Fig. 3: Increased SCHLAP1 and JAG1 in prostate ICC/IDC.

a Unsupervised graph-based clustering of epithelial cell clusters (2, 5, 6, 10, 11, 12, 21) separated by benign-enriched and ICC/IDC-enriched prostate. b, c Violin (b) and feature (c) plots of gene expression in epithelial cell clusters. d, e Representative images at 20x, bar = 10 µm (d) and quantification (e) of SCHLAP1 and JAG1 expression by RNAscope in ICC1-7 at RP for benign prostate luminal epithelial cells, Gleason pattern 3 prostate cancer, and ICC (n = 7 biologically independent samples). Quantification of SCHLAP1 and JAG1 in an extended validation RP cohort of benign prostate luminal epithelial cells (n = 20) as well as Gleason pattern 3 (n = 18), Gleason pattern 4 non-ICC (NC) (n = 14), ICC/IDC (n = 11), and Gleason pattern 5 (n = 6) prostate cancer. A total of n = 23 biologically independent samples were assessed for SCHLAP1 and JAG1 expression with samples having more than one histology. Quantification of SCHLAP1 and JAG1 expression by H-score (intensity x percent expression). Graphs are shown as mean ± SEM and analyzed by one-way ANOVA with Tukey’s multiple comparisons. f PssGSEA of hallmark pathways altered in ICC/IDC cancer cells (clusters 5, 6, and 11) compared to benign luminal epithelial cells in cluster 12. g Kaplan–Meier and log-rank test of progression-free survival in the TCGA PanCancer Atlas prostate adenocarcinoma for JAG1 by median expression (n = 492). h Percent of patient cells per cluster after re-clustering clusters 5, 6, and 11 into 7 clusters (CRIB-0 through CRIB-6). i, j UMAP visualization of re-clustering of clusters 5, 6, and 11 (CRIB-0 through CRIB-6) color-coded by cluster (i) and by patient (j). k Violin plots of gene expression in CRIB-0 through CRIB-6. l PssGSEA of hallmark pathways altered in benign epithelial clusters in ICC/IDC-enriched prostate compared to benign-enriched prostate. Source data are provided as a Source Data file.