Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression

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 ERα 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 E2‐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. Synopsis One promise of the Human Genome Project was to stimulate the translation of large‐scale functional analyses of the human genome to produce novel targets useful in the diagnosis or 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. The estrogen (E2) response is mediated in part by the estrogen receptor‐α (ERα) (Smith and O'Malley, 2004 ), a ligand‐activated and DNA sequence‐specific transcription factor that plays an integral role in the initiation, development, and metastasis of breast and uterine cancers (Yager and Davidson, 2006 ). The oncogene c ‐myc , which is upregulated by ERα in response to E2 (Dubik and Shiu, 1992 ), is one of the most broadly overexpressed oncogenes in human cancer. Because nearly 70% of breast cancers express ERα, antiestrogens remain a mainstay of therapy and prevention for these cancers. Unfortunately, this therapy is hindered by the subsequent development of tumors resistant to antiestrogen treatment through a process that often involves an E2‐autonomous c‐MYC (Jeng et al , 1998 ; Rodrik et al , 2005 ). A complete understanding of antiestrogen resistance in these tumors may depend on developing an integrated, comprehensive understand