Microarray analysis of PIN lesions from APT121 mouse prostate

High grade prostate intraepithelial neoplasia (HGPIN) is a precursor lesion for prostate cancer. The APT121 mouse is a model of early stage prostate cancer that develops PIN lesions that progress to adenocarcinoma over a period of 6 months. At 12 wks of age APT121 mouse prostate contains mostly high grade PIN lesions. We compared the transcript profile of RNA from the anterior prostate of age- and genetic background matched wild type and APT121 mice using Affymetric microarrays. Wild-type and APT121 mice were fed semi-purified AIN93G diets from weaning to 12 wks of age. Their genetics is a mixed C57BL/6J and DBA/2 background (F3 generation). 8 APT121 mice and 16 wild type mice were used. At 12 wks of age mice were killed and the anterior prostate was harvested directly into liquid nitrogen.RNA was isolated using the SV Total RNA isolation kit (Promega); prostates were crushed under liquid nitrogen and added to the kit lysis buffer to prevent RNA degradation. Genomic DNA was removed by digestion with RNAase free DNAse and RNA was repurified with the RNAeasy mini kit. After quantification, equal amounts of RNA from two mice were pooled to make 4 pooled APT121 and 8 pooled wild type samples. Profiling was done using the GeneChip Mouse Gene 1.0 ST array (affymetrix). Data from the 12 chips was normalized with RMA. Differential expression was determined using Significance Analysis for Microarrays (SAM) at 5% FDR. Functional analysis was determined using GeneGo/Metacore.