Extended Data Fig. 6: Cell state heterogeneity in primary patient samples, PDX models, single cell engrafted tumors and RD cells grown in mouse xenografts.
a–c, 3D renderings of gene expression for muscle (x axis), proliferation (z axis), mesenchymal-like (y axis) gene modules identified in RMS samples (a, FN-PDXs; b, FP-PDXs; c, primary patient samples). Individual cells are noted by dots and color coded based on cell assignments shown in Fig. 1d. Not detected (ND) denotes lack of a given cell state both in the initial UMAP cell cluster annotations and in 3D gene expression space. d, Combined UMAP visualization for all parental PDXs profiled (n = 10, and includes both replicates of MAST85) and single cell derived PDXs (n = 3). See Supplementary Table 1 for detailed information and cell numbers. e,f, Single cell RNA sequencing of RD xenograft (n = 2,619 tumor cells profiled). Heatmap showing single cells (x axis) and genes enriched for specific transcription modules (y axis, e). Cells are arranged by UMAP clusters, combined based on expression similarity, and then assigned a specific cell state as noted. f UMAP rendering of xenografted RD cells following single cell sequencing (left) and quantification of cell state composition of all 2,619 RD cells profiled (right). Similar cell states are observed in RD cells raised in 2D cell culture (see Fig. 3).
