A pilot single-cell RNA sequencing study of endothelial activation signatures in large benign prostatic hyperplasia

Benign prostatic hyperplasia (BPH) is common in aging men, but the endothelial compartment in enlarged prostates remains poorly defined. In this hypothesis-generating pilot study, we generated a single-cell RNA-seq dataset from six surgically obtained BPH specimens (three Large BPH and three Small BPH) and analyzed 56,912 cells; public datasets GSE290213 and GSE242249 were used for external context. We observed a higher sample-level fraction of Activated endothelial cells and a lower fraction of Venous-like endothelial cells in Large BPH, but these descriptive summaries were not designed for formal group inference. RNA velocity, graph ordering, and focused Slingshot/tradeSeq analyses nominated a putative endothelial-state ordering; concordance between graph pseudotime and latent time was modest (Spearman rho = 0.252). Variance decomposition suggested that AP-1/NF-κB activity was largely linked to endothelial-state composition, whereas selected IFN/HLA-II-associated programs showed stronger group-linked genetic context. MAGMA and TWAS did not support Activated endothelial markers or Large-up endothelial genes as the main genetic signal; broader stromal-vascular and HLA-related patterns were more consistent with the genetic data. These findings nominate endothelial activation signatures and a two-axis exploratory model for future validation in larger clinically annotated cohorts with protein-level testing.