Extended Data Fig. 4: Cell lines recapitulate programs of heterogeneity observed in tumor samples.
From: Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity
a–d, Combined PCA of in vitro and in vivo cells in melanoma (A-B) and HNSCC (C-D). (a, c) Top 10 genes by positive (left) and negative (right) loadings of PC1–5; Genes of respective RHPs (SkinPig. and EMT-I in melanoma, EpiSen and EMT-II in HNSCC) are emphasized (bold). (b, d) Coordinates of the three PCs associated with the respective RHPs across in vitro (left, melanoma = 3,033 cells, HNSCC = 2,780 cells) and in vivo (right, melanoma = 1,169 cells, HNSCC = 1,078 cells) cells. Cells are colored by their cell line or tumor. Similar results were obtained when PCs were not combined (not shown). (e) Heatmap shows relative expression of genes shared by paired in vivo and in vitro programs in selected melanoma (top panels) and HNSCC (bottom panels) cell lines and tumors, highlighting similar patterns of variability in vivo and in vitro. Cells are sorted according to the relative average expression of genes in each program, showing the negative correlation between the AXL and MITF programs in melanomas and the pEMT and EpiSen programs in HNSCC. Programs are annotated (right) and selected genes are indicated (left).
