Niche-labeled single-cell RNA-seq analysis of breast cancer metastatic ecosystems in brain, lung, liver, and bone.

Metastasis frequently affects multiple organs in stage IV breast cancer patients and is associated with dismal outcomes. The mechanisms enabling cancer cell colonization across diverse anatomical sites remain poorly understood, mainly due to lack of models of systemic disease and of studies in clinical samples involving multiple metastatic sites. Here, we combined metastatic niche labeling with single-cell RNA sequencing (scRNA-seq) in a mouse model of breast cancer multi-organ metastasis, and generated a cellular and molecular atlas of metastatic ecosystems encompassing >70,000 cells across brain, lung, liver, and bone.