Abstract Introduction: Recent studies have shown that cells undergoing oncogenic processes usurp normal developmental pathways to escape regulators of unsolicited growth. Basal to luminal differentiation dynamics in the prostate serves as a cellular process that can go awry, the dysregulation of which can enable oncogenesis in the prostate. Studies have found stem-like cells in prostate epithelium and speculate those to be cells of origin in prostate cancer. Methods and Results: Through single-cell RNA sequencing we investigated basal to luminal differentiation of normal human prostate epithelial cells across timepoints Days 0, 4, 8, 12, 16, and 20 by stimulating with FGF-7 (20ng/mL) and R1881 (10nM) and explored the data to identify unique populations present in the differentiation process. Our results show spatial and temporal segregation with distinct transcriptomics profile at Days 0, 8, 16, and 20. As expected, populations present at Day 0 are also present across all timepoint, though enrichment of various distinct populations emerged throughout the differentiation process. Using trajectory analysis (Monocle3) and the Cell Surface Protein Atlas, we profiled surface proteins for each cluster and identified a set of unique surface markers (SLC3A, LYPD3, TACSTD2, DSC2) from undifferentiated basal cells that express both basal (TP63+, K14+) and luminal markers (K8+, K18+), potentially serving as the bi-potent prostate epithelial cells. We further investigated our data and identified a stem-like cell (CD24+/LCN2+/KRT13+/SERPINB1+/S100A6+) population present in basal cells which was also positive for NOTCH3, a known regulator of prostate basal to luminal differentiation. Using PISCES for scRNA-seq dataset, we identified several candidate genes regulatory networks and their protein activity in the differentiation process. Conclusion: Our data have identified unique bi-potent epithelial and stem-like populations present in our human prostate differentiation model expressing both luminal and basal signatures which can be isolated using identified surface markers to investigate the role of bi-potent cells in prostate differentiation and oncogenesis. These cells exhibit markers that are known to arise in human prostate tumors. Citation Format: Hunain Khawaja, Cynthia Miranti. Identifying the regulatory network of stem-like prostate epithelial cells through scRNA-seq abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86 (2Suppl): Abstract nr B036.
Khawaja et al. (Tue,) studied this question.