Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses

The fate of cells exposed to ionizing radiation (IR) may depend greatly on changes in gene expression, so that an improved, view of gene induction pro files is important for understanding mechanisms of checkpoint control, repa ir and cell death following such exposures. We have used a quantitative flu orescent cDNA microarray hybridization approach to identify genes regulated in response gamma- irradiation in the p53 wild-type ML-1 human myeloid cel l line. Hybridization of the array to fluorescently-labeled RNA from treate d and untreated cells Has followed by computer analysis to derive relative changes in expression levels of the genes present in the array which agreed well with actual quantitative changes in expression. Forty-eight sequences , 30 not previously identified as IR-responsive, were significantly regulat ed by IR. Induction by IR and other stresses of a subset of these genes, in cluding the previously characterized CIP1/WAF1, MDM and BAX genes, as well as nine genes not previously reported to be IR-responsive, was examined in a panel of 12 human cell lines. Responses varied widely in cell lines with different tissues of origin and different genetic backgrounds, highlighting the importance of cellular contest to genotoxic stress responses. Two of t he newly identified IR-responsive genes, FRA-1 and ATF3, showed a p53-assoc iated component to their IR-induction, and this was confirmed both in isoge nic human cell lines and in mouse thymus. The majority of the IR-responsive genes, however, showed no indication of p53-dependent regulation, represen ting a potentially important class of stress-responsive genes in leukemic c ells.