PurposeClinicopathologic features and biochemical recurrence are sensitive, but not specific, predictors of metastatic disease and lethal prostate cancer. We hypothesize that a genomic expression signature detected in the primary tumor represents true biological potential of aggressive disease and provides improved prediction of early prostate cancer metastasis.MethodsA nested case-control design was used to select 639 patients from the Mayo Clinic tumor registry who underwent radical prostatectomy between 1987 and 2001. A genomic classifier (GC) was developed by modeling differential RNA expression using 1.4 million feature high-density expression arrays of men enriched for rising PSA after prostatectomy, including 213 who experienced early clinical metastasis after biochemical recurrence. A training set was used to develop a random forest classifier of 22 markers to predict for cases - men with early clinical metastasis after rising PSA. Performance of GC was compared to prognostic factors such as Gleason score and previous gene expression signatures in a withheld validation set.ResultsExpression profiles were generated from 545 unique patient samples, with median follow-up of 16.9 years. GC achieved an area under the receiver operating characteristic curve of 0.75 (0.67–0.83) in validation, outperforming clinical variables and gene signatures. GC was the only significant prognostic factor in multivariable analyses. Within Gleason score groups, cases with high GC scores experienced earlier death from prostate cancer and reduced overall survival. The markers in the classifier were found to be associated with a number of key biological processes in prostate cancer metastatic disease progression.ConclusionA genomic classifier was developed and validated in a large patient cohort enriched with prostate cancer metastasis patients and a rising PSA that went on to experience metastatic disease. This early metastasis prediction model based on genomic expression in the primary tumor may be useful for identification of aggressive prostate cancer.

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The androgen receptor (AR) plays a central role in establishing an oncogenic cascade that drives prostate cancer progression. Some prostate cancers escape androgen dependence and are often associated with aggressive phenotype. The estrogen receptor alpha (ERα) is expressed in prostate cancers, independent of AR status. However, the role of ERα remains elusive. Using a combination of chromatin immunoprecipitation (ChIP) and RNA-sequencing data, we identified an ERα specific non coding transcriptome signature. Amongst putatively ERα-regulated intergenic long non coding RNAs (lncRNAs), we identified Nuclear Enriched Abundant Transcript 1 (NEAT1) as the most significantly overexpressed lncRNA in prostate cancer. Analysis of two large clinical cohorts also revealed that NEAT1 expression is associated with prostate cancer progression. Prostate cancer cells expressing high levels of NEAT1 were recalcitrant to androgen or AR antagonists. Finally, we provide evidence that NEAT1 drives oncogenic growth by altering the epigenetic landscape of target gene promoters to favor transcription.

Purpose Prostate cancer patients with locally advanced disease after radical prostatectomy (RP) are candidates for secondary therapy. However, this higher risk population is heterogeneous and many will not metastasize even when conservatively managed. Given the limited specificity of pathologic features to predict metastasis, newer risk-prediction models are needed. This represents a validation study of a genomic classifier (GC) that predicts post-RP metastasis in a high-risk population. Materials and Methods A case-cohort design was used to sample 1,010 post-RP patients at high risk of recurrence treated between 2000-2006. Patients had preoperative PSA >20 ng/mL, Gleason ≥8, pT3b or GPSM score ≥10. Patients with metastasis at diagnosis or any prior treatment for prostate cancer were excluded. 20% random sampling created a subcohort that included all cases with metastasis. 22-marker GC scores were generated for 219 patients with available genomic data. Receiver operating characteristic and decision curves, competing risk, and weighted regression models assessed GC performance. Results GC had area under the curve of 0.79 for predicting 5-year metastasis post-RP. Decision curves showed that net benefit of GC exceeded clinical-only models. GC was the predominant predictor of metastasis in multivariable analysis. Cumulative incidence of metastasis at 5 years post-RP was 2.4%, 6.0% and 22.5% for patients with low (60% of patients), intermediate (21% of patients), and high (19% of patients) GC scores, respectively (p<0.001). Conclusions These results indicate that genomic information from the primary tumor can identify patients with adverse pathology who are most at risk for metastasis and potentially lethal prostate cancer.

Background Risk prediction models that incorporate biomarkers and clinicopathologic variables may be used to improve decision-making post radical prostatectomy (RP). We compared two previously validated post-RP classifiers—the Cancer of the Prostate Risk Assessment post-Surgical (CAPRA-S) and the Decipher genomic classifier (GC)—to predict prostate cancer-specific mortality (CSM) in a contemporary cohort of RP patients. Objective To evaluate the combined prognostic ability of CAPRA-S and GC to predict CSM. Design, Setting and Participants A cohort of 1,010 patients at high risk of recurrence post-RP was treated at Mayo Clinic between 2000–06. High-risk was defined by any of: pre-operative PSA >20ng/mL, pathological Gleason score ≥8 or stage pT3b. A case-cohort random sample identified 225 patients (cases defined as patients who experienced CSM), among whom CAPRA-S and GC could be determined for 185. Outcome Measurements and Statistical Analysis The scores were evaluated individually and in combination using concordance (c)-index, decision curve analysis, re-classification, cumulative incidence, and Cox regression for prediction of CSM. Results and Limitations Among 185 men, 28 experienced CSM. The c-index for CAPRA-S and GC were 0.75 (95% CI 0.65–0.84) and 0.78 (95% CI 0.68–0.88), respectively. GC showed higher net-benefit on decision curve analysis but a score combining CAPRA-S and GC did not improve AUC after optimism-adjusted bootstrapping. In 82 patients stratified to high-risk based on CAPRA-S score ≥6, GC scores were likewise high-risk for 33, among whom 17 had CSM events. GC reclassified the remaining 49 men as low to intermediate-risk; among these men 3 CSM events were observed. In multivariable analysis, GC and CAPRA-S as continuous variables were independently prognostic of CSM, with hazard ratios of 1.81 (p<0.001, per 0.1 unit change in score) and 1.36 (p=0.05, per one unit change in score). When categorized into risk groups, the multivariable HR for high CAPRA-S scores (≥6) was 2.36 (p=0.04), and 11.26 (p<0.001) for high GC scores (≥0.6). For patients with both high GC and CAPRA-S scores, cumulative incidence of CSM was 45% at 10 years. The study is limited by its retrospective design. Conclusions Both GC and CAPRA-S were significant independent predictors of CSM. GC was shown to re-stratify many men classified as high-risk based on CAPRA-S ≥6 alone. Patients with both high GC and CAPRA-S risk scores were at markedly elevated post-RP risk for lethal prostate cancer. If validated prospectively, these findings suggest that integration of a genomic-clinical classifier may enable better identification of those post-RP patients who should be considered for more aggressive secondary therapies and clinical trials.

Purpose To test the hypothesis that a genomic classifier (GC) would predict biochemical failure (BF) and distant metastasis (DM) in men receiving radiation therapy (RT) after radical prostatectomy (RP). Methods and Materials Among patients who underwent post-RP RT, 139 were identified for pT3 or positive margin, who did not receive neoadjuvant hormones and had paraffin-embedded specimens. Ribonucleic acid was extracted from the highest Gleason grade focus and applied to a high-density-oligonucleotide microarray. Receiver operating characteristic, calibration, cumulative incidence, and Cox regression analyses were performed to assess GC performance for predicting BF and DM after post-RP RT in comparison with clinical nomograms. Results The area under the receiver operating characteristic curve of the Stephenson model was 0.70 for both BF and DM, with addition of GC significantly improving area under the receiver operating characteristic curve to 0.78 and 0.80, respectively. Stratified by GC risk groups, 8-year cumulative incidence was 21%, 48%, and 81% for BF (P<.0001) and for DM was 0, 12%, and 17% (P=.032) for low, intermediate, and high GC, respectively. In multivariable analysis, patients with high GC had a hazard ratio of 8.1 and 14.3 for BF and DM. In patients with intermediate or high GC, those irradiated with undetectable prostate-specific antigen (PSA ≤0.2 ng/mL) had median BF survival of >8 years, compared with <4 years for patients with detectable PSA (>0.2 ng/mL) before initiation of RT. At 8 years, the DM cumulative incidence for patients with high GC and RTwith undetectable PSA was 3%, compared with 23% with detectable PSA (P=.03). No outcome differences were observed for low GC between the treatment groups. Conclusion The GC predicted BF and metastasis after post-RP irradiation. Patients with lower GC risk may benefit from delayed RT, as opposed to those with higher GC; however, this needs prospective validation. Genomic-based models may be useful for improved decision-making for treatment of high-risk prostate cancer.

Historical controls (HCs) can be used for model parameter estimation at the study design phase, adaptation within a study, or supplementation or replacement of a control arm. Currently on the latter, there is no practical roadmap from design to analysis of a clinical trial to address selection and inclusion of HCs, while maintaining scientific validity. This paper provides a comprehensive roadmap for planning, conducting, analyzing and reporting of studies using HCs, mainly when a randomized clinical trial is not possible. We review recent applications of HC in clinical trials, in which either predominantly a large treatment effect overcame concerns about bias, or the trial targeted a life-threatening disease with no treatment options. In contrast, we address how the evidentiary standard of a trial can be strengthened with optimized study designs and analysis strategies, emphasizing rare and pediatric indications. We highlight the importance of simulation and sensitivity analyses for estimating the range of uncertainties in the estimation of treatment effect when traditional randomization is not possible. Overall, the paper provides a roadmap for using HCs.

Prostate cancer is the second leading cause of cancer death among United States men. However, disease aggressiveness is varied, with low-grade disease often being indolent and high-grade cancer accounting for the greatest density of deaths. Outcomes are also disparate among men with high-grade prostate cancer, with upwards of 65% having disease recurrence even after primary treatment. Identification of men at risk for recurrence and elucidation of the molecular processes that drive their disease is paramount, as these men are the most likely to benefit from multimodal therapy. We previously showed that androgen-induced expression profiles in prostate development are reactivated in aggressive prostate cancers. Herein, we report the down-regulation of one such gene, Sparcl1, a secreted protein, acidic and rich in cysteine (SPARC) family matricellular protein, during invasive phases of prostate development and regeneration. We further demonstrate a parallel process in prostate cancer, with decreased expression of SPARCL1 in high-grade/metastatic prostate cancer. Mechanistically, we demonstrate that SPARCL1 loss increases the migratory and invasive properties of prostate cancer cells through Ras homolog gene family, member C (RHOC), a known mediator of metastatic progression. By using models incorporating clinicopathologic parameters to predict prostate cancer recurrence after treatment, we show that SPARCL1 loss is a significant, independent prognostic marker of disease progression. Thus, SPARCL1 is a potent regulator of cell migration/invasion and its loss is independently associated with prostate cancer recurrence.Hevin | synaptic cleft 1 | urogenital sinus | extracellular matrix P rostate cancer is the most common noncutaneous malignancy and the second leading cause of cancer death in United States men. Controversy currently exists over the best treatment strategy for men with high-risk disease (clinical stage ≥T2c, Gleason score 8-10 or prostate-specific antigen > 20 ng/mL) because 56-65% of these men recur after definitive local therapy (1-5). This finding highlights the need for a better understanding of the biologic determinants driving disease progression for both prognostic and therapeutic development.We and others have recently illustrated that pathways essential for prostate organogenesis are reactivated in prostate cancer (6, 7). During organogenesis, androgens induce epithelialmesenchymal interactions in the urogenital sinus (UGS) and drive its differentiation into a prostate (8). We examined early prostate organogenesis shortly after initial androgen exposure, when urogenital sinus epithelia (UGE) migrate and invade into the surrounding mesenchyme and determined that the genes defining this developmental stage were similarly regulated in the transition between low-and high-grade prostate cancers (6). Among these genes, SPARCL1 (SPARC-like 1/Hevin/SC1), a member of the secreted protein, acidic and rich in cysteine (SPARC) family of matricellular proteins, was down-regulated specifically during embryoni...