.E., Ledoux P., Evangelista C., Kim I.F., et al. NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res. 2011, 39:D1005-D1010.
23. Smyth G.K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 2004, 3. (Article 3).
24. Smyth G.K. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions Using {R} and Bioconductor 2005, 397-420. Springer, New York. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (Eds.).
25. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
26. Yang Y.H., Speed T. Design and analysis of comparative microarray experiments. Statistical Analysis of Gene Expression Microarray Data 2003, Chapman and Hall/CRC, Boca Raton, pp. 35-92. T. Speed (Ed.).
27. Irizarry R.A. From CEL files to annotated lists of interesting genes. Bioinformatics and Computational Biology Solutions Using R and Bioconductor 2005, 431-442. Springer, New York. R. Gentleman, V. Carey, W. Huber, R. Irizarry, S. Dudoit (Eds.).
28. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B: Stat. Methodol. 1995, 57:289-300.
29. G.R. Warnes, B. Bolker, L. Bonebakker, R. Gentleman, W.H.A. Liaw, T. Lumley, et al., gplots: Various R programming tools for plotting data. Available: Accessed 2013 Apr 19. http://cran%20r-project%20org/web/packages/gplots/index%20html.
30. Chen J., Bardes E.E., Aronow B.J., Jegga A.G. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 2009, 37:W305-W311.
31. Ding L.-H., Shingyoji M., Chen F., Hwang J.-J., Burma S., Lee C., et al. Gene expression profiles of normal human fibroblasts after exposure to ionizing radiation: a comparative study of low and high doses. Radiat. Res. 2005, 164:17-26.
32. Knops K., Boldt S., Wolkenhauer O., Kriehuber R. Gene expression in low- and high-dose-irradiated human peripheral blood lymphocytes: possible applications for biodosimetry. Radiat. Res. 2012, 178:304-312.
33. Amundson S.A., Do K.T., Fornace A.J. Induction of stress genes by low doses of gamma rays. Radiat. Res. 1999, 152:225-231.
34. Manning G., Kabacik S., Finnon P., Bouffler S., Badie C. High and low dose responses of transcriptional biomarkers in ex vivo x-irradiated human blood. Int. J. Radiat. Biol. 2013, in press.
35. Costes S.V., Chiolo I., Pluth J.M., Barcellos-Hoff M.H., Jakob B. Spatiotemporal characterization of ionizing radiation induced DNA damage foci and their relation to chromatin organization. Mutat. Res. 2010, 704:78-87.
36. Stenerlöw B., Karlsson K.H., Cooper B., Rydberg B. Measurement of prompt DNA double-strand breaks in mammalian cells without including heat-labile sites: results for cells deficient in nonhomologous end joining. Radiat. Res. 2003, 159:502-510.
37. Gong B., Chen Q., Almasan A. Ionizing radiation stimulates mitochondrial gene expression and activity. Radiat. Res. 1998, 150:505-512.
38. Nishimaki N., Tsukimoto M., Kitami A., Kojima S. Autocrine regulation of ?-irradiation-induced DNA damage response via extracellular nucleotides-mediated activation of P2Y6 and P2Y12 receptors. DNA Repair (Amst.) 2012, 11:657-665.
39. Tsukimoto M., Homma T., Ohshima Y., Kojima S. Involvement of purinergic signaling in cellular response to gamma radiation. Radiat. Res. 2010, 173:298-309.
40. Marchetti F., Coleman M.A., Jones I.M., Wyrobek A.J. Candidate protein biodosimeters of human exposure to ionizing radiation. Int. J. Radiat. Biol. 2006, 82:605-639.