Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells.
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.
Chuang
Yao-Yu Eric
YY
Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA.
Chen
Yidong
Y
Gadisetti
Chandramouli
V R
VR
Cook
John A
JA
Coffin
Deborah
D
Tsai
Mong-Hsun
MH
DeGraff
William
W
Yan
Hailing
H
Zhao
Shuping
S
Russo
Angelo
A
Liu
Edison T
ET
Mitchell
James B
JB
D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism; D016000:Cluster Analysis; D015870:Gene Expression / Q000187:drug effects*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D006861:Hydrogen Peroxide / Q000494:pharmacology; D020411:Oligonucleotide Array Sequence Analysis; D016877:Oxidants / Q000494:pharmacology*; D018384:Oxidative Stress / Q000235:genetics; D015203:Reproducibility of Results; D015533:Transcriptional Activation; D014407:Tumor Cells, Cultured; D024483:Vitamin K 3 / Q000494:pharmacology; D020122:tert-Butylhydroperoxide / Q000494:pharmacology
D016877:Oxidants; D024483:Vitamin K 3; D020122:tert-Butylhydroperoxide; D006861:Hydrogen Peroxide