Use of quantitative gene expression in primary and highest Gleason pattern cancers to identify genes associated with clinical recurrence after radical prostatectomy.

Abstract

39 Background: Prostate biopsy may not adequately sample small, secondary or tertiary Gleason pattern tumors which can drive clinical outcome. We conducted a study to determine whether tumor-derived gene expression profiling could identify a distinct underlying biology associated with clinical recurrence (cR) after radical prostatectomy (RP) across both the primary and highest Gleason pattern (GP) samples. Methods: All patients (pts) with clinical stage T1/T2 prostate cancer treated with RP at Cleveland Clinic from 1987 to 2004 were identified (n∼f2,600). A cohort sampling design was used to select 127 patients with cR and 374 patients without cR after RP. Each patient had two spatially distinct tumor specimens sampled that included the primary GP and the highest GP. Surgical GS and clinical data were centrally reviewed. RNA was extracted from 6 manually dissected 10 μ m fixed paraffin embedded tissue sections obtained from the RP tumor specimens and expression of 732 cancer-related and reference genes was quantified using RT-PCR. Clinical recurrence-free interval (cRFI) was analyzed using Cox PH regression. Results: Blocks from 441 patients were evaluable. Median F/U was 5.8 years. Pts were mostly Caucasian (83%), clinical stage T1 (66%), had baseline PSA <10 ng/mL (82%), and had surgical GS ≤7 (87%). As expected, surgical GP, biopsy GP, path T- stage, clin T-stage, baseline PSA, and year of surgery (p<0.05, unadj) were associated with cRFI. In the primary and highest GP specimens respectively, 295 and 297 genes were significantly associated (unadj. p<0.05) with cRFI. 235 genes were associated with cRFI in both specimens, well in excess of the number expected by chance. In a multivariate model adjusted for AUA risk group and allowing a 10% false discovery rate, 289 genes remained significantly and strongly associated with cRFI. Conclusions: Gene expression analysis using quantitative RT-PCR identified a large number of genes, and underlying biology, that are strongly associated with clinical recurrence in both the primary and highest GP. This information can be used to develop a biopsy-based assay that distinguishes indolent versus aggressive disease. [Table: see text]