Androgen Deprivation Alters the Transcriptome of Endothelial Cells More Dramatically in Human Prostate Cancer Tissue than in Benign Prostate Tissue. Androgen Deprivation Alters the Transcriptome of Endothelial Cells More Dramatically in Human Prostate Cancer Tissue than in Benign Prostate Tissue

Purpose: Examine the cell type specific (Epithelial, Endothelial, and Stromal) transcriptome profile between prostate primary tissue xenografts of prostate tissue tumor tissue and uninvolved tissue (named non-tumor hereafter) in response testosterone (T) deprivation. Additional cell type specific untreated fresh tissue from both tumor and non-tumor samples is included for additional validation. Related samples previously uploaded to GEO are found under accession number GSE145641. Method: Nude-Fox1nu mice were castrated and silastic tubing containing dry T was inserted providing “humanized” levels of circulating T. 5-8 pieces of fresh human prostate tissue was then inserted subcutaneously along the flank of the animal. For samples not subjected to T-deprivation, after 30 days the animal was euthanized, and tissue was harvested. For samples undergoing T-deprivation, after 30 days with humanized circulating T levels, T-deprivation was performed by surgical removal of silastic tubing after which serum T levels dropped below the level of detection within 24 hours. Samples were then harvested at Pre T-deprivation time point, an early T-deprivation time point (3-days) or late T-deprivation timepoint (15-17 days) post-surgery. Tissue from fresh human prostate or tissue from xenograft and was then enriched into endothelial, epithelial and the remaining stromal compartments using magnetic bead enrichment. RNA-Seq was then preformed on cell types from both origins and the results compared to determine the cell type specific effects of T-deprivation on the human prostate transcriptome. Overall design: This data set contains 127 samples from 24 individuals across three cell types (Endothelial, Epithelial, and Stroma) across two tissue types (tumor and non-tumor) and in both Fresh prostate Xenografts and fresh prostate tissue. Samples from fresh porstate xenografts were subjected to T-deprivation and harvested at one of three timepoints (Pre T-deprivation, Early T-deprivation (3 days), or late T-deprivation (15-17 days))