MyProstateScore in men considering repeat biopsy: validation of a simple testing approach

BACKGROUND

Men with persistent risk of Grade Group (GG) ≥ 2 cancer after a negative biopsy present a unique clinical challenge. The validated MyProstateScore test is clinically-available for pre-biopsy risk stratification. In biopsy-naïve patients, we recently validated a straightforward testing approach to rule-out GG ≥ 2 cancer with 98% negative predictive value (NPV) and 97% sensitivity. In the current study, we established a practical MPS-based testing approach in men with a previous negative biopsy being considered for repeat biopsy.

METHODS

Patients provided post-digital rectal examination urine prior to repeat biopsy. MyProstateScore was calculated using the validated, locked model including urinary PCA3 and TMPRSS2:ERG scores with serum PSA. In a clinically-appropriate primary (i.e., training) cohort, we identified a lower (rule-out) threshold approximating 90% sensitivity and an upper (rule-in) threshold approximating 80% specificity for GG ≥ 2 cancer. These thresholds were applied to an external validation cohort, and performance measures and clinical outcomes associated with their use were calculated.

RESULTS

MyProstateScore thresholds of 15 and 40 met pre-defined performance criteria in the primary cohort (422 patients; median PSA 6.4, IQR 4.3-9.1). In the 268-patient validation cohort, 25 men (9.3%) had GG ≥ 2 cancer on repeat biopsy. The rule-out threshold of 15 provided 100% NPV and sensitivity for GG ≥ 2 cancer and would have prevented 23% of unnecessary biopsies. Use of MyProstateScore >40 to rule-in biopsy would have prevented 67% of biopsies while maintaining 95% NPV. In the validation cohort, the prevalence of GG ≥ 2 cancer was 0% for MyProstateScore 0-15, 6.5% for MyProstateScore 15-40, and 19% for MyProstateScore >40.

CONCLUSIONS

In patients who previously underwent a negative prostate biopsy, the MyProstateScore values of 15 and 40 yielded clinically-actionable rule-in and rule-out risk groups. Using this straightforward testing approach, MyProstateScore can meaningfully inform patients and physicians weighing the need for repeat biopsy.

Abstract P4-02-04: Serial monitoring of circulating tumor cells and circulating tumor DNA in metastatic lobular breast cancer identifies intra-tumor heterogeneity and precision and immuno-oncology biomarkers of therapeutic importance

Clinical decisions on precision and immuno-oncology therapies are based on predictive biomarkers commonly obtained from a single metastatic biopsy or archived primary tumor tissue. Circulating genomic biomarkers offer a minimally invasive approach to monitor intra-patient tumor heterogeneity and detect in real-time the clinically-relevant evolving clonal architecture. Although currently underutilized, we hypothesize that single-cell DNA next generation sequencing (scNGS) of circulating tumor cells (CTC) is a particularly well-suited method to complement biomarker information obtained from tissue and cell-free circulating tumor DNA (ctDNA). In this study we analyzed 113 individual CTC, 21 ctDNA, and 15 white blood cells (WBC) samples, from 15 CTC-positive lobular breast cancer patients, four of whom had CTC available at both metastatic baseline and after progression on a variety of therapies chosen at their physician’s discretion. Clinical NGS data from 15 tumor tissue biopsies obtained using a ~1700-gene DNA panel and whole transcriptome sequencing were available for comparison. CTC were enriched with the CellSearch® system and isolated as single cells with the DEPArray™ system. Whole genome amplified CTC and WBC, as well as ctDNA underwent scNGS with the Oncomine Comprehensive Assay covering ~500 genes and 1.1Mb of genomic space to detect mutations, copy number alterations, tumor mutation burden (TMB) and microsatellite instability (MSI). 99.1% of single cells and 95.2% of ctDNA samples were informative, with a mean sequencing depth of 664x. Using our previously developed, CTC-based precision medicine reporting platform, MI-CTCSeq, CTC in 9 of 15 patients (60%) had mutations that were actionable by FDA-approved targeted therapies including in the oncogenes PIK3CA and FGFR2 and HER2. 3 of these 9 patients (33%) harbored actionable alterations not shared between all 3 analyte types (tissue, CTC and ctDNA). These included 3 actionable mutations found in CTC and ctDNA only, 1 in tissue and ctDNA only, and 1 in ctDNA only. However, 2 of those ctDNA mutations were identified near the limit of detection and with a priori knowledge of their presence from tissue or CTC. Further, 1 patient with plentiful CTC had no detectable ctDNA and one patient’s tissue biopsy was inadequate for sequencing while both liquid biopsy analytes were abundant. 13 patients (87%) displayed intra-patient, inter-CTC genomic heterogeneity of putative driver mutations. 1 of 4 (25%) patients with CTC available in >1 timepoint displayed fluctuations in their CTC subclonal makeup between timepoints. Data from this patient’s 2 tissue biopsies, 3 ctDNA samples, and 27 individual CTC over 4 timepoints combined to reveal in unprecedented detail inter-metastatic lesion and inter-CTC heterogeneity and tumor evolution in response to endocrine and immunotherapy selective pressures. ScNGS of CTC helped provide an additional level of detail not appreciated by sequencing of the other two analyte types. In another patient, CTC were composed of 2 subclones which were indistinguishable by ctDNA, 1 of which appears to have not been sampled by the tissue biopsy. Using a novel method, we enabled detection of single-cell CTC TMB and MSI. CTC TMB scores (dichotomized as above/below 10 mutations/Mb) were 100% concordant with those measured in the corresponding tissue biopsies. Further, in a novel observation, we detected intra patient, inter-CTC heterogeneity of TMB and MSI, which has potential implications for immunotherapy response and development of resistance. Taken together, these data support the non-invasive biomarker interrogation and monitoring by liquid biopsy that incorporates CTC scNGS and complements tissue in informing precision and immuno-oncology approaches. This may have important implications for appropriate treatment selection and identification of therapeutic resistance mechanisms.

Citation Format: Andi Cani, Emily Dolce, Alissa Turnbull, Kevin Hu, Chia-Jen Liu, Elizabeth Darga, Dan Robinson, Yi-Mi Wu, Dafydd G. Thomas, Costanza Paoletti, Scott Tomlins, James Rae, Aaron Udager, Arul Chinnaiyan, Erin F. Cobain, Daniel F. Hayes. Serial monitoring of circulating tumor cells and circulating tumor DNA in metastatic lobular breast cancer identifies intra-tumor heterogeneity and precision and immuno-oncology biomarkers of therapeutic importance [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-02-04.

Crizotinib in patients with tumors harboring ALK or ROS1 rearrangements in the NCI-MATCH trial

The NCI-MATCH was designed to characterize the efficacy of targeted therapies in histology-agnostic driver mutation-positive malignancies. Sub-protocols F and G were developed to evaluate the role of crizotinib in rare tumors that harbored either ALK or ROS1 rearrangements. Patients with malignancies that progressed following at least one prior systemic therapy were accrued to the NCI-MATCH for molecular profiling, and those with actionable ALK or ROS1 rearrangements were offered participation in sub-protocols F or G, respectively. There were five patients who enrolled on Arm F (ALK) and four patients on Arm G (ROS1). Few grade 3 or 4 toxicities were noted, including liver test abnormalities, and acute kidney injury. For sub-protocol F (ALK), the response rate was 50% (90% CI 9.8-90.2%) with one complete response among the 4 eligible patients. The median PFS was 3.8 months, and median OS was 4.3 months. For sub-protocol G (ROS1) the response rate was 25% (90% CI 1.3-75.1%). The median PFS was 4.3 months, and median OS 6.2 months. Data from 3 commercial vendors showed that the prevalence of ALK and ROS1 rearrangements in histologies other than non-small cell lung cancer and lymphoma was rare (0.1% and 0.4% respectively). We observed responses to crizotinib which met the primary endpoint for ALK fusions, albeit in a small number of patients. Despite the limited accrual, some of the patients with these oncogenic fusions can respond to crizotinib which may have a therapeutic role in this setting.

SAT-549 Identification of Somatic Mutations in CLCN2 as a Cause of Aldosterone-Producing Adenomas

Background: Primary aldosteronism (PA) results from both unilateral and bilateral adrenal disease. Unilateral disease is most often caused by aldosterone-producing adenomas (APAs). We recently identified aldosterone-driver somatic mutations in approximately 90% of APAs using an aldosterone synthase (CYP11B2) immunohistochemistry (IHC)-guided DNA sequencing approach. In the present study, we analyzed DNA from APA samples found to be mutation negative. Methods: Formalin-fixed paraffin-embedded tissue samples from PA patients who underwent adrenalectomy were studied. Genomic DNA was isolated from 118 APAs (identified by CYP11B2 IHC). Next generation sequencing (NGS) was performed to identify known aldosterone-driver mutations in KCNJ5, ATP1A1, ATP2B3, and CACNA1D. APA DNA that was mutation negative and the adjacent normal adrenal tissue DNA were subjected to Whole Exome Sequencing (WES). Results: Targeted NGS and WES detected two variants in the voltage-gated chloride channel ClC-2 (encoded by CLCN2), which were confirmed by Sanger sequencing. One of the CLCN2 mutations (p.Gly24Asp) was identical to that previously found to cause germline early-onset PA. The second CLCN2 mutation, which would affect the same region of the protein, was an unreported PA mutation (p.Met22fs). The presence of these variants in two tumors suggests that CLCN2 mutations as a cause of APAs are rare with an approximate prevalence of 1.7% (2/118 APAs). Conclusion: In this study, we identified somatic mutations in CLCN2, in two of 118 APAs. Germline variants in this gene have previously been shown to cause of familial hyperaldosteronism type II and the current findings indicate that similar mutations cause a small proportion of APAs. These findings also indicate that WES of CYP11B2-guided mutation negative APAs can help determine rarer genetic causes of sporadic PA.

SAT-352 Comprehensive Genetic Analysis of Cortisol-Producing Adenomas

Background: Cortisol-producing adenomas (CPA) are the most common cause of adrenal Cushing’s syndrome. Next-generation sequencing (NGS) has recently facilitated the identification of somatic mutations that cause autonomous cortisol production by these tumors. The most commonly mutated gene in CPAs is PRKACA, resulting in hyper-activation of the protein kinase A (PKA) signaling pathway. Somatic mutations of GNAS, PRKAR1A, and CTNNB1 have also been identified in CPAs. However, direct mutation analysis of CPAs using formalin-fixed paraffin-embedded (FFPE) materials and immunohistochemistry (IHC)-guided targeted NGS has not been done before. Objective: To investigate the prevalence of somatic mutations in CPAs using FFPE tissue sections and targeted NGS. Methods: FFPE adrenal tumor tissue from 37 patients with Cushing’s syndrome who underwent adrenalectomy in our institution was used. IHC of HSD3B2 and CYP17A1 was performed. Aldosterone synthase (CYP11B2) IHC was also performed on tumors with low CYP17A1 expression and one from a patient with concomitant primary aldosteronism with Cushing’s syndrome. IHC-guided gDNA isolation was performed from 40 functional tumor samples [38 CPAs and two CPA-adjacent aldosterone-producing adenomas (APAs)]. Targeted NGS was implemented to identify somatic mutations involved in the tumors. The panel of targeted NGS included PKA pathway related genes (PRKACA, PRKAR1A, GNAS) and β-catenin (CTNNB1), as well as aldosterone-driver genes (KCNJ5, CACNA1D, ATP1A1, ATP2B3). Results: Somatic mutations were found in 63% (24/38) of CPAs. The two most commonly mutated genes were PRKACA (29%, n= 11/38) and CTNNB1 (24%, n= 9/38). GNAS mutations were found in 8% (3/38) of the CPAs and a PRKAR1A mutation was found in one CPA (3%). Of the two CPA-adjacent APAs, one had a KCNJ5 mutation, while the other had a CACNA1D mutation. Clinically, the autonomous cortisol production resulting from these CPAs was dichotomized into either overt or subclinical Cushing’s syndrome. Intriguingly, the majority of PRKACA mutations were found in the overt Cushing’s syndrome group (62%, n= 8/13) compared to only 1/23 (4%) of the subclinical Cushing’s syndrome cohort. The overt Cushing’s syndrome group also contained the single PRKAR1A mutation (8%, n=1/13). Furthermore, CTNNB1 (39%, n= 9/23) and GNAS (13%, n= 3/23) mutations were exclusively observed in subclinical Cushing’s syndrome patients. Conclusion: Targeted NGS on FFPE CPA tissue identified somatic mutations in 63% of tumors. CPAs causing overt Cushing’s syndrome appear to have a distinct mutation profile compared to the tumors observed in subclinical Cushing’s syndrome.

Abstract 098: Aldosterone-Producing Cell Clusters in Essential Hypertension

Introduction: Primary aldosteronism (PA) is one of the major causes of secondary hypertension and has two major subtypes. One is unilateral aldosterone-producing adenoma (APA), which is positive for aldosterone synthase (CYP11B2) by immunohistochemistry (IHC), and the other is bilateral idiopathic hyperaldosteronism (IHA), which has image-undetectable CYP11B2-positive cell clusters (termed aldosterone-producing cell clusters, APCC) beneath the adrenal capsule. We and others have previously shown that APCC present in normotensive adrenals and the number is significantly less than IHA adrenals, supporting the disease-causing role of APCC in hyperaldosteronism of IHA. Furthermore, we have also shown that most of APCCs in the IHA and normotensive adrenals harbor somatic mutations in a L-type calcium channel, CACNA1D , whereas most of APA has been previously shown to harbor those in a potassium channel, KCNJ5 . These mutations are reported to increase intracellular calcium levels, resulting in aldosterone overproduction. Here, we seek for the first time to identify the potential role of APCC in non-PA hypertensive patients and to clarify whether these adrenals could be precursor of APA or IHA by performing next-generation sequencing (NGS) on observed APCC.

Method and Results: We selected fifteen adrenal glands with the evidence of hypertension and/or antihypertensive agents from a cohort of serial Japanese autopsy cases. None of the cases harbored adrenal tumors, but instead nine cases harbored 23 APCCs. We then isolated DNA from each APCC and performed NGS targeting genes mutated in APA. Of observed APCCs, 9 (39%) APCCs harbored somatic mutations in CACNA1D .

Interpretations: These results show that autonomous aldosterone production in a part of patients with essential hypertension is caused by APCCs with aldosterone-driving somatic mutations. In addition, the mutation spectrum observed in this cohort suggests that essential hypertension could potentially develop into IHA through aldosterone overproduction by APCC.

Molecular Correlates of In Vitro Responses to Dacomitinib and Afatinib in Bladder Cancer

Background:

The HER family of proteins (EGFR, HER2, HER3 and HER4) have long been thought to be therapeutic targets for bladder cancer, but previous clinical trials targeting these proteins have been disappointing. Second generation agents may be more effective.

Objective:

The aim of this study was to evaluate responses to two second-generation irreversible tyrosine kinase inhibitors, dacomitinib and afatinib, in bladder cancer cell lines.

Methods:

Cell lines were characterized by targeted next generation DNA sequencing, RNA sequencing, western blotting and flow cytometry. Cell survival responses to dacomitinib or afatinib were determined using (3-[4,5-dimethylthioazol-2-yl]-2,5-diphenyl tetrazolium bromide) (MTT) or [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) and phenazine methosylfate (PMS) cell survival assays.

Results:

Only two cell lines of 12 tested were sensitive to afatinib. Sensitivity to afatinib was significantly associated with mutation in either HER2 or HER3 (p < 0.05). The two cell lines sensitive to afatinib were also responsive to dacomitinib ralong with an additional 4 other cell lines out of 16 tested. No characteristic was associated with dacomitinib sensitivity. Molecular profiling demonstrated that only two genes were high in both afatinib and dacomitinib sensitive cells. Further rhigher expression of RAS pathway genes was noted for dacomitinib responsive cells.

Conclusions:

This study confirms that cell line screening can be useful in pre-clinical evaluation of targeted small molecule inhibitors and suggests that compounds with similar structure(s) and target(s) may have distinct sensitivity profiles. Further rcombinational targeting of additional molecularly relevant pathways may be important in enhancing responses to HER targeted agents in bladder cancer.

Abstract 057: Cellular and Genetic Causes of Idiopathic Hyperaldosteronism

Background: Primary aldosteronism (PA) affects ~10% of hypertensive patients and has unilateral and bilateral forms (30%:70%). Unilateral PA is caused by aldosterone-producing adenomas (APA), which express CYP11B2 (aldosterone synthase) and frequently harbor somatic mutations in aldosterone regulating genes ( KCNJ5>>CACNA1D ). We recently demonstrated that adrenals from normotensive patients present with pockets of cell expressing aldosterone synthase (CYP11B2). These aldosterone-producing foci (APF) have somatic gene mutations similar to those found in APA ( CACNA1D >> KCNJ5 ). Bilateral PA, which is typically treated by mineralocorticoid receptor (MR) blockade rather than surgery, is termed idiopathic hyperaldosteronism (IHA). Its pathobiology is largely unknown but has been thought to be due to zona glomerulosa (ZG) hyperplasia.

Methods: We studied 11 IHA patients (7 males, 4 females) who had unilateral adrenalectomy. Immunohistochemistry for CYP11B2 and next generation sequencing (NGS) targeting genes found in APA were performed on formalin fixed paraffin embedded adrenal tissue. Results were compared to previously described cohorts of 53 age-matched normotensive patients (29 males, 24 females) which were evaluated similarly.

Results: CYP11B2 expression was absent from intervening ZG cells in 8/11 (73%) IHA adrenals, but all adrenals harbored at least one APF. The median number and size of APF per case were significantly larger in IHA than normotensive controls (6.1 vs 0 APF/cm 2 of adrenal cortex and 0.25 vs. 0.16 mm 2 , respectively; p<0.0001 and p<0.006). In this IHA cohort, NGS identified CACNA1D and KCNJ5 somatic mutations in 44/71 (62%) and 1/71 (1%) of APF, respectively. Interpretations. Diffuse CYP11B2 expression in adrenal ZG cells was only observed in 3/11 IHA cases, arguing against ZG hyperplasia as the major underlying pathobiology. Rather, we demonstrated increased and enlarged APF in IHA adrenals compared to normotensive controls, supporting potential contribution to the clinical manifestations of hyperaldosteronism. The frequent occurrence of aldosterone-dysregulating CACNA1D somatic mutations in APF support CACNA1D as a potential therapeutic target in IHA to complement current MR blockade approaches.

Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors

Approximately 20% of metastatic prostate cancers harbor mutations in genes required for DNA repair by homologous recombination repair (HRR) such as BRCA2 HRR defects confer synthetic lethality to PARP inhibitors (PARPi) such as olaparib and talazoparib. In ovarian or breast cancers, olaparib resistance has been associated with HRR restoration, including by BRCA2 mutation reversion. Whether similar mechanisms operate in prostate cancer, and could be detected in liquid biopsies, is unclear. Here, we identify BRCA2 reversion mutations associated with olaparib and talazoparib resistance in patients with prostate cancer. Analysis of circulating cell-free DNA (cfDNA) reveals reversion mutation heterogeneity not discernable from a single solid-tumor biopsy and potentially allows monitoring for the emergence of PARPi resistance.Significance: The mechanisms of clinical resistance to PARPi in DNA repair-deficient prostate cancer have not been described. Here, we show BRCA2 reversion mutations in patients with prostate cancer with metastatic disease who developed resistance to talazoparib and olaparib. Furthermore, we show that PARPi resistance is highly multiclonal and that cfDNA allows monitoring for PARPi resistance. Cancer Discov; 7(9); 999-1005. ©2017 AACR.See related commentary by Domchek, p. 937See related article by Kondrashova et al., p. 984See related article by Goodall et al., p. 1006This article is highlighted in the In This Issue feature, p. 920.

Abstract LB-115: TPRKB dependency in p53-deficient cancers

TP53 (p53) is an extensively studied tumor suppressor mutated in approximately 50% of all cancers. Identification of vulnerabilities imposed by p53 alterations may enable effective targeted therapy development. Thus, this study aimed to identify and characterize novel vulnerabilities in this context. Through analyzing shRNA screening data from the Broad Institute’s Project Achilles, we identified TPRKB, a poorly characterized member of the tRNA-modifying EKC/KEOPS complex, as the most significant vulnerability in p53 mutated cancer cell lines. In vitro, across multiple benign-immortalized and cancer cell lines, we confirmed that TPRKB knockdown in p53-deficient cells significantly inhibited proliferation, while there was little to no effect in p53 wild-type cells. Furthermore, p53 reintroduction into TPRKB-sensitive p53-null cells resulted in loss of TPRKB sensitivity, confirming the importance of p53 status in this context. To determine whether this response was unique to TPRKB or a result of impairment of the EKC/KEOPS complex, we knocked down other members of the complex: PRPK, OSGEP, and LAGE3. PRPK loss showed minor changes between p53 wild type versus deficient cells; while OSGEP and LAGE3 loss resulted in a significant decrease regardless of p53 status. For the first time, we have demonstrated a potential role for TPRKB in cancer, and our results suggest that effects of TPRKB knockdown in p53-deficient cancer cells may be independent of its role in the EKC/KEOPS complex.

Citation Format: Kelly VanDenBerg, Moloy Goswami, Lei Lucy Wang, Bhavneet Singh, Travis Weiss, Sumin Han, Dan Rhodes, Felix Feng, Scott Tomlins. TPRKB dependency in p53-deficient cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-115. doi:10.1158/1538-7445.AM2017-LB-115

Abstract 5874: Cdk4/6 kinase inhibitor resistance in prostate cancer

Non-organ confined prostate cancer (PCa) is often effectively, but only transiently treated by targeting the androgen receptor (AR) signaling axis through androgen depletion strategies, often coupled with AR antagonists. Unfortunately, disease recurs within a median of 3-4 years, presenting as castration resistant PCa (CRPC), for which there are limited therapeutic options. This emphasizes the need for more efficacious drugs and a patient-tailored approach towards cancer therapy to improve disease outcome. One class of drugs currently tested clinically, Cdk4/6 kinase inhibitors, blocks phosphorylation of the retinoblastoma (RB) tumor suppressor, thereby boosting its function, and likely preventing castration resistance. As Cdk4/6 inhibitor resistance has already been reported in other cancers, some PCa patients are anticipated to develop drug resistance. Here, we created palbociclib-resistant PCa cell models by continuously culturing them in presence of the drug to unravel mechanisms of acquired resistance, and assessed them for cross-resistance to ribociclib and response to other therapeutics. While the parental PCa cell models, Cdk4/6 inhibitors efficiently induce a G1 cell cycle arrest, the resistant cell lines bypass this cell cycle checkpoint. Although loss of RB is a known mechanism for Cdk4/6i resistance, none of the models lost RB expression. Strikingly, these originally hormone-sensitive cell lines, upon developing Cdk4/6 inhibitor resistance display altered response to selected therapeutic regimens. Mechanisms of resistance, as informed by Whole Exome Sequencing and RNASeq, will be discussed.

Citation Format: Renee de Leeuw, Matthew J. Schiewer, Christopher McNair, Michael A. Augello, Akihiro Yoshida, Edward S. Hazard, Sean Courtney, Gerard T. Hardiman, Justin Drake, Felix Y. Feng, Scott Tomlins, Maha H. Hussain, J Alan Diehl, William K. Kelly, Karen E. Knudsen. Cdk4/6 kinase inhibitor resistance in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5874. doi:10.1158/1538-7445.AM2017-5874

Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors

Approximately 20% of metastatic prostate cancers harbor mutations in genes required for DNA repair by homologous recombination repair (HRR) such as BRCA2 HRR defects confer synthetic lethality to PARP inhibitors (PARPi) such as olaparib and talazoparib. In ovarian or breast cancers, olaparib resistance has been associated with HRR restoration, including by BRCA2 mutation reversion. Whether similar mechanisms operate in prostate cancer, and could be detected in liquid biopsies, is unclear. Here, we identify BRCA2 reversion mutations associated with olaparib and talazoparib resistance in patients with prostate cancer. Analysis of circulating cell-free DNA (cfDNA) reveals reversion mutation heterogeneity not discernable from a single solid-tumor biopsy and potentially allows monitoring for the emergence of PARPi resistance.Significance: The mechanisms of clinical resistance to PARPi in DNA repair-deficient prostate cancer have not been described. Here, we show BRCA2 reversion mutations in patients with prostate cancer with metastatic disease who developed resistance to talazoparib and olaparib. Furthermore, we show that PARPi resistance is highly multiclonal and that cfDNA allows monitoring for PARPi resistance. Cancer Discov; 7(9); 999-1005. ©2017 AACR.See related commentary by Domchek, p. 937See related article by Kondrashova et al., p. 984See related article by Goodall et al., p. 1006This article is highlighted in the In This Issue feature, p. 920.

Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium

The cancer community understands the value of blood profiling measurements in assessing and monitoring cancer. We describe an effort among academic, government, biotechnology, diagnostic, and pharmaceutical companies called the Blood Profiling Atlas in Cancer (BloodPAC) Project. BloodPAC will aggregate, make freely available, and harmonize for further analyses, raw datasets, relevant associated clinical data (e.g., clinical diagnosis, treatment history, and outcomes), and sample preparation and handling protocols to accelerate the development of blood profiling assays.

The Molecular Evolution of Castration-resistant Prostate Cancer

CONTEXT

Androgen deprivation therapy (ADT) is the backbone of treatment for advanced prostate cancer. However, castration-resistant prostate cancer (CRPC) nearly invariably develops through a range of different molecular mechanisms accompanied by progression to a more aggressive phenotype.

OBJECTIVE

To understand the key molecular mechanisms leading to CRPC and the functional implications of this progression. Understanding molecular evolutionary mechanisms in CRPC is essential for the development of novel curative therapeutic approaches.

EVIDENCE ACQUISITION

A systematic literature search to identify relevant original articles was conducted using PubMed. Findings verified in independent studies and supported by in vivo data were prioritised. From the eligible collection, 50 papers were selected.

EVIDENCE SYNTHESIS

The majority of CRPC tumours harbour alterations in the androgen receptor (AR) at the DNA, RNA, and/or protein level, and/or other alterations involving the AR signalling pathway, so this central molecule is the focus of this review. To survive and resume growth despite low levels of circulating androgens, prostate cancer cells can also adapt androgen synthesis or induce alternative pathways.

CONCLUSIONS

Despite more efficient ADT strategies, most evidence points to persistent AR signalling as a major mechanism of progression to CRPC. Resistance due to transdifferentiation or AR independence is also emerging as a mechanism of resistance. The diversity of potential resistance mechanisms supports the need for combination treatment and serial monitoring for adaptive treatment strategies.

PATIENT SUMMARY

In this review, we summarise how prostate cancer cells evade androgen deprivation therapy and become more aggressive. Defining the molecular mechanisms will be critical for the development of new treatment approaches and hence improved survival.

Abstract A03: Analyses of a prostate cancer patient-derived xenografts series, a resource for translational research

Patients with metastatic prostate cancer (PCa) have effective therapy options, but none of them are curative. Thus, their mortality rates are persistently high. Essential to furthering our progress in PCa research and therapy development is a spectrum of models that reflect the heterogeneity of the disease at each tumor site as well as the different histological variants of PCa (e.g., adenocarcinoma, small cell carcinoma). To address this challenge, we developed a strategy to establish PCa patient-derived xenografts (PDXs), using PCa tissue specimens taken from PCa sites demonstrating clinical progression. This approach provided a diverse repository of PDXs that can be linked prospectively with clinical progression and led to the identification of clinically relevant therapy targets and have proven valuable for testing drugs. We studied the first 50 PDXs developed under our program to a) define the histopathological features of paired human PCa and corresponding PDXs applying the clinically defined morphological characterization groupings of human cancer to the PDX tumors; b) assess the expression of genes known to play roles in PCa pathogenesis (e.g., androgen receptor, PTEN, ETS gene fusions) in PDXs and the human tumors of origin using immunohistochemistry and fluorescence in situ hybridization and c) perform array comparative genomic hybridization to 42 PDXs. We found that the histopathological and molecular pattern of these PDXs maintain the fidelity with the human tumor of origin. Furthermore, of the 50 cases studied, 32 (64%) were adenocarcinomas, and 16 (32%) were small cell carcinomas, poorly differentiated neuroendocrine carcinomas or mixed adenocarcinoma/ small cell carcinomas. In our cohort, we also have one sarcomatoid tumor and one ductal adenocarcinoma. Of the 32 adenocarcinomas in this cohort, 26 were AR-positive (81%), and 11 of the 27 AR-positive adenocarcinomas (41%) had aberrant expression of genes frequently involved in recurrent rearrangement (e.g., ERG, ETV1, ETV5). Also, SCCs and poorly differentiated neuroendocrine carcinomas did not express AR and were negative for ERG. This distribution recapitulates that of human PCa in the general population. Comparative genomic hybridization demonstrated gains and losses previously reported in PCa with a defined cluster of genomic aberrations. Significant differences in oncogenic pathways activation in pairs of PDXs derived from different areas of the same tumor suggesting divergent cellular progression. Finally, using this platform, we identified a focal deletion of speckle-type POZ protein-like (SPOPL) gene in 7/28 PDX. SPOPL is a MATH-BTB protein that shares an overall 85% sequence identity with SPOP (a SPOPL paralog). SPOP was recently reported to be mutated in about 8% of PCa and to define a molecular subclass of PCa. No mutations were found in SPOP in our cohort. In support of our findings, deletions on SPOPL were also found in about 7% of the PCa in TCGA data suggesting that our cohort is a reliable platform for discovery. In conclusion, we have developed a dynamic repository of clinically annotated samples that can be used as a discovery platform. Furthermore, these clinically annotated samples can be linked prospectively to clinical progression/response to therapy and thus will help define therapeutic targets for subpopulations of men and to identify likely responders to previous and upcoming therapies.

Citation Format: Nallasivam Palanisamy, Jun Yang, Xinhai Wan, Elsa M. li Ning Tapia, John C. Araujo, Eleni Efstathiou, Estefania Labanca, Louis Pisters, Ana Aparicio, Ritu Bhalla, Scott Tomlins, Lakshmi P. Kunju, Arul Chinnaiyan, Christopher J. Logothetis, Patricia Troncoso, Nora M. Navone. Analyses of a prostate cancer patient-derived xenografts series, a resource for translational research. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr A03.

The Potential of MicroRNAs as Prostate Cancer Biomarkers

CONTEXT

Short noncoding RNAs known as microRNAs (miRNAs) control protein expression through the degradation of RNA or the inhibition of protein translation. The miRNAs influence a wide range of biologic processes and are often deregulated in cancer. This family of small RNAs constitutes potentially valuable markers for the diagnosis, prognosis, and therapeutic choices in prostate cancer (PCa) patients, as well as potential drugs (miRNA mimics) or drug targets (anti-miRNAs) in PCa management.

OBJECTIVE

To review the currently available data on miRNAs as biomarkers in PCa and as possible tools for early detection and prognosis.

EVIDENCE ACQUISITION

A systematic review was performed searching the PubMed database for articles in English using a combination of the following terms: microRNA, miRNA, cancer, prostate cancer, miRNA profiling, diagnosis, prognosis, therapy response, and predictive marker.

EVIDENCE SYNTHESIS

We summarize the existing literature regarding the profiling of miRNA in PCa detection, prognosis, and response to therapy. The articles were reviewed with the main goal of finding a common recommendation that could be translated from bench to bedside in future clinical practice.

CONCLUSIONS

The miRNAs are important regulators of biologic processes in PCa progression. A common expression profile characterizing each tumor subtype and stage has still not been identified for PCa, probably due to molecular heterogeneity as well as differences in study design and patient selection. Large-scale studies that should provide additional important information are still missing. Further studies, based on common clinical parameters and guidelines, are necessary to validate the translational potential of miRNAs in PCa clinical management. Such common signatures are promising in the field and emerge as potential biomarkers.

PATIENT SUMMARY

The literature shows that microRNAs hold potential as novel biomarkers that could aid prostate cancer management, but additional studies with larger patient cohorts and common guidelines are necessary before clinical implementation.

Characterization of urothelial carcinoma with seminal vesicle involvement in locally advanced bladder cancer

440

Background: Muscle-invasive bladder cancer is associated with poor clinical outcomes, especially in locally advanced (pT4) disease. There is a paucity of data, however, regarding the clinical impact of seminal vesicle (SV) involvement. Therefore, we sought to characterize clinicopathologic features of patients with urothelial carcinoma involving seminal vesicles, and evaluate clinical outcomes in patients with locally advanced (pT4) bladder cancer with or without SV involvement. Methods: After institutional review board (IRB) approval, we retrospectively identified all men with pT4 (per the 7th edition of the AJCC Cancer Staging Manual) bladder cancer who underwent radical cystectomy between 2002 and 2013 at a single large academic institution. Clinicopathologic and follow-up data for all patients were obtained from the electronic medical record. The presence or absence of divergent differentiation, including aggressive forms (plasmacytoid, nested, micropapillary, and sarcomatoid), was recorded. Estimates of overall survival (OS) were compared by plotting Kaplan-Meier curves and using log-rank test. Results: A total of 62 patients were eligible for analysis. The median age and follow-up duration were 72 (range: 46 – 87) years and 12 (range: 0 – 141) months respectively. SV involvement was present in 17.7% (11/62) of patients. The frequency of divergent differentiation (including aggressive forms), angiolymphatic invasion, nodal disease (pN1-3), and positive soft tissue margins was relatively higher among those with SV involvement (not significant, all p >0.05). The 1 and 2-year OS for patients with SV involvement were 32.7% and 0% respectively, compared with 51.0 % and 24.9% respectively for patients without SV involvement. There was no statistically significant difference between the median OS of men with and without SV involvement (9 vs. 13 months, respectively; p = 0.19). Conclusions: In this relatively limited sample size cohort, we did not observe any difference in the overall survival of locally advanced bladder cancer patients with and without SV involvement.

Molecular and clinical characterization of 1,577 primary prostate cancer tumors to reveal novel clinical and biological insights into its subtypes

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Background: Prostate cancer molecular subtypes based on ETS gene fusions and SPINK1 were originally identified through outlier gene expression profiling analysis. Such molecular subtypes may have utility in disease stratification and clonality assessment, complementing available purely prognostic tests. Hence, we determined the analytical validity of molecular subtyping in a large sample of PCa treated with radical prostatectomy. Methods: We analyzed Affymetrix Human Exon 1.0ST GeneChip expression profiles for 1,577 patients from 8 radical prostatectomy (RP) cohorts. Multi-feature random forest classifiers and outlier analysis were used to define microarray-based molecular subtypes. Results: A random forest (RF) classifier was trained and validated to predict ERG fusion status using a subset with known ERG rearrangement status defined by FISH, achieving >95% sensitivity and specificity in the validation subset. Less frequent rearrangements involving other ETS genes or SPINK1 over-expression were predicted based on gene expression outlier analysis. Across cohorts, 45%, 9% 8% and 38% of PCa were classified as ERG+, ETS+, SPINK+, and Triple Negative, respectively. Global gene expression analysis shows that the four subtypes could be collapsed into three entities (ERG+, ETS+ and SPINK+/Triple Negative) based on expression patterns and clinical characteristics similarity. A series of multivariable analyses further revealed, ERG+ to be associated with lower pre PSA and Gleason scores but more likely to have EPE and occur in patients with European American ancestry compared to the ETS+, SPINK+/Triple Negative tumors (p<0.001). In contrast, patients with ETS+ were more likely to have SVI compared to both ERG+ and SPINK/Triple Negative (p=0.01), while SPINK+/Triple Negative had higher Gleason scores and were more likely to occur in African Americans (p<0.001). Conclusions: The Decipher platform can accurately determine ERG rearrangement status and PCa molecular subtypes. Inclusion of molecular subtyping, such as m-ERG status, may enable additional precision medicine opportunities in prognostic tests

Aggressive variants of castration-resistant prostate cancer

A subset of patients with advanced castration-resistant prostate cancer may eventually evolve into an androgen receptor (AR)-independent phenotype, with a clinical picture associated with the development of rapidly progressive disease involving visceral sites and hormone refractoriness, often in the setting of a low or modestly rising serum prostate-specific antigen level. Biopsies performed in such patients may vary, ranging from poorly differentiated carcinomas to mixed adenocarcinoma-small cell carcinomas to pure small cell carcinomas. These aggressive tumors often demonstrate low or absent AR protein expression and, in some cases, express markers of neuroendocrine differentiation. Because tumor morphology is not always predicted by clinical behavior, the terms "anaplastic prostate cancer" or "neuroendocrine prostate cancer" have been used descriptively to describe these rapidly growing clinical features. Patients meeting clinical criteria of anaplastic prostate cancer have been shown to predict for poor prognosis, and these patients may be considered for platinum-based chemotherapy treatment regimens. Therefore, understanding variants within the spectrum of advanced prostate cancer has important diagnostic and treatment implications.

Papillary renal cell carcinoma revisited: a comprehensive histomorphologic study with outcome correlations

Papillary renal cell carcinoma (P-RCC) is the second most common type of malignant renal epithelial tumor and can be subclassified into type 1, which demonstrates simple cuboidal low-grade epithelium and type 2, which demonstrates pseudostratified high-grade epithelium with abundant eosinophilic cytoplasm. Despite this clinically useful subclassification, P-RCCs exhibit considerable histomorphologic diversity, with many cases having features differing from classically described type 1 and type 2 tumors. To our knowledge, there has been no recent study that has methodically evaluated the histomorphologic features of a series of P-RCCs. To address this, we evaluated a cohort of P-RCCs diagnosed between 1997 and 2004 with long-term clinical follow-up data (n = 56). Histomorphologic features previously described in the spectrum of type 1 and type 2 P-RCCs were recorded for each tumor, including nuclear grade, complete tumor capsule, and cytoplasmic eosinophilia as well as several other features. The current TNM staging (American Joint Committee on Cancer, seventh edition) was assigned to all cases. Histomorphologic features were diverse, demonstrating classic type 1 P-RCC and classic type 2 P-RCC morphology and several tumors with nonclassic features. Four patients in this cohort had distant metastasis. The primary tumor was equally divided between type 1 (2 cases) and type 2 (2 cases) morphology in the cases with metastasis. All P-RCC cases with metastases demonstrated presence of high nuclear grade and high tumor stage in the primary tumor. Cluster analysis using staging parameters and histomorphologic features divided tumors into 2 primary clusters. All primary tumors associated with metastasis were in the same cluster.

Abstract 2780: Xenografts of human prostate cancer - a genetic profile analysis

Prostate cancer (PCa) is the second leading cause of cancer-related death in the US. Recent clinical trials have shown responses in a subpopulation of patients; thus we need methods to identify likely responders. The genetic basis of PCa is understood to the extent that patients can be classified based on underlying molecular aberrations: 50-60% of PCas have rearrangements in ERG, ETV1, ETV4, ETV5, BRAF, and RAF1 and overexpression of SPINK1 and AR. PCas with PTEN deletion along with ERG have altered clinical behavior. We developed a strategy to establish PCa xenografts with tissue taken directly from men and implanted subcutaneously in SCID mice. After its growth, the tumor is harvested and sequentially passaged over 4 or 5 mice. We have established 62 PCa xenografts since the program's inception. These xenografts, which are often developed while the donor PCa patient is alive, have proven valuable for testing drugs and have led to initiation of a promising clinical study (ClinicalTrials.gov: NCT00831792). In the study reported here we systematically characterized 51/62 xenografts for the presence of known PCa markers by immunohistochemistry and fluorescence in situ hybridization. The PCa xenografts were derived from PCas in the prostate or direct extensions to adjacent organs (21) or from metastases to bone (4), lymph node (3), liver (6), thyroid (1), testis (1), adrenal gland (2), brain (3), and unusual sites (skin, chest wall, soft tissue) (4) or ascites (3), and pleural effusions (3). 81% of xenografts derived from prostatic adenocarcinomas were AR positive (27/33); 16 were small-cell, poorly differentiated neuroendocrine carcinomas or ductal adenocarcinomas and did not express AR. One sarcomatoid and 1 ductal adenocarcinoma expressed AR; 77% of evaluable tumors had a deletion in PTEN (31/40); 48% of AR-positive tumors expressed recurrent gene fusions (eg, ERG, ETV1, ETV5) (13/27). Together, these results in this cohort_AR and recurrent gene fusion expression and PTEN deletion_nicely correlate with findings in human PCa. We next assessed whether PCa xenografts maintained histopathologic and molecular fidelity with the human tumor of origin in selected cases (n=16). Histopathologic pattern and recurrent gene fusion expression were the same in the paired human and mouse tissue. The AR and PTEN status were the same in most paired human and mouse samples. In 4 cases, AR expression was lost or PTEN deleted in the PCa xenograft, suggesting that selection for more aggressive genotypes may occur during xenograft development and that PCa xenografts develop by selecting cells’ drivers of cancer progression. In conclusion, we have developed a protocol for xenograft development that has fidelity with human PCa. This approach has provided a repository of clinically annotated samples that can be linked prospectively to clinical progression/response to therapy and thus will help identify therapy responders.

Citation Format: Nallasivam Palanisamy, Jun Yang, Xinhai Wan, John C. Araujo, Eleni Efstathiou, Louis Pisters, Ritu Bhalla, Scott Tomlins, Lakshmi P. Kunju, Arul Chinnaiyan, Christopher J. Logothetis, Patricia Troncoso, Nora M. Navone. Xenografts of human prostate cancer - a genetic profile analysis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2780. doi:10.1158/1538-7445.AM2013-2780

Abstract 3664: Breast cancer companion diagnostic platform based on objectively defined tumor co-expression patterns stratifies multiple clinical and therapeutic endpoints comparison to existing molecular subtyping definitions

Gene expression profiles of human breast tumors have greatly expanded our understanding of the genes and pathways that underlie breast cancer. Profiling studies have also supported a molecular classification of breast cancer. The resulting molecular subtypes Luminal, Basal-like, ERBB2+, and Normal-like were shown to have different prognostic and predictive characteristics. Related studies have led to a proliferation of multigene prognostic and predictive diagnostic tests. Two independent multigene tests, OncoType Dx and MammaPrint, have been shown to be helpful in predicting the risk of recurrence of patients with early stage breast cancer. Current multigene tests consistently prioritize the proliferation, estrogen receptor (ER), and ERBB2 pathways. An alternative approach to identifying key molecular variables within breast cancer is based on a definition of objectively defined tumor co-expression patterns. To this end, we defined co-expression patterns within 56 independent breast cancer molecular profiling datasets representing &gt;5,000 unique patients. We then performed a meta-analysis across datasets to define the most robust, consistently occurring co-expression patterns. These patterns, termed modules, recapitulate the proliferation, ER, and ERBB2 pathways, but also monitor expression of other important variables including core cancer cell growth pathways, immune signaling and microenvironment, and hallmark genomic aberrations. An important feature of co-expression patterns is that a small number of genes serve as an effective surrogate for each module. Thus, we created a single multigene qPCR test that measures the expression of 18 distinct breast cancer modules and validated the test for use with formalin-fixed paraffin-embedded (FFPE) tumor samples. In retrospective microarray scoring analyses with key clinical datasets, and with analysis of FFPE specimens from breast cancer cohorts, we demonstrate that breast cancer modules can be used to recapitulate the molecular subtypes of breast cancer and to have prognostic and predictive properties similar to the current multigene tests. Because they recapitulate existing molecular tests, while also reading out many additional axes of molecular variability, breast cancer modules provide a universal assay with broad application to companion diagnostics development.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3664. doi:1538-7445.AM2012-3664

P1-07-04: Gene Expression Module Biomarkers To Stratify Multiple Clinical and Therapeutic Endpoints for Universal Breast Cancer Companion Diagnostic

Gene expression patterns are increasingly capable of stratifying patients based on prognosis and response to therapy. Given the limited availability of sample tissue, however, it is not feasible to run many tests, suggesting the need for a universal companion diagnostic assay that is informative with respect to multiple clinical and therapeutic endpoints. Key challenges are identification of appropriate gene expression biomarkers, translation of biomarkers to clinical assays, and development of reliable gene expression profiling of formalin-fixed clinical specimens. Here, we describe a meta-analysis approach that identifies novel biomarker modules that results in multiple clinical and therapeutic read-outs.

A co-expression meta-analysis of 5,339 breast tumors from 56 microarray datasets identified highly co-expressed sets of genes (modules) across multiple datasets. These module based biomarkers were tested for their ability to associate with prognostic and predictive targets in published datasets. In addition, each module was reduced from 10 - 1,000 genes to the top performing 2–3 genes based on the degree of co-expression across the meta-analysis and validation by quantitative PCR in an independent panel of FFPE tumor samples. This study demonstrates that a single 96 gene qPCR test utilizing multiple module biomarkers is not only capable of stratifying patients by standard histopathological parameters (ER, PR and Her2), but also stratifies by other diverse elements of the disease (cell lineage, dysregulated core biological functions, factors of cell growth, underlying genomic aberrations and the tumor microenvironment). Taken together, these biological variables represent the major biological diversity present within the breast cancer population. A series of retrospective analyses demonstrated that different single module and combinations of modules were capable of predicting a variety of clinical endpoints, including 5-year survival, neoadjuvant chemotherapy response in ER- patients and targeted therapy response in model systems.The molecular heterogeneity of breast cancer can be summarized by discrete gene expression modules that individually represent distinct biological pathways, and that collectively can be represented by as few as 96 genes. These breast cancer modules, together with outlier genes, allow for summation of the entire transcriptional program and provide a universal assay with broad application to companion diagnostics development.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-07-04.

The tumor suppressor gene rap1GAP is silenced by miR-101-mediated EZH2 overexpression in invasive squamous cell carcinoma

Rap1GAP is a critical tumor suppressor gene that is downregulated in multiple aggressive cancers, such as head and neck squamous cell carcinoma, melanoma and pancreatic cancer. However, the mechanistic basis of rap1GAP downregulation in cancers is poorly understood. By employing an integrative approach, we demonstrate polycomb-mediated repression of rap1GAP that involves Enhancer of Zeste Homolog 2 (EZH2), a histone methyltransferase in head and neck cancers. We further demonstrate that the loss of miR-101 expression correlates with EZH2 upregulation, and the concomitant downregulation of rap1GAP in head and neck cancers. EZH2 represses rap1GAP by facilitating the trimethylation of histone 3 at lysine 27, a mark of gene repression, and also hypermethylation of rap1GAP promoter. These results provide a conceptual framework involving a microRNA-oncogene-tumor suppressor axis to understand head and neck cancer progression.

Abstract 953: Mechanistic rationale for inhibition of Poly(ADP-Ribose) Polymerase in ETS gene fusion positive prostate cancer

Recurrent fusions of ETS genes are considered driving mutations in a diverse array of cancers including Ewing's sarcoma, acute myeloid leukemia, and epithelial tumors such as prostate cancer. However, transcription factors like the ETS genes have been notoriously difficult to target therapeutically. In fact, while approximately 50% of all prostate cancers harbor ETS gene fusions, the most common variant fuses an androgen regulated promoter and the 5’-UTR of TMPRSS2 to the second exon of ERG resulting in the pathogenic overexpression of a slightly truncated ERG transcription factor. Here, we use IP-mass spectrometry to characterize the ETS protein interactome in prostate cancer. We show that the TMPRSS2:ERG gene fusion product interacts with the enzymes poly(ADP-ribose)polymerase 1 (PARP1) and the catalytic subunit of DNA protein kinase (DNA-PKcs) in a DNA-independent manner in both prostate cancer cells and tissues. ETS gene fusion-mediated transcription of several target genes including the invasion associated gene EZH2 requires both PARP1 and DNA-PKcs expression and activity. Likewise, cell invasion driven by ETS gene overexpression is inhibited by small molecule inhibitors or siRNA against these enzymes in matrigel coated transwell invasion assays (in vitro) as well as chicken chorioallantoic membrane intravasation and metastasis assays (in vivo). Importantly, pharmacological inhibition of PARP1 selectively inhibited the growth of 4 ETS positive, but not 5 ETS negative, prostate cancer cell xenografts. This analysis includes several prostate cancer cell lines, an isogenic model of hormone refractory prostate cancer and primary human tumors that were serially grown in mice. Finally, we find that TMPRSS2:ERG gene fusion overexpression leads to increased DNA double strand breaks as assessed by gamma-H2A.X staining and COMET assays. This DNA damage is then potentiated by PARP1 inhibition in a manner similar to that of BRCA1/2-deficiency.Thus, we propose that the ETS:PARP1 interaction axis may represent a novel target for therapeutic intervention in cancers with ETS gene fusions and that future clinical trials will help determine if this subgroup of patients preferentially benefits from the addition of PARP inhibitor therapy. Moreover, our study suggests that inhibition of co-factors necessary for function may represent a new paradigm of treatment for malignancies driven by oncogenic transcription factors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 953. doi:10.1158/1538-7445.AM2011-953

Abstract LB-262: Estimation of tumor content from exome sequencing data

In cancer genomics studies, variation in sample purity can greatly influence the ability to detect cancer-specific genomic aberrations. Genomics datasets are often analyzed as if samples consist of 100% cancerous or benign cells, which is rarely true in practice. Particularly in prostate tumors, one always expects tumor samples to consist of a mixture of cancer cells, stromal cells, and benign cells. Here we use next-generation exome sequencing data to estimate the proportion of cancer cells by sample, which may then be used for downstream analysis.

Using human whole-exome capture data from 14 prostate tumors and matched benign tissues from the same patients, we developed a statistical method for estimating tumor content. Specifically, we generated a list of single-nucleotide variant (SNV) candidates derived from the sequencing data and used these candidates to fit a two-component binomial mixture model. The two components are assumed to consist of a set of experimental artifacts such as sequencing errors which tend to exhibit low fractions of variant reads, and a set of true SNVs whose variant fractions are related to the unknown tumor content. Estimation, achieved via the EM algorithm, results in a probabilistic classification of the SNV candidates as well as an estimated proportion of cancer cells in each sample.

As expected, 6 of 7 metastatic samples had high estimated tumor content (&gt;70%). In contrast, among the set of 7 localized cancer samples, most of which exhibited an absence of copy number aberrations by aCGH, only 3 had enough SNVs to reliably estimate tumor content. Tumor content in these samples varied: two of the three samples had tumor content of approximately 70% while the third was estimated to be 35%.

Knowledge of a sample's tumor content may be used in any downstream analysis of genomic data; here we point out three applications. First, this method allows for rigorous quality control and exclusion of samples based on tumor content as estimated from the data. Second, it can improve the quality of SNV calling from next-generation sequencing data. To test this, we performed Sanger sequencing on 30 SNV candidates from one of our localized cancer samples and compared validation status with the predictions from our model. Notably, our model predicted validation status perfectly (18 validated; 12 did not) on this set of candidates. Third, precise knowledge of tumor content enabled us to explain variation in copy number profiles by aCGH. We found that log-ratios for regions of gain and loss were smaller in magnitude for samples with lower tumor content; this has major implications for calling aberrant regions from aCGH data. Thus, we anticipate that the methodology described here will be useful in refining many standard methods of analysis so that a clearer picture of aberrations in prostate cancer can emerge.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-262. doi:10.1158/1538-7445.AM2011-LB-262

Abstract 899: TMPRSS2:ERG urine test identifies Gleason score upgrading and significant prostate cancer

Objective: In men diagnosed with prostate cancer (PCa) at biopsy, a major challenge is correctly stratifying those with indolent versus significant PCa for treatment selection. The extent and grade of PCa is assessed in part based on standard risk factors, biopsy Gleason score (bx GS) and the number of positive biopsy cores. However, due to under-sampling at biopsy, upgrading in Gleason score is often seen from biopsy to prostatectomy. In this study we evaluated a TMPRSS2:ERG (T2:ERG) urine test for its ability to identify significant cancer and upgrading at prostatectomy.

Methods: Post-DRE urine specimens were prospectively collected from 218 men referred for prostatectomy. T2:ERG mRNA copies were quantified using a transcription-mediated amplification assay and normalized to PSA mRNA copies to calculate a T2:ERG score. The prototype T2:ERG urine assay detects the gene fusion mRNA isoform TMPRSS2 exon 1 to ERG exon 4. T2:ERG score was correlated to prostatectomy Gleason score (px GS) and significant cancer as defined by the Epstein criteria at prostatectomy.

Results: Of 185 men scheduled for radical prostatectomy, 61 had low risk of significant cancer based on having bx GS&lt;6 and % positive biopsy cores&lt;33%, yet upon prostatectomy, 57% of these men were found to harbor a significant PCa. The T2:ERG assay identified an additional 31% prostatectomy significant cancer in the biopsy low-risk disease cancer group. In a multivariate model, adding T2:ERG to bx GS and % positive cores significantly increased the accuracy for predicting significant PCa at prostatectomy from 0.84 to 0.89 (p=0.0002). Sensitivity increased by 8% for detecting prostatectomy significant cancer when T2:ERG was added to these biopsy criteria (sens/spec=85%/87% vs 77%/87%). T2:ERG also significantly correlated with Gleason score upgrading from biopsy to prostatectomy (bx GS/px GS = 6/ 6 vs bx GS/px GS = 6/&gt;7, p = 0.0076). At biopsy, 70 men were found to have low-grade cancer (bx GS&lt;6), but upon prostatectomy, upgrading was seen in 50% of these men. T2:ERG was able to identify 40% of men with bx GS&lt;6 that were later upgraded.

Conclusions: A T2:ERG urine test may help identify significant cancers and Gleason score upgrading, and increase predictive accuracy when used in combination with currently available methods.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 899. doi:10.1158/1538-7445.AM2011-899

Abstract 2795: An onco-protein axis linking polycomb repressive complex 2 and polycomb repressive complex 1 through miRNAs in cancer

Enhancer of Zeste Homolog 2 (EZH2) is the catalytic histone methyltransferase subunit of the Polycomb Repressive Complex 2 (PRC2), that trimethylates histone H3 at lysine 27 (H3K27me3) resulting in the silencing of target genes. PRC2 plays a critical role in many basic cellular processes including cell proliferation, differentiation, early embryogenesis, and X chromosome inactivation. In cancer, EZH2 upregulation is implicated in metastasis and tumor aggressiveness of prostate and breast cancer and several other solid tumors. Recently our lab reported the genomic loss of miR-101 microRNA accompanying EZH2 overexpression in tumor cells. Here we identified several microRNAs that were downregulated by EZH2 and their levels were restored upon EZH2 depletion in cancer cell lines, and expression levels of these microRNAs were negatively correlated with EZH2 in human prostate tumors. Additionally, H3K27me3 modification was observed in the upstream regions of the miRNAs, suggesting a direct role for EZH2 in their regulation. Ectopic overexpression of the miRNAs suppressed cell proliferation, invasion, anchorage-independent growth, sphere formation and xenograft tumor growth of aggressive prostate and breast cancer cell lines. Finally, our investigations showed that the miRNAs also repress the expression of Polycomb Repressive Complex 1 (PRC1) members BMI1 and RING2, leading to a global decrease in the epigenetic marker, ubiquityl-H2A-K119 (uH2A) in cells, a key step in PRC1-mediated silencing. Our findings provide compelling argument for a regulatory axis joining PRC2 and PRC1 through miRNAs. This novel link between PRC2 and PRC1 indicates a coordinated mechanism by polycomb group proteins to promote an aggressive cancer phenotype.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2795. doi:10.1158/1538-7445.AM2011-2795