Fig. 3
Subpopulations of malignant epithelial cells share common expression profiles. a t-SNE plot of epithelial cells showing the five identified clusters. Patient-specific effects have been excluded through linear regression analysis. b Heatmap depicting the cluster assigned to each cell (top) and the corresponding expression of three normal breast epithelial subtypes signatures: ML (mature luminal), basal, and LP (luminal progenitor). c Average expression of each of the three normal breast epithelial subtype signatures in the epithelial clusters. Clusters 2 and 4 most strongly express the LP signature, while cluster 3 most highly expresses the ML signature. d Heatmap depicting the cluster assigned to each cell (top) and the corresponding expression of the four TNBCtype-4 subtype signatures and the Intrinsic Basal signature. e Average expression of each of the four TNBCtype-4 subtype signatures in the epithelial clusters. Clusters 2 and 4 most strongly express the proliferative Basal-Like 1 signature, while cluster 3 prominently expresses this signature and the luminal AR signature. f Assignment of each TNBC epithelial cell to a single normal breast epithelial subtype signature, depending on the difference between its average expression of the upregulated genes characterizing the signature, and the average expression of the downregulated genes. The plurality of cells in all tumors is LP-like, except for tumor 84, which is predominantly comprised of ML-like cells. g Assignments of each TNBC epithelial cell to a single TNBCtype-4 subtype signature depending on the difference between its average expression of the upregulated genes characterizing the signature, and the average expression of the downregulated genes. Multiple TNBCtype-4 subtypes are expressed among the cells of each tumor
