The responses of a line of normal human mammary epithelial cells, HME87, to treatment with the ultimate carcinogen benzo[a]pyrene diol epoxide (BPDE) were analyzed using a directed gene expression analysis technique, RAGE. Under conditions where cell number was decreased by 50% 24 or 48 h post-treatment, flow cytometry demonstrated no establishment of a G(1)/S arrest nor induction of apoptosis; cells continued to enter S phase from G(1) for at least 24 h but were blocked at G(2)/M. Using the RAGE technique, changes in gene expression were assayed for over 1000 genes, and multiple time-point data were collected for approximately 90 genes. In accord with the cell cycle studies, expression of the p21-WAF1 gene, the major mediator of p53-dependent G(1)/S arrest, did not increase until 24 h post-treatment. The expression of other target genes for transactivation by p53 was increased at early time points, including GADD45, an effector of the G(2)/M checkpoint, and WIP1. Analyses of proteins in treated cells indicated that p53 was phosphorylated at Ser15 but not at Ser20 within 30 min of treatment, and this correlated with an increase in the total amount of p53 protein. Significant expression changes were noted in a number of transcription factor genes, including ATF3 and E2A, genes that have not been previously connected to a response to DNA damage involving bulky chemical adducts. In addition, expression of the XPC gene was induced by BPDE treatment; the XPC product is thought to be involved in recognition of DNA damage by the nucleotide excision repair system.

Current techniques for analysis of gene expression either monitor one gene at a time, for example northern hybridization or RT-PCR methods, or are designed for the simultaneous analysis of thousands of genes, for example microarray hybridization or serial analysis of gene expression. To provide a flexible, intermediate scale alternative, a PCR-based method for the rapid analysis of gene expression has been developed which allows expression changes to be determined in either a directed search of known genes, or an undirected survey of unknown genes. A single set of reagents and reaction conditions allows analyses of most genes in any eukaryote. The method is useful for assaying on the order of tens to hundreds of genes in multiple samples. Control experiments indicate reliable detection of changes in gene expression 2-fold and greater, and sensitivity of detection better than 1 in 10 000. Analyses of over 400 genes in a mouse system transgenic for the E2F1 gene have identified several new downstream targets of E2F1, including Brca1 and Cdk7, in addition to several unidentified genes that are upregulated in the transgenic mice. Changes in expression of several genes related to apoptosis suggest a possible potentiation of apoptotic pathways in the transgenic keratinocytes.