Transcriptional changes in the mammary gland during lactation revealed by single cell sequencing of cells from human milk

Findings: from epidemiological studies suggest that breast cancer risk is influenced by parity in an age-dependent manner. However, human mammary tissue remodelling that takes place during pregnancy and lactation remain little understood due to the challenge of acquiring samples. Here, we present an approach to overcome this using single-cell RNA sequencing to examine viable primary mammary epithelial cells isolated from human milk compared to resting, non-lactating breast tissue. Thereby, we determined that separate to breast tissue, human milk largely contains epithelial cells belonging to the luminal lineage, as well as immune cells. Our data reveal the presence of two distinct secretory luminal cell clusters in milk which highly express luminal progenitor signatures akin to non-lactating breast tissue luminal cells. Taking advantage of the fact that both the resting and lactating mammary gland contain a luminal compartment, we focussed on comparing these transcriptomes and identified differences in mammary cell function and metabolism between these maturation states. These findings provide the basis to dissect human luminal differentiation and milk biosynthesis pathways that in the future, may be interrogated to determine how parity influences luminal cell metabolism and breast cancer risk.