Identification of genes involved in the proliferative response to estrogen (E2)

The Human Genome Project promised to promote large-scale functional analyses necessary for the diagnosis and treatment of complex diseases. Here we demonstrate an integrated approach to the study of a transcriptional regulatory cascade involved in the progression of breast cancer and we identify a protein associated with disease progression. Using chromatin immunoprecipitation and genome tiling arrays, whole genome mapping of transcription factor binding sites was combined with gene expression profiling to identify genes involved in the proliferative response to estrogen (E2). Using RNA interference, selected ERa and c-Myc gene targets were knocked down to identify mediators of E2-stimulated cell proliferation. Tissue microarray screening revealed that high expression of an epigenetic factor, the estrogen-inducible histone variant H2A.Z, is significantly associated with lymph node metastasis and decreased breast cancer survival. Detection of H2A.Z levels independently increased the prognostic power of biomarkers currently in clinical use. This integrated approach has accelerated the identification of a molecule linked to breast cancer progression, has implications for diagnostic and therapeutic interventions, and can be applied to a wide range of cancers. Keywords: treated vs. untreated MCF7 cells treated with E2 (10nM) or Ctrl (vehicle) for 4, 12 or 24 hours. Each hormone treatment time was performed at least three times and hybridizations included dye swaps.