Functional heterogeneity of mouse prostate stromal cells revealed by single cell RNA-seq

We perform a single cell RNA-seq analysis to investigate the phenotypic and functional heterogeneity of the adult mouse prostate stromal cells. Our analysis identifies three major cell populations representing the smooth muscle cells and two types of fibroblast cells enriched by CD90 and CD34, respectively. The CD90+ stromal cells are in direct contact with the epithelial cells and express plentiful growth factors and genes associated with cell motility, developmental process, and androgen biosynthesis. This suggests that they may regulate epithelial cell survival and growth. The CD34+ stromal cells highly express genes associated with the extracellular matrix and cytokine-mediated signaling pathways, indicating a role in tissue repair and immune responses. The CD34+ stromal cells significantly suppress the luminal differentiation of the basal cells in the organoid culture assay. Our study identifies novel surface markers enabling physical separation of stromal cell subpopulations and generate gene expression profiles that imply their cellular functions. Prostate stromal cells were FACS-isolated from 8-10 week old C57Bl/6 mice based on their surface antigen expression profile (Lin-CD24-CD49f-). We employed the iCell8 single cell system from Wafergen BioSystems for single cell capture to achieve an intermediate in-depth expression profiling of single prostate stromal cells. In-chip RT-PCR amplification and single cell RNA-seq library construction were performed following the iCELL8 single cell polyA transcriptome amplification hands-on workflow checklist and preparation guide.