Effects of Ras signaling on gene expression analyzed by customized microarrays.

Many signal transduction processes converge on Ras proteins that serve as molecular switches to couple external stimuli with cytoplasmic and nuclear targets. Oncogenic mutations lock Ras proteins in their activated state. Cellular responses to permanent Ras activation such as the induction of neoplastic phenotypes are mediated by distinct transcriptional alterations. A number of studies have reported alterations of the genetic program because of short-term or long-term activation of Ras signaling pathways. However, a consistent pattern of Ras-related transcriptional alterations has not yet emerged, because currently available investigations were based on different methods for assessing mRNA expression profiles, on different types of cells, and on heterogeneous experimental conditions. Here we describe the "Ras signaling target array" (RASTA) representing approximately 300 Ras-responsive target genes. This customized oligonucleotide array is a universal tool for assessing transcriptional patterns of cells or tissues expressing oncogenic Ras genes, as well as upstream and downstream effectors. To validate the results obtained by array-based expression profiling, we have compared the data with those obtained by suppression subtractive hybridization and conventional expression analysis by Northern blotting. Target RNAs were prepared from preneoplastic rat ovarian surface epithelial cells (ROSE) and the KRAS-transformed derivative A2/5. By interrogating Ras signaling target arrays with mRNAs prepared from the same types of cells as hybridization target, we correctly recognized 85% of genes differentially expressed on conversion of normal ovarian epithelial cells to the Ras-transformed state.