Fig. 2: A Prostate Tumor Gene Signature distinguishes normal and malignant luminal epithelial cells.

a Joint embedding represent the detailed annotation of epithelial subpopulations in prostate tissues. b RNA velocity analysis of the transitions of epithelial cells, estimated on different sample fraction. c Violin plot showing the expression of genes panel of “Prostate Tumor Gene Signature” in malignant cells and in the epithelial luminal cells of healthy, adj-normal, and tumor prostate samples. d Boxplot representing the epithelial-mesenchymal transition (EMT) score in malignant cells (n = 6) and the luminal epithelial cells of healthy (n = 5), adj-normal (n = 14), and tumor (n = 17) prostate samples. The box is bounded by the first and third quartile with a horizontal line at the median and whiskers extend to the maximum and minimum value. Significance was assessed using two-sided Wilcoxon rank-sum test (Malignant vs. adj-normal *p = 0.02; Malignant vs. Healthy *p = 0.03). e Spatial presentation of epithelial subpopulations in healthy (n = 4), adj-normal (Adj-normal LG n = 2) and two tumor tissues collected from low-grade (Tumor-LG n = 2) and high-grade (Tumor-HG n = 2) patients. Patinets ID from Supplementary Data 2 represented here as healthy is HP1, adj-normal of LG case is Benign04, tumor tissue of LG case is Tumor08, tumor tissue of HG case is Tumor02. f Dotplot representing key-marker genes expression in epithelial subpopulations in Slide-seqV2. The color represents scaled average expression of marker genes in each cell type, and the size indicates the proportion of cells expressing marker genes. g Spatial presentation for “Prostate Tumor Gene Signature” average expression in healthy, adjacent-normal (HG) and tumor (HG) Slide-SeqV2 pucks. h A schematic view of the admixture problem in the Slide-seqV2 puck. The barplot shows the cell type composition in two different contexts within the same puck. The barplot related to the tumor context contains substantial admixture from nearby tumor cells whereas the one related to tumor-adjacent context is a heterogeneous mixture of different cell types. Source data are provided as a Source Data file.