The study of mammary epithelial cell differentiation dynamics and breast cancer development by single cell RNA sequencing


Session type:


Walid Khaled1,Sara Pensa2,Kyren Lazarus1,Karsten Bach3,Maria Francesca Santolla3,Jason Carroll4,David Adams5,Carlos Caldas4,John Marioni4
1University of Cambridge,2University Cambridge,3Univeristy of Cambridge,4University of Cambridge - CI,5Sanger Institute



Characterising the hierarchy of mammary epithelial cells (MECs) and how they are regulated during adult development is important for understanding how breast cancer arises.  


Here we report the use of single-cell RNA sequencing (scRNAseq) to determine the gene expression profile of MECs across four developmental stages in wild type (WT) mice and during early stages of triple negative breast cancer (TNBC) development in the p53/Brca1 mouse model.


Our analysis of 23,184 cells across the four developmental time points identifies 15 clusters of MECs, few of which could be fully characterised by a single marker gene. We argue instead that the epithelial cells especially in the luminal compartment should rather be conceptualised as being part of a continuous spectrum of differentiation. Furthermore, our data supports the existence of a common luminal progenitor cell, giving rise to intermediate, restricted alveolar and hormone-sensing progenitors (Bach K. et al. Nat. Comm 2017). Understanding the biology of luminal progenitor cells is important given their proposed cell of origin role in TNBC. We then performed scRNAseq combined with genetic lineage tracing and in situ imaging to show that the transcription factor Bcl11a, a gene upregulated in TNBC, is expressed in long-lived luminal progenitor cells that expand in response to MPA/DMBA mediated oncogenesis. Furthermore, we show that deletion of Bcl11a protects mice from developing tumours in the Brca1/p53 mouse model of TNBC. Single cell transcriptomics of pre-cancerous MECs revealed that the luminal progenitor compartment in the Brca1/p53 mouse model undergoes aberrant differentiation towards secretory cells, which in WT mice are only found during pregnancy/lactation. Interestingly, Bcl11a deletion fully reverses this abnormal phenotype.


In summary, our results provide an unbiased view of adult MEC differentiation and calls for a review of the protective effects of parity in BRCA1 mutation carriers.