Gene Expression Profiling of Prostate Benign and Malignant Tissue

We profiled genome-wide gene expression of human prostate benign and malignant tissue to identify potential biomarkers and immunotherapy targets. We stratified malignant specimens according to their TMPRSS2:ERG gene fusion status. Radical prostatectomy tissue samples were obtained from the Hershey Foundation Prostate Cancer Serum and Tumor Bank at our institution. Morphologic diagnosis was done by a pathologist. OCT blocks containing >30% of PCa tissue (with Gleason score of 6 or 7) were selected for RNA purification. A biopsy punch was used to select the PCa tissues from the OCT sample blocks. Benign or PCa tissues were homogenized using a TissueLyser (Qiagen) at 28 Hz for 5 min. Total RNA was isolated using Trizol reagent. RNA was quantified by NanoDrop ND-1000 spectrophotometer, and quality was evaluated with Agilent RNA 6000 NanoChip and the 2100 Bioanalyzer, with 28S/18S ratios and RIN determined by 2100 Expert software.