Molecular targeted approaches have broadened the treatment options for breast cancer and have significantly improved therapeutic outcomes. Gene expression-based molecular subtyping has also been broadly applied to breast cancer to aid treatment decisions 3, 4. Genome alteration-matched treatment of breast cancer to target amplification of human epidermal growth factor receptor 2 gene (Erb-B2 receptor tyrosine kinase 2, ERBB2 also known as HER2) is an example of a successful gene-targeted therapy 2. Many molecular-targeted treatments for breast cancer have been evaluated since the application of endocrine therapy for oestrogen receptor (ER)-positive tumour types 1. These results illustrate that the breast cancer transcriptome has a wide range of intratumoral heterogeneity, which is shaped by the tumour cells and immune cells in the surrounding microenvironment. T lymphocytes and macrophages both display immunosuppressive characteristics: T cells with a regulatory or an exhausted phenotype and macrophages with an M2 phenotype. Most of the non-cancer cells are immune cells, with three distinct clusters of T lymphocytes, B lymphocytes and macrophages. At a single-cell resolution, carcinoma cells display common signatures within the tumour as well as intratumoral heterogeneity regarding breast cancer subtype and crucial cancer-related pathways. Inferred copy number variations from the single-cell RNA-seq data separate carcinoma cells from non-cancer cells. Here we adopt this powerful approach to breast cancer and analyse 515 cells from 11 patients. Single-cell transcriptome profiling of tumour tissue isolates allows the characterization of heterogeneous tumour cells along with neighbouring stromal and immune cells.
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