Extended Data Fig. 4: Gene signatures of malignant cell types.
a) Sankey plot (left) shows the distribution and relationship of n = 2,520 cells assigned to malignant clusters 1 and 2 versus NSC-like, intermediate, and neuron-like clusters. NSC-like and neuron-like cells almost entirely derive from malignant clusters 1 and 2, respectively. The intermediate population derives from both malignant clusters. Bar plot (right) shows the fractions of malignant cell types per fresh-sorted ETMR sample. b) Heatmap shows relative expression of signature genes specific to cycling, NSC-like, intermediate, and neuron-like cells in the fresh-sorted ETMR scRNAseq dataset (n = 2,520 cells). Sample annotation, cycling cells, and cell type assignment are indicated on top of the heatmap. Genes of interest are highlighted on the right. c) Proportional venn diagrams highlight the overlap of genes associated with different single cell-derived signatures. d) Sankey plot (left) shows the distribution and relationship between n = 2,520 cells assigned to the NSC-like, intermediate, and neuron-like clusters versus the cell cycle state. Bar plot (right) shows the fractions of cycling and non-cycling cells per fresh-sorted ETMR sample. e) tSNE visualization of the fresh-sorted ETMR scRNAseq dataset (n = 2,520 cells), overlaid with differentiation trajectories defined by RNA velocity analysis. f) Images show representative multiplexed immunofluorescence stainings of three primary ETMR samples for PAX6 (NSC-like cells, red), NEUROD1 (Intermediate cells, green) and PEG3 (neuron-like cells, magenta) TFs. Scale bars = 500 µm. This experiment was performed at least three times for each tumor sample. g) Pseudo images of in silico phenotyped cells of the images shown in panel (f). Coordinates and phenotypes of cells were determined as described in the methods. Pseudo images are resolved by marker genes PAX6 (NSC-like cells, red), NEUROD1 (Intermediate cells, green) and PEG3 (neuron-like cells, magenta). This experiment was performed at least three times for each tumor sample. Related to Fig. 2.
