Fig. 6: Transcriptional signal enrichment analysis identifies treatment-persistent cells in prostate cancer.

a t-Distributed stochastic neighbor embedding (tSNE) visualization of cell types from 13 treatment-naive prostate tumors from Chen et al.³⁸. b Gene set variation analysis (GSVA) enrichment scores for gene signatures in luminal, basal/intermediate, and fibroblast cells from Chen et al. GSVA enrichment scores were generated from the average expression profile of each cell type. c-d tSNE plot of prostate tumor cells from Chen et al. colored according to their average expression of the genes in c the Persist signature and d the PROSGenesis signature. The adjacent histograms show the distribution of average expression scores in the cells, with a red dashed line marking the 90th percentile of scores. e Percentage of cells scoring at or above the 90th percentile for the Persist and PROSGenesis signatures belonging to each prostate tumor from Chen et al. f–h Spatial transcriptomics (ST) from a prostate cancer tissue section, Prostate A. f The left panel shows the hematoxylin and eosin (H&E) staining of the tissue section. In the middle, the uniform manifold approximation and projection (UMAP) visualization shows the clusters of spots on the ST slide. Each cluster is labeled according to its histological tissue type, with BE referring to benign epithelium. The right panel shows the UMAP clusters of spots overlaid on the H&E slide. g Sensitivity analysis of Persist and PROSGenesis signatures scores in ST against the score distributions of control housekeeping gene signatures (see “Methods”). h The leftmost panel shows the ST UMAP clusters of spots overlaid on the H&E slide. Each spot was scored according to its expression of genes in the Persist, PROSGenesis, and cluster-10 signatures. For each signature, spots scoring at or above the 90th percentile (high) are colored in red, while spots scoring below the 90th percentile (low) are colored in yellow. The barplots indicate the percentage of spots in each cluster scoring high or low for each signature. The bars are labeled with the cluster histology and the cluster number in parentheses, with BE referring to benign epithelium. Differences in proportions of high-scoring spots between clusters were tested with the chi-square test. See also Supplementary Fig. 6.