Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development

Abstract

The mammary gland consists of cells with gene expression patterns reflecting their cellular origins, function, and spatiotemporal context. However, knowledge of developmental kinetics and mechanisms of lineage specification is lacking. We address this significant knowledge gap by generating a single-cell transcriptome atlas encompassing embryonic, postnatal, and adult mouse mammary development. From these data, we map the chronology of transcriptionally and epigenetically distinct cell states and distinguish fetal mammary stem cells (fMaSCs) from their precursors and progeny. fMaSCs show balanced co-expression of factors associated with discrete adult lineages and a metabolic gene signature that subsides during maturation but reemerges in some human breast cancers and metastases. These data provide a useful resource for illuminating mammary cell heterogeneity, the kinetics of differentiation, and developmental correlates of tumorigenesis.

Mammary stem cells and progenitors: targeting the roots of breast cancer for prevention

“…Claudin-low breast cancers have expression profiles similar to the mammary stem cellenriched ER-PR-subpopulation (Lim et al, 2009;Molyneux et al, 2010). Aggressive metastatic triple-negative (ER À PR À HER2 À ) breast cancers also show remarkable gene expression similarities to fetal murine mammary stem cells at embryonic days 16 and 18, stages known to have high stem cell capacity (Spike et al, 2012;Giraddi et al, 2018). Basal-like breast cancers have expression similarities to ER À PR À luminal progenitors (Lim et al, 2009;Molyneux et al, 2010;Shehata et al, 2012).…”

“…For instance, in a meta-analysis of 40 studies, BRCA1 promoter methylation was statistically significantly higher in breast cancers negative for both ER, PR and with a triple-negative phenotype (Zhang & Long, 2015). Given the current momentum in utilizing drugs tailored to epigenetic machinery in oncology, understanding the epigenomes of mammary lineages has become an active area (Maruyama et al, 2011;Pellacani et al, 2016;Dravis et al, 2018). Mammary cell proteomes have exposed the enrichment of key epigenetic regulators in the luminal lineage (Casey et al, 2018).…”

“…Despite ongoing discussion in this area, a considerable body of work supports specific mammary populations as the candidate cells‐of‐origin for breast cancer subtypes. Finally, techniques such as scRNA‐seq and mass cytometry (CyTOF) are exposing heterogeneity within the basal and luminal compartments (Bach et al , ; Pal et al , ; Giraddi et al , ; Nguyen et al , ), indicating the necessity of further dissecting precursor–progeny relationships and developmental correlates of tumorigenesis.…”

Mammary stem cells, where art thou?

“…We anticipate that advancement in single cell biology, including better analytic methods and the improvement on doing multi-omics should further extend and enhance our understanding of lineage development in the mammary gland (Kester & van Oudenaarden, 2018). 5.2 | Mammary gland stem cells are heterogeneous and likely "primed" for a certain lineage before cell differentiation Interestingly, single cell transcriptomics also have shown a surprising amount of molecular heterogeneity in the stem cell pool of the mammary gland (Giraddi et al, 2018;Wuidart et al, 2018). Similar molecular heterogeneity has been observed in other stem cell systems, including the hematopoietic stem cells (HSCs) (Laurenti & Gottgens, 2018;Paul et al, 2015), thus suggesting it is a common feature of stem cell pools.…”

“…Despite being a well-accepted concept and a long-time interest, research on embryonic mammary gland stem cells has not gained much tractions until recently (Giraddi et al, 2018;Lilja et al, 2018;Trejo, Luna, Dravis, Spike, & Wahl, 2017;Wuidart et al, 2018). This is in contrast to the research on adult stem cell biology, which has blossomed over the past decade due in a large part to a strong interest in its supposed therapeutic applications and in regenerative medicine.…”