Single-cell transcriptional profiling of indolent and aggressive mammary lesions

We performed transcriptional profiling of tumor cells from indolent and aggressive lesions isolated from a mouse model of breast cancer. To initiate formation of mammary lesions, we delivered lentiviral particles carrying constitutively-activated Erbb2 tagged with HA and GFP (caErbB2) through the lactiferous glands of adult virgin female. Mammary glands bearing lesions were visualized under a fluorescence stereoscope, and regions harboring aggressive (>2mm, comprised of invasive lesions) and indolent (<2mm, enriched for in situ lesions) lesions were dissected away from each other. Lesions from multiple animals were pooled to obtain sufficient material for downstream analysis. Following tissue digestion, GFP-expressing epithelial cells and CD45+ immune cells were isolated by fluorescence-activated cell sorting (FACS), and then subjected to single-cell RNA-sequencing. Single-cell transcriptional profiles of tumor and immune cells from indolent and aggressive mouse mammary lesions were generated from a pool of animals