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Gene Expression after Treatment with Hydrogen Peroxide, Menadione, or t-Butyl Hydroperoxide in Breast Cancer Cells

Radiation Biology Branch, Center for Cancer Research, National Cancer Institute [Y-Y. E. C., G. V. R. C., J. A. C., D. C., M-H. T., W. D., H. Y., S. Z., A. R., J. B. M.], and Cancer Genetics Branch, National Human Genome Research Institute [Y. C.], NIH, Bethesda, Maryland 20892, and Genome Institute of Singapore, Singapore 117528 [E. T. L.]

Global gene expression patterns in breast cancer cells after treatment with oxidants (hydrogen peroxide, menadione, and t-butyl hydroperoxide) were investigated in three replicate experiments. RNA collected after treatment (at 1, 3, 7, and 24 h) rather than after a single time point, enabled an analysis of gene expression patterns. Using a 17,000 microarray, template-based clustering and multidimensional scaling analysis of the gene expression over the entire time course identified 421 genes as being either up- or down-regulated by the three oxidants. In contrast, only 127 genes were identified for any single time point and a 2-fold change criteria. Surprisingly, the patterns of gene induction were highly similar among the three oxidants; however, differences were observed, particularly with respect to p53, IL-6, and heat-shock related genes. Replicate experiments increased the statistical confidence of the study, whereas changes in gene expression patterns over a time course demonstrated significant additional information versus a single time point. Analyzing the three oxidants simultaneously by template cluster analysis identified genes that heretofore have not been associated with oxidative stress.

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