Fig. 2
Clustering, genomic CNVs, and correlation maps classify most epithelial cells as malignant. a t-SNE plot of all 1112 classified cells, demonstrating separation of non-epithelial cells by cell type. b t-SNE plot of the 244 non-epithelial cells, demonstrating separation by cell type, and no distinguishable patient effect. c t-SNE plot of the 868 epithelial cells, showing mixed separation by patient, and substantial clustering of cells from different patients, suggesting pronounced intra-tumor heterogeneity. d Inferred CNVs from the single-cell gene expression data. Columns represent individual cells, and rows represent a selected set of genes, arranged according to their genomic coordinates (chromosome number indicated at left). A set of 240 normal mammary epithelial cells is shown on the left for comparison, and epithelial cells from all TNBC cases are shown, clustered separately for each patient. Amplifications (red) or deletions (blue) are inferred by computing, for each gene, a 100-gene moving average expression score, centered at the gene of interest. Prominent subclones defined by shared CNVs in tumors 39 and 81 are indicated by brackets on the top (“clonal”). e WES data for four of the six TNBC cases demonstrates high concordance with the CNV calls inferred from the transcriptomes of single cells (d). Genomic coordinates are arranged as in d from top to bottom, and mean copy number for each region (“CNV mean”) is indicated on a continuous scale, with red representing gain and blue representing loss. Accordingly, scanning from left (d) to right (e) allows for a comparison of inferred CNVs (d) and actual CNVs (e) for the same regions. f Correlation map among the expression profiles of the normal epithelial cells and the TNBC epithelial cells, depicted in the same order from left to right as d. Normal cells, as well as malignant clonal subpopulations defined by shared CNVs for tumors 39 and 81 (indicated as “clonal” at top), are correlated. The remaining non-clonal epithelial populations in all tumors show relatively poor correlation, supporting their identity as malignant cells
