Fig. 3: PyMT⁺ cells in primary and relapsed tumors.

a UMAP visualization of epithelial cell heterogeneity. Tspan8⁺ and Aldh1a3⁺ cancer stem cell populations are demarcated with black dashed lines. A Sankey plot compares the frequencies of different epithelial subsets. b RNA velocity-based pseudo-temporal trajectory of epithelial subtypes using partition-based graph abstraction. Arrows indicate predicted differentiation directions. c UMAP projection demonstrating PyMT expression restriction to Ly6a⁻ cells. d InferCNV analysis comparing aneuploidy scores between Ly6a⁻ and Ly6a⁺ epithelial cells. e Gene set enrichment analysis revealing upregulation of estrogen response pathway in PyMT⁻ Ly6a⁺ epithelial cells. f UMAP showing cellular composition of myoepithelial cells (yellow) and epithelial cells (cyan). Feature plots showing the expression of PyMT and other EMT markers. g InferCNV analysis showing that a myoepithelial subpopulation shares aneuploidy score with PyMT⁺ epithelial population. h Differential gene set analysis showing significant upregulation of mesenchymal signatures in PyMT⁺ myoepithelial versus PyMT⁺ epithelial cells.