Fig. 3

Analysis of ProstaTrend genes in the developed PCa single-cell atlas. A We embedded about 90,000 cells of 41 PCa patients from 5 publicly available datasets (Chen et al. 2021; Dong et al. 2020; Ma et al. 2020; Song et al. 2022; Tuong et al. 2021) into a two-dimensional space by the t-distributed stochastic neighbor embedding (tSNE) method. Each dot represents a single cell. Cells are colored according to cell identity. B We applied a simplified TRS to each cell from the tumor samples using the ProstaTrend and ProstaTrend-ffpe signatures. Each area containing cells on the tSNE was divided into hexagonal bins, and cells within each bin were averaged. The bins are colored according to TRS. C For tumor samples, TRS were grouped based on the ProstaTrend(-ffpe) signatures and colored according to luminal and tumor-specific luminal (T-luminal) cells (****p-value < 0.0001, Wilcoxon rank-sum test). PT ProstaTrend, PT-ffpe ProstaTrend-ffpe. The y-axis depicts the TRS. D UpSet plot of ProstaTrend(-ffpe) DE genes (FDR < 0.05) of four cell lineages. The squares in the matrix represent unique or overlapping DE genes for the cell lineages. The stacked bar graph above the matrix summarizes the number of ProstaTrend(-ffpe) DE genes for each unique lineage. The top stacked bar plot shows the fraction of DE genes with log hazard ratio > 0 or < 0. E Heat map of the highest ranked DE genes for the ProstaTrend(-ffpe) genes. Genes are ranked by log2 fold change. 15 genes (if present) are depicted for each cell lineage. Each column depicts the average expression value for one patient, grouped by cell lineage and tissue source. Average gene expression values are standardized. F UpSet plot of ProstaTrend(-ffpe) DE genes for cell types. G Pathological annotations of a human prostate stage III adenocarcinoma biopsy, which was FFPE preserved and processed using the Visium spatial gene expression for FFPE workflow. H Standardized overall enrichment (OE) scores of cell type markers for each spot were estimated using the AddModuleScore function implemented in Seurat. I OE of DE genes (T-luminal vs. luminal cells from the PCa Cell Atlas) for each spot. J TRS was applied to gene expression spots using the ProstaTrend(-ffpe) signatures