Introduction

Current tissue-based prognostic biomarker assays claim that genetic assessment of a single focus is sufficient to predict disease behavior. We analyzed and compared the genetic profiles of multifocal prostate cancer (PCa) with concordant lymph node metastasis (LNM) to determine if expression based prognostic tests are robust to multifocality.

Methods

This IRB-approved study comprised patients who underwent radical prostatectomy and lymph node dissection that revealed N1 disease or discordant multifocal disease (low- and high-grade foci). DNA and RNA were co-isolated from each tumor focus pre-identified on formalin fixed paraffin embedded specimens. High depth, targeted DNA and RNA next generation sequencing was performed to characterize the genetic and transcriptional signature of each sample, using the Oncomine Comprehensive (11 patients) or Comprehensive Cancer (DNA, 3 patients) Panels and a custom targeted RNAseq panel comprising genes for deriving prognostic signatures.

Results

A total of 67 primary tumor and 17 LMN foci (with control tissue when available) from 14 patients were analyzed. We observed significant intra- and inter-patient molecular heterogeneity. For example, in patient #1, while all four regions of high-grade primary tumor showed TP53 somatic mutations and some broad copy number alterations (CNAs) with two samples from the LNM, tumor areas near the positive margin showed more complete concordance than intraprostatic regions. Critically, a low-grade primary tumor focus in this case showed no somatic mutation or CNA overlap with the high-grade or LNM samples. In patient #4, all tumor and LNM foci shared a large number of somatic mutations, including a frameshift mutation in PTEN, with no high level CNA identified, consistent with a hypermutated genotype. By targeted RNAseq, low-grade and high-grade tumors from the same patient showed distinct expression profiles using genes included in available prognostic signatures (Figure 1)._x000D_

Conclusions

Our results challenge the claim that expression based prognostic tests are robust to multifocality. Additional molecular studies are needed to better characterize the biologically dominant lesion in multi-focal PCa and hold promise for the development of improved prognostic biomarkers.

Funding

Prostate Cancer Foundation