In silico Computed Clusters of Prostate Luminal Progenitors Match FACS-Enriched LSCmed cells

Several groups recently published single-cell (sc) expression atlases of the adult mouse prostate cells based on RNA sequencing (scRNA-seq) data. All studies identified one computerized cluster of non-secretory luminal progenitor cells enriched in luminal and stemness-related gene transcripts. The actual correspondence between these luminal progenitor cell clusters has not been investigated. In addition, the presence of Krt4 (encoding cytokeratin 4) in these in silico-identified luminal progenitors suggested the overlap with FACS-enriched LSCmed luminal progenitor cells earlier identified as a stem-like, castration-tolerant and tumor-initiating cell population. Here, we used a unified bioinformatics pipeline to re-analyze published prostate scRNA-seq datasets and perform various pan-transcriptomic comparisons including the LSCmed cell signature. Our study demonstrates that i) the mouse prostate luminal progenitor cell clusters identified in the different scRNA-seq studies largely overlap and can be defined by a common 15-gene signature including Krt4, ii) mouse LSCmed cells match both mouse and human luminal progenitors identified by scRNA-seq analysis. Bridging these in silico-identified and ex vivo-characterized prostate luminal progenitor subsets should benefit our understanding of their actual involvement in prostate diseases.

Time-resolved single-cell analysis of Brca1 associated mammary tumourigenesis reveals aberrant differentiation of luminal progenitors

It is unclear how genetic aberrations impact the state of nascent tumour cells and their microenvironment. BRCA1 driven triple negative breast cancer (TNBC) has been shown to arise from luminal progenitors yet little is known about how BRCA1 loss-of-function (LOF) and concomitant mutations affect the luminal progenitor cell state. Here we demonstrate how time-resolved single-cell profiling of genetically engineered mouse models before tumour formation can address this challenge. We found that perturbing Brca1/p53 in luminal progenitors induces aberrant alveolar differentiation pre-malignancy accompanied by pro-tumourigenic changes in the immune compartment. Unlike alveolar differentiation during gestation, this process is cell autonomous and characterised by the dysregulation of transcription factors driving alveologenesis. Based on our data we propose a model where Brca1/p53 LOF inadvertently promotes a differentiation program hardwired in luminal progenitors, highlighting the deterministic role of the cell-of-origin and offering a potential explanation for the tissue specificity of BRCA1 tumours.

Integrating Single Cell RNA-Sequencing Analyses and Functional Assays to Decipher Cell Differentiation Hierarchies in the Mammary Epithelium

The identification and molecular characterization of cellular hierarchies in complex tissues is key to understanding both normal cellular homoeostasis and tumorigenesis. The mammary epithelium is a heterogeneous tissue consisting of two main cellular compartments, an outer basal layer containing myoepithelial cells and an inner luminal layer consisting of estrogen receptor negative (ER-) ductal cells and secretory alveolar cells (in the fully functional differentiated tissue) and hormone responsive estrogen receptor positive (ER+) cells. Recent publications in Nature Communications used single cell RNA-sequencing (scRNA-seq) analysis to decipher epithelial cell differentiation hierarchies in human (Nguyen et al., 2018) and murine (Pal et al., 2017) mammary glands and report the identification of new cell types based on the expression of the luminal progenitor cell marker KIT (c-Kit). However, there are several inaccuracies and unfortunate omissions in the citation of previous research in each of these studies. As a result, the overall conclusions on the significance of these reports, in particular the claimed identification of new cell types is not accurate. Here we discuss these studies in the context of our previous research (Regan et al., 2012), in which we identified c-Kit as a luminal progenitor cell marker and functionally characterized cellular subpopulations analogous to those reported in the recent scRNA-seq studies.