A spatially resolved single-cell genomic atlas of the adult human breast

The adult human breast is comprised of an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue 1 – 3 . Although most previous studies have focused on the breast epithelial system 4 – 6 , many of the non-epithelial cell types remain understudied. Here we constructed the comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics study profiled 714,331 cells from 126 women, and 117,346 nuclei from 20 women, identifying 12 major cell types and 58 biological cell states. These data reveal abundant perivascular, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Spatial mapping using four different technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide a reference of the adult normal breast tissue for studying mammary biology and diseases such as breast cancer. The Human Breast Cell Atlas identifies 12 major breast cell types and 58 biological cell states, revealing abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states.