Prediction of Toxicant-Specific Gene Expression Signatures after Chemotherapeutic Treatment of Breast Cell Lines

Abstract

Global gene expression profiling has demonstrated that the predominant cellular response to a range of toxicants is a general stress response. This stereotyped environmental stress response commonly includes repression of protein synthesis and cell-cycle-regulated genes and induction of DNA damage and oxidative stress-responsive genes. Our laboratory recently characterized the general stress response of breast cell lines derived from basal-like and luminal epithelium after treatment with doxorubicin (DOX) or 5-fluorouracil (5FU) and showed that each cell type has a distinct response. However, we expected that some of the expression changes induced by DOX and 5FU would be unique to each compound and might reflect the underlying mechanisms of action of these agents. Therefore, we employed supervised analyses (significance analysis of microarrays) to identify genes that showed differential expression between DOX-treated and 5FU-treated cell lines. We then used cross-validation analyses and identified genes that afforded high predictive accuracy in classifying samples into the two treatment classes. To test whether these gene lists had good predictive accuracy in an independent data set, we treated our panel of cell lines with etoposide, a compound mechanistically similar to DOX. We demonstrated that using expression patterns of 100 genes we were able to obtain 100% predictive accuracy in classifying the etoposide samples as being more similar in expression to DOX-treated than to 5FU-treated samples. These analyses also showed that toxicant-specific gene expression patterns, similar to general stress responses, vary according to cell type.

Scoring of senescence signalling in multiple human tumour gene expression datasets, identification of a correlation between senescence score and drug toxicity in the NCI60 panel and a pro-inflammatory signature correlating with survival advantage in peritoneal mesothelioma

“…We first validated the approach using public data sets involving interventions in which increased senescence would be expected. The sets chosen for this analysis examine radiotherapy of colon adenocarcinoma [24], doxorubicin and 5-FU treatment of breast cancer cell lines [25], and replicative senescence of mesenchymal stem cells [26]. In each case, we find that the scoring approach does indeed report increased pro-senescence signalling and allows dissection of the relative contributions of DAS and mSS subtypes.…”

Enhancement of chemotherapeutic efficacy in hypermethylator breast cancer cells through targeted and pharmacologic inhibition of DNMT3b

“…The IC 50 for DOX, PAX, and 5-FU have been reported for the breast cancer cell lines used in this study [38][39][40]. However, these IC 50 values vary widely from laboratory to laboratory and with specific experimental conditions.…”

Interaction between p53 and estradiol pathways in transcriptional responses to chemotherapeutics

“…Previous studies have established cell type-specific responses to DOX and 5FU as well as other drugs. 42 Notably, only H19 and INPP5D consistently exhibited transcriptional cooperation between E2 and DOX, 5FU and nutlin treatments. Using p53-deficient MCF7 cells, the dependency on p53 was examined for eight genes and confirmed for the newly identified p53 target genes GDNF, KRT15, and SOX9 as well as the previously reported TLR5, 35 INPP5D, 43 NOTCH1 61 and EPHA2.…”