A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells

Summary Single-cell RNA sequencing (scRNA-seq) is an evolving technology used to elucidate the cellular architecture of adult organs. Previous scRNA-seq on breast tissue utilized reduction mammoplasty samples, which are often histologically abnormal. We report a rapid tissue collection/processing protocol to perform scRNA-seq of breast biopsies of healthy women and identify 23 breast epithelial cell clusters. Putative cell-of-origin signatures derived from these clusters are applied to analyze transcriptomes of ~3,000 breast cancers. Gene signatures derived from mature luminal cell clusters are enriched in ~68% of breast cancers, whereas a signature from a luminal progenitor cluster is enriched in ~20% of breast cancers. Overexpression of luminal progenitor cluster-derived signatures in HER2+, but not in other subtypes, is associated with unfavorable outcome. We identify TBX3 and PDK4 as genes co-expressed with estrogen receptor (ER) in the normal breasts, and their expression analyses in >550 breast cancers enable prognostically relevant subclassification of ER+ breast cancers.
Graphical abstract
Highlights Healthy breast contains 23 subclusters of epithelial cells Breast cancers may originate from 3 luminal mature and 1 progenitor subclusters TBX3 and PDK4, co-expressed with estrogen receptor (ER), subclassify ER+ breast cancers
Bhat-Nakshatri et al. describe the single-cell atlas and document 23 epithelial cell subclusters in the healthy breast. Although experimentally validating cell of origin of a tumor is technically challenging, overlap analysis of subcluster-enriched gene signatures with breast tumor transcriptomes revealed dominant representation of differentiated luminal subclusters-derived signatures in breast cancers.