Fig. 4: Transcriptional states in enzalutamide resistance.

a Average expression of cell cycle-related genes (S- and G2/M phases) in cells from the single-cell (sc) RNA-seq data. b, c Dot plot of average gene expression of the b indicated genes and of the c genes within the Persist signature in each scRNA-seq cluster. The size of the dot reflects the percentage of cells in the cluster that express each gene. d Uniform manifold approximation and projection (UMAP) visualization showing the average expression score of each cell for the genes in the PROSGenesis gene signature derived from Karthaus et al.³⁰. e Cells in VCaP and VCaP–ENZ48 (enzalutamide treated for 48 h) scored for their expression of Persist and PROSGenesis gene signatures. f Boxplots of predicted cluster-differentiation states in the four LNCaP scRNA-seq samples based on cytoTRACE. Each cell is visualized as a point within its scRNA-seq cluster. Clusters are ordered from left to right in order of decreasing predicted differentiation potential. The scRNA-seq clusters are labeled with numbers. The boxplots show the 25th percentile, median, and 75th percentile, with the whiskers indicating the minimum and maximum values within the 1.5x interquartile range. The two-sided Wilcoxon rank sum test was used to assess for differences in average cluster cytoTRACE scores and p-values are shown within the figure (n = 111, 106, 122, and 126 for cluster-11 cells in LNCaP, LNCaP-ENZ48, RES-A, and RES-B; n = 127, 160, 379, and 226 for cluster-9 cells in LNCaP, LNCaP-ENZ48, RES-A, and RES-B; and n = 135, 451 for cluster-8 cells in LNCaP–ENZ48 and RES-A). g RNA velocities based on scRNA-seq depicted as streamlines. Clusters are shown in different colors and are numbered. ENZ = enzalutamide. See also Supplementary Fig. 4.