Global Transcriptome Analysis of Formalin-Fixed Prostate Cancer Specimens Identifies Biomarkers of Disease Recurrence

Abstract

Prostate cancer remains the second leading cause of cancer death in American men and there is an unmet need for biomarkers to identify patients with aggressive disease. In an effort to identify biomarkers of recurrence, we performed global RNA sequencing on 106 formalin-fixed, paraffin-embedded (FFPE) prostatectomy samples from 100 patients at three independent sites, defining a 24-gene signature panel. The 24 genes in this panel function in cell cycle progression, angiogenesis, hypoxia, apoptosis, PI3K signaling, steroid metabolism, translation, chromatin modification and transcription. Sixteen genes have been associated with cancer with five specifically associated with prostate cancer (BTG2, IGFBP3, SIRT1, MXI1 and FDPS). Validation was performed on an independent publicly available dataset of 140 patients, where the new signature panel outperformed markers published previously in terms of predicting biochemical recurrence (BCR). Our work also identified differences in gene expression between Gleason Pattern 4+3 and 3+4 tumors, including several genes involved in the epithelial to mesenchymal transition and developmental pathways. Overall, this study defines a novel biomarker panel that has the potential to improve the clinical management of prostate cancer.

The Landscape of Prognostic Outlier Genes in High-Risk Prostate Cancer

“…Molecular biomarkers are a promising class of prognostic biomarker candidates, but these studies in prostate cancer have been limited by follow-up insufficient for study of metastatic progression or survival because of the long disease course (16). Separately, outlier analysis has identified preeminent prostate cancer genes TMPRSS2-ERG fusions and SPINK1 (19,20), but has been limited to comparisons of cancer versus normal samples.…”

“…Prognostic studies in prostate cancer are hampered by the long disease course, resulting in follow-up of insufficient length to study associations with the most meaningful outcomes of metastatic progression, prostate cancer death, and overall survival. Thus, many studies have been limited to the intermediate outcome of biochemical recurrence (16).…”

The Role of SIRT1 in Cancer

“…4 This includes several studies in prostate cancer, which are in agreement with the findings of Di Sante et al 5 Furthermore, chemical inhibition of SIRT1 in prostate cancer has been shown to reduce cellular growth, viability, and chemoresistance, and a recent analysis of prostate cancer tissues showed SIRT1 to be a reliable biomarker of disease recurrence. 6 It would be logical to conclude from these findings that SIRT1 has a tumor promoter function in prostate cancer. However, Di Sante et al 5 have found that in prostate cancer patients, a low level of SIRT1 is associated with decreased recurrence-free survival, supporting a tumor suppressor function of SIRT1 in prostate cancer.…”

Biomarker, Molecular, and Technologic Advances in Urologic Pathology, Oncology, and Imaging

“…We performed RNA sequencing on prostatectomy samples from 100 patients and identified a new set of biomarkers of biochemical recurrence composed of a 24-gene panel. 82 This panel showed significant improvement of prediction of biochemical recurrence over clinical parameters alone and over previously described biomarker panels based on cellular proliferation. 83 The findings were especially significant in demonstrating that RNAseq analysis of formalinfixed, paraffin-embedded prostate cancer specimens is feasible and can provide critical insights into the mechanisms of prostate cancer progression that may be translated into clinically useful biomarkers, which can then be used in institutions and settings that may not have access to frozen, banked specimens.…”

“…83 The findings were especially significant in demonstrating that RNAseq analysis of formalinfixed, paraffin-embedded prostate cancer specimens is feasible and can provide critical insights into the mechanisms of prostate cancer progression that may be translated into clinically useful biomarkers, which can then be used in institutions and settings that may not have access to frozen, banked specimens. 82 …”