Impact of therapy on gene expression in high-risk prostate cancer (PCA) treated with neoadjuvant docetaxel and androgen deprivation therapy.
8 Background: Molecular analyses of neoadjuvant post-treatment radical prostatectomy (RP) specimens has been challenging as often times only microscopic foci remain present at time of RP precluding RNA-seq. DNA analysis alone in the absence of expression may be suboptimal in elucidating complex mechanisms of resistance and/or prognostic risk stratification. We therefore set out to develop an assay that could quantify mRNA expression in treated and untreated PCA using formalin fixed paraffin embedded (FFPE) tissues. Methods: We evaluated 40 untreated and post-treatment FFPE specimens as well as patient-matched pre-treated needle biopsies and baseline clinical data from patients enrolled on CALGB 90203: a randomized phase 3 trial comparing noeadjuvant docetaxel and ADT followed by RP vs RP alone for men with high risk localized PCA. High-density tumor areas were selected for RNA extraction (min 50ng RNA). We used NanoString nCounter to quantify gene expression of a custom panel of 75 genes including AR and androgen regulated, neural/neuroendocrine (NE), EMT, cell cycle, hormone receptors, TMPRSS-ERG, ARv7 splice variant, and housekeeper genes. mRNA data was integrated with matched whole exome sequencing data. Frozen specimens and RNA-Seq (n = 7) were used for QC and comparative analysis. Results: Quantitative expression using Nanostring showed high correlation with RNA-seq of patient-matched frozen tissue (Spearman coefficient 0.9). There was significant upregulation of AR and the ARv7 expression following treatment, as well as a subset of NE and EMT genes; three high chromogranin A outlier cases were identified in the treatment arm. There was an overall higher AR score in treated cases (based on expression of 30 AR signaling genes) compared to untreated, along the spectrum of CRPC. Conclusions: These data support the feasibility of quantifying gene expression in neoadjuvant-treated PCA cases with limited FFPE tissue requirement. Extensive characterization of AR status and NE/EMT genes identifies molecular outliers that can arise post-treatment and provides new insight into the heterogeneity of treatment response and potential early markers of resistance. Clinical trial information: NCT00430183.