Gene expression profiling of three human prostate epithelial subpopulations

The human prostate epithelium is predominantly comprised of two cell-types: basal and luminal. While basal cells exhibit significant progenitor activity in a variety of functional assays, luminal cells are depleted of this activity. Recent studies indicate that approximately 1% of luminal cells exhibit progenitor activity. We have discovered that differential expression of the glycoprotein CD38 can fractionate the luminal population into two subsets: CD38+ and CD38-low. In functional assays, the CD38-low luminal cells exhibit roughly 5-fold increased progenitor activity compared to the remaining CD38+ population. Therefore, we propose that CD38-low luminal cells represent an enriched luminal progenitor population while the CD38+ subset is predominantly comprised of mature non-progenitor luminal cells. In this microarray experiment, we have performed expression profiling of three epithelial subsets (basal, CD38-low luminal progenitor, and CD38+ mature luminal) purified by Fluorescence Activated Cell Sorting from the benign prostate of four different patients. Benign human prostate from four different patients, provided to researchers in a de-identified manner, were enzymatically and mechanically digested to single cells using a combination of collagenase, dispase and trypsin as described in Goldstein et al (Nature Protocols, 2011). Single cells were stained for antibodies against CD45, EpCAM, CD49f and CD38. CD45-EpCAM+ epithelial cells were further sorted into basal (CD49f-hi), luminal progenitor (CD49f-lo CD38-lo) and mature luminal (CD49f-lo CD38+). Cell pellets were frozen and later lysed in buffer RLT to isolate RNA using the Qiagen RNEasy micro kit. Samples were subjected to microarray analysis on the Affymetrix platform at the UCLA Clinical Microarray Core.