Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks

Abstract

The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines. Each genome-wide analysis contains profiles for six histone marks, methylated DNA, and RNA transcripts. Analysis of these datasets shows that each cell type has unique features, primarily within genomic regulatory regions, and that the cell lines group together. Analyses of the promoter and enhancer profiles place the luminal progenitors in between the basal cells and the non-progenitor luminal subset. Integrative analysis reveals networks of subset-specific transcription factors.

Epigenomics of mammary gland development

“…Luminal cells differentiate into milk-secreting alveolar cells in preparation for lactation, which results in decreased repressive marks and increased active marks in key luminal differentiation and milk-production genes. Similar results were found in sorted human mammary epithelial populations [28, 40]. Interestingly, the genes repressed in luminal and basal subsets are often present in large regions enriched for H3K27Me3 marks (K27 blocs), which may allow for cell-type specific co-ordinated gene silencing [28].…”

“…The diverse chromatin states that distinguish between mammary epithelial subpopulations are as extensive as those that distinguish epithelial subpopulations from developmentally unrelated stromal cells [40]. The largest variations in chromatin state occurred in enhancer regions, although there were also significant variations in promoter regions [40]. This shows that the chromatin state of cell-specific regulatory elements is a key determinant of cell type, even within the same epithelial lineage.…”

“…Luminal progenitor cells have intermediate promoter features between basal and mature luminal cells. For example, promoters of genes involved in basal functions (such as extracellular matrix organisation) are marked by H3K4Me3 in basal cells, are bivalent in luminal progenitors, and are marked with H3K27Me3 in mature luminal cells [40]. This corresponds with a decrease in gene expression [40].…”

Basal-like Breast Cancers: From Pathology to Biology and Back Again

“…The human CD49f + KIT + luminal (EpCAM + CD24 + CD133 + ) cells thus obtained display quite different molecular features and functional properties than the luminal cells that are CD49f − and KIT − . These include differences in expression of epidermal growth factor receptors (EGFR), which are higher on the CD49f + subset of luminal cells (Pellacani et al., 2016, Visvader and Stingl, 2014), and are coupled with a selective ability to proliferate in response to EGF stimulation (in concert with other factors) in vitro, a property shared with some CD49f + basal cells (Kannan et al., 2013, Kannan et al., 2014). Interestingly, the CD49f + EpCAM + luminal cells generate only progeny with features of luminal cells, whereas the CD49f + basal cells make both basal and luminal progeny (Raouf et al., 2008).…”

“…The cells in this subset also contain, and are resistant to, higher levels of reactive oxygen species, which results in their accumulation of detectable oxidative DNA damage (Kannan et al., 2014). Comprehensive epigenomic and deep global transcriptome data further underscore the biologic differences exhibited by these three phenotypes of normal human mammary cells: i.e., EpCAM + luminal cells with and without surface CD49f, and EpCAM − basal cells that are also CD49f + (Kannan et al., 2013, Lim et al., 2009, Pellacani et al., 2016, Raouf et al., 2008). …”