RNA-seq profiling of single cells from normal human breast tissue reveals unexpected nuclear receptor segregation
J Dinny Graham, Heidi N Hilton, Tram B Doan, Audrey Silvestri, Barbara Guild, Nicole Santucci, Ying Cao, Christine L Clarke
The Westmead Institute for Medical Research, University of Sydney, Australia
The human breast is remarkably dynamic, undergoing multiple developmental cycles throughout adult life. The epithelial component of the breast forms a branching structure of ducts lined by a single layer of secretory luminal cells encased by contractile myoepithelial cells. Both cell types descend from a common stem cell via a hierarchy that is only partially understood, but which includes bipotent and committed progenitor stages. There is considerable interest in better elucidating the cell types and their developmental drivers as a step towards identifying the precursors of malignancy. Breast cancers are highly heterogeneous, suggesting multiple epithelial subtypes may be targets of carcinogenesis. Breast cancer is a hormone-dependent disease: most breast cancers express receptors for estrogen (ER) and progesterone (PR), and progesterone analogues are linked to increased breast cancer risk. Yet characterization to date has suggested that stem and progenitor cells are largely receptor negative, raising further questions about the cell origins of breast cancer. We conducted single cell RNA-seq in primary cultured normal breast epithelial organoids. Transcripts from sorted single cells were amplified using SmartSeq2, and sequenced on the Illumina platform. Principal component anaylsis revealed 3 major cell populations expressing known luminal, myoepithelial and progenitor markers. Expression of ER was observed in a subset of luminal cells, as expected. Strikingly, PR and ER were largely non-overlapping, and most PR+ cells coexpressed markers suggestive of progenitor properties. Moreover, PR expression tracked with higher proliferation in that cell type. Examination of the 48 members of the nuclear receptor family revealed additional receptors that discriminated lineage and developmental stage, suggesting key roles in normal breast development and biology.