Breast carcinogenesis involves genetic and epigenetic alterations that cause aberrant gene function. Recent progress in the knowledge of epigenomics has had a profound impact on the understanding of mechanisms leading to breast cancer, and consequently the development of new strategies for diagnosis and treatment of breast cancer. Epigenetic regulation has been known to involve three mutually interacting events -DNA methylation, histone modifications and nucleosomal remodeling. These processes modulate chromatin structure to form euchromatin or heterochromatin, and in turn activate or silence gene expression. Alteration in expression of key genes through aberrant epigenetic regulation in breast cells can lead to initiation, promotion and maintenance of carcinogenesis, and is even implicated in the generation of drug resistance. We currently review known roles of the epigenetic machinery in the development and recurrence of breast cancer. Furthermore, we highlight the significance of epigenetic alterations as predictive biomarkers and as new targets of anticancer therapy.Keywords breast cancer; CpG islands; demethylating agents; DNA methylation; epigenetics; histone deacetylase inhibitors; histone modifications; nucleosomal rem odeling Breast cancer is among the most frequently diagnosed neoplasias and the second leading cause of cancer death among American women. Generally, cancer has been viewed as a disease that is driven by progressive genetic abnormalities, involving mutations in oncogenes and tumor suppressor genes, and chromosomal abnormalities [1,2]. However, it has been shown that breast cancer, similar to other types of cancer, is also a disease that is driven by epigenetic alterations, which do not affect the primary DNA sequence [3,4]. The outcome of these alterations is aberrant transcriptional regulation that results in a change in expression patterns of genes implicated in cellular proliferation, survival and differentiation [3,5,6]. Epigenetic alterations occur at the chromosomal level in transformed cells. These involve changes in DNA methylation and histone modifications, and altered expression and function of factors implicated in regulating assembly and remodeling of nucleosomes [5][6][7][8][9]. Alterations in DNA methylation include global hypomethyation and focal hypermethylation. Global hypomethylation has been found to increase with age and is linked to genomic instability and activation of oncogene expression [10][11][12]. By contrast, gene-locus-specific hypermethylation can lead to the transcriptional silencing of tumor suppressor genes [3,[5][6][7][8][9]. In addition to DNA methylation, post-translational histone modification is another epigenetically regulated mechanism that can modulate chromatin structure to regulate gene expression [5][6][7][8]13]. DNA methylation is often associated with some specific types of histone modifications that can Correspondence to: Saraswati Sukumar. NIH Public Access Author ManuscriptPharmacogenomics. Author manuscript; available in PMC 2009 Oc...

The expression of several members of the FOX gene family is known to be altered in a variety of cancers. We show that in breast cancer, FOXF1 gene is a target of epigenetic inactivation and that its gene product exhibits tumor-suppressive properties. Loss or downregulation of FOXF1 expression is associated with FOXF1 promoter hypermethylation in breast cancer cell lines and in invasive ductal carcinomas. Methylation of FOXF1 in invasive ductal carcinoma (37.6% of 117 cases) correlated with high tumor grade. Pharmacologic unmasking of epigenetic silencing in breast cancer cells restored FOXF1 expression. Re-expression of FOXF1 in breast cancer cells with epigenetically silenced FOXF1 genes led to G 1 arrest concurrent with or without apoptosis to suppress both in vitro cell growth and in vivo tumor formation. FOXF1-induced G 1 arrest resulted from a blockage at G 1 -S transition of the cell cycle through inhibition of the CDK2-RB-E2F cascade. Small interfering RNAmediated depletion of FOXF1 in breast cancer cells led to increased DNA re-replication, suggesting that FOXF1 is required for maintaining the stringency of DNA replication and genomic stability. Furthermore, expression profiling of cell cycle regulatory genes showed that abrogation of FOXF1 function resulted in increased expression of E2F-induced genes involved in promoting the progression of S and G 2 phases. Therefore, our studies have identified FOXF1 as a potential tumor suppressor gene that is epigenetically silenced in breast cancer, which plays an essential role in regulating cell cycle progression to maintain genomic stability.

Differentiation is an epigenetic program that involves the gradual loss of pluripotency and acquisition of cell type–specific features. Understanding these processes requires genome-wide analysis of epigenetic and gene expression profiles, which have been challenging in primary tissue samples due to limited numbers of cells available. Here we describe the application of high-throughput sequencing technology for profiling histone and DNA methylation, as well as gene expression patterns of normal human mammary progenitor-enriched and luminal lineage-committed cells. We observed significant differences in histone H3 lysine 27 tri-methylation (H3K27me3) enrichment and DNA methylation of genes expressed in a cell type–specific manner, suggesting their regulation by epigenetic mechanisms and a dynamic interplay between the two processes that together define developmental potential. The technologies we developed and the epigenetically regulated genes we identified will accelerate the characterization of primary cell epigenomes and the dissection of human mammary epithelial lineage-commitment and luminal differentiation.