Molecular sampling of prostate cancer: a dilemma for predicting ­disease progression. BMC Med Genomics 3:8

Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, NY, USA.
BMC Medical Genomics (Impact Factor: 2.87). 03/2010; 3(1):8. DOI: 10.1186/1755-8794-3-8
Source: PubMed


Current prostate cancer prognostic models are based on pre-treatment prostate specific antigen (PSA) levels, biopsy Gleason score, and clinical staging but in practice are inadequate to accurately predict disease progression. Hence, we sought to develop a molecular panel for prostate cancer progression by reasoning that molecular profiles might further improve current clinical models.
We analyzed a Swedish Watchful Waiting cohort with up to 30 years of clinical follow up using a novel method for gene expression profiling. This cDNA-mediated annealing, selection, ligation, and extension (DASL) method enabled the use of formalin-fixed paraffin-embedded transurethral resection of prostate (TURP) samples taken at the time of the initial diagnosis. We determined the expression profiles of 6100 genes for 281 men divided in two extreme groups: men who died of prostate cancer and men who survived more than 10 years without metastases (lethals and indolents, respectively). Several statistical and machine learning models using clinical and molecular features were evaluated for their ability to distinguish lethal from indolent cases.
Surprisingly, none of the predictive models using molecular profiles significantly improved over models using clinical variables only. Additional computational analysis confirmed that molecular heterogeneity within both the lethal and indolent classes is widespread in prostate cancer as compared to other types of tumors.
The determination of the molecularly dominant tumor nodule may be limited by sampling at time of initial diagnosis, may not be present at time of initial diagnosis, or may occur as the disease progresses making the development of molecular biomarkers for prostate cancer progression challenging.

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Available from: Andrea Sboner
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    • "Using Significance Analysis of Microarrays, prostate cancer cDNA microarray datasets were examined for gene expression positively (red) and negatively (green) correlated with NUSAP1 expression. Sboner et al., 2010 dataset [15]: 281 prostate cancer samples and 5,657 genes. "
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    ABSTRACT: BACKGROUND Overexpression of NUSAP1 is associated with poor prognosis in prostate cancer, but little is known about what leads to its overexpression. Based on previous observations that NUSAP1 expression is enhanced by E2F1, we hypothesized that NUSAP1 expression is regulated, at least in part, by loss of RB1 via the RB1/E2F1 axis.METHODS Using Significance Analysis of Microarrays, we examined RB1, E2F1, and NUSAP1 transcript levels in prostate cancer gene expression datasets. We compared NUSAP1 expression levels in DU145, LNCaP, and PC-3 prostate cancer cell lines via use of cDNA microarray data, RT-qPCR, and Western blots. In addition, we used lentiviral expression constructs to knockdown RB1 in prostate cancer cell lines and transient transfections to knockdown E2F1, and investigated RB1, E2F1, and NUSAP1 expression levels with RT-qPCR and Western blots. Finally, in DU145 cells or PC-3 cells that stably underexpress RB1, we used proliferation and invasion assays to assess whether NUSAP1 knockdown affects proliferation or invasion.RESULTSNUSAP1 transcript levels are positively correlated with E2F1 and negatively correlated with RB1 transcript levels in prostate cancer microarray datasets. NUSAP1 expression is elevated in the RB1-null DU145 prostate cancer cell line, as opposed to LNCaP and PC-3 cell lines. Furthermore, NUSAP1 expression increases upon knockdown of RB1 in prostate cancer cell lines (LNCaP and PC-3) and decreases after knockdown of E2F1. Lastly, knockdown of NUSAP1 in DU145 cells or PC-3 cells with stable knockdown of RB1 decreases proliferation and invasion of these cells.CONCLUSION Our studies support the notion that NUSAP1 expression is upregulated by loss of RB1 via the RB1/E2F1 axis in prostate cancer cells. Such upregulation may promote prostate cancer progression by increasing proliferation and invasion of prostate cancer cells. NUSAP1 may thus represent a novel therapeutic target. Prostate © 2015 Wiley Periodicals, Inc.
    Full-text · Article · Jan 2015 · The Prostate
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    • "The Gleason score ranged from 5 to 10, where the majority of the patients had a score of 7a (n ¼ 28) or 7b and above (n ¼ 27). GSE16560 contained data of 281 patients in a Swedish watchful waiting cohort, including expression of 6100 genes from the cDNA-mediated annealing, selection, ligation and extension (DASL) platform and up to 30 years follow-up for survival (Sboner et al, 2010). The patients had either died from prostate cancer or survived more than 10 years without metastases. "
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    ABSTRACT: Background: The hypoxia marker pimonidazole is a candidate biomarker of cancer aggressiveness. We investigated the transcriptional programme associated with pimonidazole staining in prostate cancer. Methods: Index tumour biopsies were taken by image guidance from an investigation cohort of 52 patients, where 43 patients received pimonidazole before prostatectomy. Biopsy location within the index tumour was verified for 46 (88%) patients, who were included for gene expression profiling and immunohistochemistry. Two independent cohorts of 59 and 281 patients were used for validation. Results: Expression of genes in proliferation, DNA repair and hypoxia response was a major part of the transcriptional programme associated with pimonidazole staining. A signature of 32 essential genes was constructed and showed positive correlation to Ki67 staining, confirming the increased proliferation in hypoxic tumours as suggested from the gene data. Positive correlations were also found to tumour stage and lymph node status, but not to blood prostate-specific antigen level, consistent with the findings for pimonidazole staining. The association with aggressiveness was confirmed in validation cohorts, where the signature correlated with Gleason score and had independent prognostic impact, respectively. Conclusions: Pimonidazole staining reflects an aggressive hypoxic phenotype of prostate cancer characterised by upregulation of proliferation, DNA repair and hypoxia response genes.
    Full-text · Article · Dec 2014 · British Journal of Cancer
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    • "a duplication of the TMPRSS2-ERG fusion together with an interstitial deletion (HR: 6.1) [21]. Results from a watchful waiting cohort that compared 161 men who died from PCa with 111 men surviving at least 10 yr after diagnosis showed that ERG gene–rearranged men were more likely to be in the lethal PCa group than in the long-termsurvival group (odds ratio: 7.2) [22]. Lin et al. recently reported that TMPRSS2-ERG levels in post-DRE urine were associated with higher tumour volume and GS in subsequent biopsies [6], and data indicate that high values of TMPRSS2-ERG fusion mRNA in expressed prostatic secretion are associated with an increased risk of tumour upgrading and upstaging in AS candidates undergoing immediate RP [23]. "
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    ABSTRACT: Background Compelling biomarkers identifying prostate cancer patients with a high risk of progression during active surveillance (AS) are needed. Objective To examine the association between ERG expression at diagnosis and the risk of progression during AS. Design, setting, and participants This study included 265 patients followed on AS with prostate-specific antigen (PSA) measurements, clinical examinations, and 10–12 core rebiopsies from 2002 to 2012 in a prospectively maintained database. ERG immunohistochemical staining was performed on diagnostic paraffin-embedded formalin-fixed sections with a ready-to-use kit (anti-ERG, EPR3864). Men were characterised as ERG positive if a minimum of one tumour focus demonstrated ERG expression. Outcome measurements and statistical analysis Overall AS progression was defined as clinical progression: increased clinical tumour category ≥cT2b by digital rectal examination and ultrasound, and/or histopathologic progression: upgrade of Gleason score, more than three positive cores or bilateral positive cores, and/or PSA progression: PSA doubling time <3 yr. Risk of progression was analysed using multiple cause-specific Cox regression and stratified cumulative incidences (Aalen-Johansen method). Curatively intended treatment, watchful waiting, and death without progression were treated as competing events. Results and limitations A total of 121 of 142 ERG-negative and 96 of 123 ERG-positive patients had complete diagnostic information. In competing risk models, the ERG-positive group showed significantly higher incidences of overall AS progression (p < 0.0001) and of the subgroups PSA progression (p < 0.0001) and histopathologic progression (p < 0.0001). The 2-yr cumulative incidence of overall AS progression was 21.7% (95% confidence interval [CI], 14.3–29.1) in the ERG-negative group compared with 58.6% (95% CI, 48.7–68.5) in the ERG-positive group. ERG positivity was a significant predictor of overall AS progression in multiple Cox regression (hazard ratio: 2.45; 95% CI, 1.62–3.72; p < 0.0001). The main limitation of this study is its observational nature. Conclusions In our study, ERG positivity at diagnosis can be used to estimate the risk of progression during AS. If confirmed, ERG status can be used to individualise AS programmes. Patient summary The tissue biomarker ERG identifies active surveillance patients with an increased risk of disease progression.
    Full-text · Article · Nov 2014 · European Urology
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