Stress-specific signatures: expression profiling of p53 wild-type and -null human cells

Abstract

Gene expression responses of human cell lines exposed to a diverse set of stress agents were compared by cDNA microarray hybridization. The B-lymphoblastoid cell line TK6 (p53 wild-type) and its p53-null derivative, NH32, were treated in parallel to facilitate investigation of p53-dependent responses. RNA was extracted 4 h after the beginning of treatment when no notable decrease in cell viability was evident in the cultures. Gene expression signatures were defined that discriminated between four broad general mechanisms of stress agents: Non-DNAdamaging stresses (heat shock, osmotic shock, and 12-Otetradecanoylphorbol 13-acetate), agents causing mainly oxidative stress (arsenite and hydrogen peroxide), ionizing radiations (neutron and c-ray exposures), and other DNAdamaging agents (ultraviolet radiation, methyl methanesulfonate, adriamycin, camptothecin, and cis-Platinum(II)diammine dichloride (cisplatin)). Within this data set, non-DNA-damaging stresses could be discriminated from all DNA-damaging stresses, and profiles for individual agents were also defined. While DNA-damaging stresses showed a strong p53-dependent element in their responses, no discernible p53-dependent responses were triggered by the non-DNA-damaging stresses. A set of 16 genes did exhibit a robust p53-dependent pattern of induction in response to all nine DNA-damaging agents, however.

MicroRNA Responses to Cellular Stress

“…Notably, we saw no significant change in miRNA expression profiles with exposure to 2.5 Gy of g-irradiation after 4 hours or 6 days, compared with mock-treated controls. Studies have shown that these cells, similarly exposed, exhibit a potent alteration in gene expression after 4 hours, all the while exhibiting no marked changes in viability (30). Therefore, these cells react to the stress (administered in this fashion) through a significant transcriptional response; however, our results show that ionizing radiation, which directly damages DNA, does not change the miRNA expression profile.…”

“…The 6-day time period was chosen based on previous reports showing that folate deficiency for this period can lead to altered S-adenosyl methionine levels and can alter global genomic methylation without severe consequences for cell viability (29). Similarly, the dose of g-irradiation was chosen based on previous data showing it to elicit alterations in gene expression, without a marked change in cell viability at the 4-hour or 6-day time point (30). The miRNA profile was delineated using a novel microarray-based platform, the mirVana miRNA Bioarray (Ambion), which simultaneously examines 385 known human miRNAs.…”

Gene expression profiles modulated by the human carcinogen aristolochic acid I in human cancer cells and their dependence on TP53

“…In Eker and WT rats treated with 10 mg/kg bw of AA (41% AAI, 56% AAII) for up to 14 days the TP53-regulated genes CDKN1A and CCNG1 were changed (upregulated) in a time-dependent manner (Stemmer et al, 2007). We found that CDKN1A and CCNG1 were changed in HCT116 cells exposed to AAI and these genes were identified as discriminating TP53 status in TK6 cells after DNA-damaging treatments (Amundson et al, 2005).…”

Gene expression response to cisplatin treatment in drug-sensitive and drug-resistant ovarian cancer cells

“…Gene expression profiling techniques such as microarrays and serial analysis of gene expression (SAGE) have allowed the identification of genes whose expression is acutely affected by cisplatin exposure (Amundson et al, 2005;Kerley-Hamilton et al, 2005), as well as genes differentially expressed in cells that have developed cisplatin resistance (Sherman-Baust et al, 2003;Kang et al, 2004;Whiteside et al, 2004;Roberts et al, 2005;Cheng et al, 2006). In addition, these techniques have also allowed for the identification of gene expression signatures that may help predict cisplatin sensitivity in various cancers (Akervall et al, 2004;Takata et al, 2005).…”