Targeted RNA Sequencing of FFPE Prostate Biopsies and Matched Prostatectomies

One of the significant challenges with management of prostate cancer is discriminating between aggressive and indolent disease at the time of diagnosis, in order to make clinical decisions on the optimal course of therapy. While biopsies are critical for definitive diagnosis of prostate cancer, it is not known whether RNA biomarker signatures that have been developed using prostatectomy tissues are adequately represented by biopsy specimens. Additionally, the fact that prostate cancers are subject to significant clonal heterogeneity adds to the challenge of applying prognostic signatures to biopsy‐derived RNA. To interrogate whether it is feasible to use prognostic RNA signatures with biopsy tissues, we employed targeted RNA‐Seq on 24 matched biopsy‐radical prostatectomy (RP) pairs and 70 unmatched biopsies. We optimized the Agilent Sure Select Targeted RNA‐Seq protocol to enable targeted RNA‐seq of FFPE RNA, and generated 135 sequencing libraries. Our targeted sequencing panel included 295 genes derived from multiple published prognostic RNA signatures, including our own published 24 gene signature (Sig24), which is prognostic of biochemical recurrence following radical prostatectomy. We identified a subset of 9 out of 295 genes, 1 of which belonged to the Sig24 signature, that were consistently expressed among biopsies and exhibit a relatively high correlation in matched RPs. We also found insignificant gene expression variation among multiple biopsies within the same patient. We calculated Sig24 scores for each matched biopsy‐radical prostatectomy pair, and found that only 8 out of 24 patients had biopsy‐RP pairs with consistent grouping, suggesting that non‐targeted biopsies may not reliably reflect the gene patterns expressed in corresponding primary tumors. Taken together, these data support the use of targeted biopsies and demonstrate the feasibility of targeted RNA‐seq of FFPE biopsy samples. Support or Funding Information Atlanta Clinical and Translational Science Institute (ACTSI) NIH UL1TR000454‐06 ACTSI, NIH U01CA113913‐suppl, Winship Prostate Pilot Award, NIH Cancer Center Support Grant P30CA138292.