Van Der Kwast Research Articles

Abstract 4305: Germline structural variants shape prostate cancer clinical and molecular evolution

Abstract Inherited genetic variation profoundly influences cancer risk and outcome. While the impact of germline single nucleotide polymorphisms has been well-studied in several cancer types, the effects of germline structural variants (gSVs) on cancer biology and clinical outcomes is largely unknown. From our cohort of 300 men with localized, intermediate risk prostate cancer, we identified 6,003 gSVs present in at least 3% of patients; 48 were associated with recurrent somatic alterations or clinical outcome. Of these, approximately 50% were associated with expression of nearby genes or intersected with exons or regulatory regions. Using external cohorts, we validated three gSVs that were strongly associated with poor clinical outcomes, including an inversion at chr14q24.1 present in ~20% of patients. Notably, a strong synergistic effect on outcome was observed in patients with somatic TP53 alterations or high genomic instability, defining a new aggressive prostate cancer subtype with chr14INV as a novel, recurrent biomarker. Citation Format: Nicholas K. Wang, Alexandre Rouette, Kathleen E. Houlahan, Takafumi N. Yamaguchi, Julie Livingstone, Chol-Hee Jung, Peter Georgeson, Michael Fraser, Yu-Jia Shiah, Cindy Q. Yao, Vincent Huang, Natalie S. Fox, Natalie Kurganovs, Katayoon Kasaian, Veronica Y. Sabelnykova, Jay Jayalath, Kenneth Weke, Helen Zhu, Theodorus van der Kwast, Tony Papenfuss, Housheng H. He, Niall M. Corcoran, Robert G. Bristow, Alexandre R. Zlotta, Christopher Hovens, Paul C. Boutros. Germline structural variants shape prostate cancer clinical and molecular evolution. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4305.

Unraveling the epitranscriptome of small non-coding RNAs in vascular cells

Unraveling the epitranscriptome of small non-coding RNAs in vascular cells

Author Reply

All authors of the article “Predictive value of Cribriform and Intraductal Carcinoma for the Nomogram-Based Selection of Prostate Cancer Patients for Pelvic Lymph Node Dissection” sincerely appreciate the editorial comment. Although multiple retrospective studies have shown that nodal metastases are significantly more common in patients with CR/IDC, 1 Ericson KJ Wu SS Lundy SD Thomas LJ Klein EA McKenney JK. Diagnostic accuracy of prostate biopsy for detecting cribriform Gleason pattern 4 carcinoma and intraductal carcinoma in paired radical prostatectomy specimens: implications for active surveillance. The Journal of urology. 2020; 203: 311-319 Crossref PubMed Scopus (0) Google Scholar , 2 Wang L Deng FM Huang H Lee P Melamed J.M Zhou M. Gleason score 7 and 8 prostate cancer with cribriform morphology diagnosed in prostate biopsy is more likely to have seminal vesicle invasion and pelvic lymph node metastasis in radical prostatectomy. Mod Pathol. 2017; 30: 266A Google Scholar , 3 Downes MR Xu B van der Kwast TH. Cribriform architecture prostatic adenocarcinoma in needle biopsies is a strong independent predictor for lymph node metastases in radical prostatectomy. Eur J Cancer [Internet]. 2020; (Available from)https://linkinghub.elsevier.com/retrieve/pii/S0959804920305244 PubMed Google Scholar CR/IDC status did not improve the prediction of nodal metastases in our study. However, the “Letter to the Editor” clearly points out that presence of cribriform and intraductal carcinoma (CR/IDC) could allow the selection of intermediate-risk prostate cancer patients for extended pelvic lymph node dissection. Unfortunately, the number of intermediate-risk patients in our study leave us underpowered to validate the clinical benefit of a CR/IDC-enriched nomogram in this cohort. Recently, Yu et al. retrospectively demonstrated that the addition of CR/IDC status to pretreatment prostate cancer classification tools (ie, the Cancer of Prostate Risk Assessment and National Comprehensive Cancer Network [NCCN] risk scores) particularly improves the outcome stratification of intermediate-risk prostate cancer patients. 4 Yu Y Lajkosz K Finelli A Fleshner N van der Kwast TH Downes MR Impact of cribriform pattern 4 and intraductal prostatic carcinoma on National Comprehensive Cancer Network (NCCN) and Cancer of Prostate Risk Assessment (CAPRA) patient stratification. Modern Pathol. 2022; : 1-7 PubMed Google Scholar Alterations in the risk stratification may eventually affect treatment recommendations for these patients. Given the increased interest in integrating CR/IDC into clinical decision making, not only for guiding nodal dissections, but eg also for the selection of patient for active surveillance, 5 Ericson KJ Wu SS Lundy SD Thomas LJ Klein EA McKenney JK. Diagnostic accuracy of prostate biopsy for detecting cribriform Gleason pattern 4 carcinoma and intraductal carcinoma in paired radical prostatectomy specimens: implications for active surveillance. J Urol. 2020; 203: 311-319 Crossref PubMed Scopus (21) Google Scholar prospective studies evaluating the value of biopsy-identified CR/IDC for oncological outcomes and clinical decision making in intermediate-risk prostate cancer patients are needed.

FOXA1 regulates alternative splicing in prostate cancer.

SummaryDysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by AR, ERG, FOXA1, and MYC. Here, we show that FOXA1 functions as the primary orchestrator of alternative splicing dysregulation across 500 primary and metastatic prostate cancer transcriptomes. We demonstrate that FOXA1 binds to the regulatory regions of splicing-related genes, including HNRNPK and SRSF1. By controlling trans-acting factor expression, FOXA1 exploits an “exon definition” mechanism calibrating alternative splicing toward dominant isoform production. This regulation especially impacts splicing factors themselves and leads to a reduction of nonsense-mediated decay (NMD)-targeted isoforms. Inclusion of the NMD-determinant FLNA exon 30 by FOXA1-controlled oncogene SRSF1 promotes cell growth in vitro and predicts disease recurrence. Overall, we report a role for FOXA1 in rewiring the alternative splicing landscape in prostate cancer through a cascade of events from chromatin access, to splicing factor regulation, and, finally, to alternative splicing of exons influencing patient survival.

PD63-01 ONCOLOGICAL LONG-TERM BENEFIT OF RE-RESECTION IN T1 BLADDER CANCER: A POPULATION-BASED COHORT STUDY FROM ONTARIO

You have accessJournal of UrologyBladder Cancer: Non-invasive III (PD63)1 Sep 2021PD63-01 ONCOLOGICAL LONG-TERM BENEFIT OF RE-RESECTION IN T1 BLADDER CANCER: A POPULATION-BASED COHORT STUDY FROM ONTARIO Marian S. Wettstein, Nancy N. Baxter, Rinku Sutradhar, Muhammad Mamdani, Song Pham, Syed R. Qadri, Kathy Li, Ning Liu, Theodorus van der Kwast, Thomas Hermanns, and Girish S. Kulkarni Marian S. WettsteinMarian S. Wettstein More articles by this author , Nancy N. BaxterNancy N. Baxter More articles by this author , Rinku SutradharRinku Sutradhar More articles by this author , Muhammad MamdaniMuhammad Mamdani More articles by this author , Song PhamSong Pham More articles by this author , Syed R. QadriSyed R. Qadri More articles by this author , Kathy LiKathy Li More articles by this author , Ning LiuNing Liu More articles by this author , Theodorus van der KwastTheodorus van der Kwast More articles by this author , Thomas HermannsThomas Hermanns More articles by this author , and Girish S. KulkarniGirish S. Kulkarni More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002107.01AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: A second transurethral resection within 2 to 6 weeks after the initial resection (i.e. re-resection) is recommended for patients diagnosed with primary T1 bladder cancer as prior studies suggest therapeutic, diagnostic, and prognostic benefits. Results on survival endpoints, however, are sparse, conflicting, and often affected by various biases. Hence, we aimed to provide real-world evidence by investigating the survival benefit of re-resection in T1 bladder cancer at the population level. METHODS: Retrospective population-wide observational cohort study based on pathology reports linked to health administrative data. We identified patients who were diagnosed with T1 bladder cancer in the province of Ontario (01/2001-12/2015) and used billing claims to ascertain whether they received re-resection within 2 to 10 weeks. The time-dependent effect of re-resection on survival outcomes was modeled by Cox proportional hazards regression (unadjusted and adjusted for numerous assumed patient- and surgeon-level confounding variables). Effect measures were presented as hazard ratios and 95% confidence intervals. RESULTS: We identified 7,666 patients of which 2,162 (28.7%) underwent re-resection after a median time of 45 days (interquartile range: 35-56 days). The probability of dying from bladder cancer was consistently lower than the probability of dying from other causes (5 years: 15.8% versus 25.0%, 10 years: 18.7% versus 40.9%). Patients who received re- resection were less likely to die from any causes (0.68 [0.63-0.74], p<0.001) and from bladder cancer (0.66 [0.57-0.76], p<0.001) during any time of follow-up. After adjusting for all assumed confounding variables, re-resection was still significantly associated with a lower overall mortality (0.88 [0.81-0.95], p<0.001) while the association with cancer-specific survival marginally lost its statistical significance (0.87 [0.75-1.02], p=0.08). CONCLUSIONS: To the best of our knowledge, this population-wide study represents the largest cohort of patients diagnosed with T1 bladder cancer and provides real-world evidence supporting the utilization of re-resection in this group of patients. Source of Funding: None © 2021 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 206Issue Supplement 3September 2021Page: e1138-e1138 Advertisement Copyright & Permissions© 2021 by American Urological Association Education and Research, Inc.MetricsAuthor Information Marian S. Wettstein More articles by this author Nancy N. Baxter More articles by this author Rinku Sutradhar More articles by this author Muhammad Mamdani More articles by this author Song Pham More articles by this author Syed R. Qadri More articles by this author Kathy Li More articles by this author Ning Liu More articles by this author Theodorus van der Kwast More articles by this author Thomas Hermanns More articles by this author Girish S. Kulkarni More articles by this author Expand All Advertisement Loading ...

Abstract IA-018: Molecular landmarks of tumor hypoxia across cancer types

Abstract Many primary tumor sub-regions have low levels of molecular oxygen, termed hypoxia. Hypoxic tumors are at elevated risk for local failure and distant metastasis, but the molecular hallmarks of tumor hypoxia remain poorly defined. To fill this gap, we quantified hypoxia in 8,006 tumors across 19 tumor types. In ten tumor types, hypoxia was associated with elevated genomic instability. In all 19 tumor types, hypoxic tumors exhibited characteristic driver mutation signatures. We observed widespread hypoxia-associated dysregulation of miRNAs across cancers and functionally validated miR-133a-3p as a hypoxia-modulated miRNA. In localized prostate cancer, hypoxia was associated with elevated rates of chromothripsis, allelic loss of PTEN and shorter telomeres. These associations are particularly enriched in polyclonal tumors, representing a constellation of features resembling tumor nimbosus – an aggressive cellular phenotype. Overall, this work establishes that tumor hypoxia may drive aggressive molecular features across cancers and shape the clinical trajectory of individual tumors. Citation Format: Vinayak Bhandari, Christianne Hoey, Lydia Liu, Emilie Lalonde, Jessica Ray, Julie Livingstone, Robert Lesurf, Yu-Jia Shiah, Tina Vujcic, Xiaoyong Huang, Shadrielle M.G. Espiritu, Lawrence E. Heisler, Fouad Yousif, Vincent Huang, Takafumi N. Yamaguchi, Cindy Q. Yao, Veronica Y. Sabelnykova, Michael Fraser, Melvin L.K. Chua, Theodorus van der Kwast, Stanley K. Liu, Paul C. Boutros, Robert G. Bristow. Molecular landmarks of tumor hypoxia across cancer types [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr IA-018.

Abstract B23: FGFR3 mutations and their relation to FGFR3 expression and clinical outcome in a large radical cystectomy cohort: Implications for anti-FGFR3 bladder cancer treatment?

Abstract Objective: Fibroblast growth factor receptor 3 (FGFR3) is a potentially actionable target in bladder cancer (BC). FGFR3 mutations are associated with favorable prognosis in non-muscle invasive (NMI) BC and MIBC. Overexpression of FGFR3 was reported in up to 40% of FGFR3 wild-type MIBC. p53 alterations rarely coincide with FGFR3 mutations. We analyzed FGFR3 mutations and protein-expression of FGFR3 and p53 and assessed their prognostic value in a multicenter, multilaboratory setting. Methods: We included 1,000 cN0M0, chemotherapy-naive patients who underwent radical cystectomy (RC) with pelvic node dissection. Specimens were reviewed by eight uropathologists. At seven laboratories, FGFR3 mutation status was examined using PCR-SNaPshot. p53 and FGFR3 expression were determined by immunohistochemistry (IHC). FGFR3 mutation status, p53 and FGFR3 protein expression were correlated to each other, clinicopathologic parameters, and disease-specific survival (DSS). Results: FGFR3 mutations were found in 107/1,000 RCs (11%), of which 67 were S249C. Overexpression of FGFR3 was found in 279/1,000 (28%) of tumors. p53 overexpression (cut-off&amp;gt;10%) was found in 638/926 (69%) of available cases. Among FGFR3 mutant tumors, 73% had FGFR3 overexpression. Among FGFR3 wild-type tumors, 22% had FGFR3 overexpression. FGFR3 mutations were associated with lower pT-stage (P&amp;lt;0.001), lower grade (G2-WHO 1973) (P&amp;lt;0.001), absence of CIS (P=0.009), pN0 (P&amp;lt;0.001), normal p53 (P&amp;lt;0.001), and prolonged DSS (Plog-rank=0.001). FGFR3 overexpression was associated with lower pT-stage (P&amp;lt;0.001) and G2 (P&amp;lt;0.001) but not with absence of CIS (P=0.860), pN0 (P=0.230), normal p53, (P=0.330) nor prolonged DSS (Plog-rank=0.204). We found no significant difference in DSS for patients with FGFR3 mutant tumors comparing normal vs. overexpression of FGFR3 (Plog-rank=0.444). Furthermore, we also found no significant difference in DSS for patients with FGFR3 wild-type tumors comparing normal vs. overexpression of FGFR3 (Plog-rank=0.754). Conclusions: FGFR3 mutations identified patients with favorable BC with fewer p53 alterations at RC. FGFR3 overexpression was not associated with DSS in patients with FGFR3 wild-type tumors. Our results suggest that FGFR3 mutations (driver effect) have a distinct functional role than FGFR3 overexpression (passenger effect). Hence, patients with FGFR3 mutations may be more likely to benefit from anti-FGFR3 therapy than patients with only overexpression of FGFR3. Citation Format: Bas van Rhijn, Laura Mertens, Roman Mayr, Peter Bostrom, Mirari Marques, Geert van Leenders, Stefanie Gotz, Michiel van der Heijden, Michael Jewett, Francisco Real, Robert Stohr, Alexandre Zlotta, Markus Eckstein, Yanish Soorojebally, Max Burger, Wolfgang Otto, Francois Radvanyi, Damien Pouessel, Theo van der Kwast, Nuria Malats, Arndt Hartmann, Yves Allory, Deric van der Schoot, Ellen Zwarthoff, Tahlita Zuiverloon. FGFR3 mutations and their relation to FGFR3 expression and clinical outcome in a large radical cystectomy cohort: Implications for anti-FGFR3 bladder cancer treatment? [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2019 May 18-21; Denver, CO. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(15_Suppl):Abstract nr B23.

Abstract B100: High-risk pathologic and genomic features of BRCA2-mutant prostate cancer

Abstract Germline BRCA mutations are associated with an increased risk of developing aggressive prostate cancer with poor clinical outcomes. However, the mechanisms by which BRCA mutations contribute to clinical aggressiveness are not completely understood. Previously, we showed that BRCA2-mutant prostate cancers often have intraductal carcinoma of the prostate (IDC-P), a distinct growth pattern of prostate cancer that is associated with adverse clinical features. Despite this, IDC-P is not routinely reported in pathology and its functional significance remains poorly understood. Thus, we investigated the clinical relevance of IDC-P as well as the underlying molecular features of localised BRCA2-mutant prostate cancers with and without IDC-P. To define the prevalence of IDC-P across cohorts of sporadic and familial prostate cancer, we conducted a systematic review in accordance with PRISMA guidelines. This analysis of over 7,000 patient specimens revealed that the prevalence of IDC-P rises from 2.1% in low-risk cohorts to 56% in cohorts with metastatic/recurrent disease. Since these data showed that IDC-P is a prominent feature of high-risk prostate cancer, we next studied the biologic features of IDC-P using patient-derived xenografts (PDXs). PDXs were established from three patients with germline BRCA mutations and compared to PDXs from four high-risk sporadic cases. IDC-P was successfully grown within the PDXs, maintaining its characteristic morphologic features for up to 800 days. Using classical castration-hormone regeneration experiments, we showed that IDC-P contains a subset of “castrate-tolerant” cells that persist after androgen deprivation and subsequently regenerate the tumor. Notably, we found that PDXs derived from BRCA-mutant tumors have the same response to androgen deprivation as sporadic cases. To further investigate the aggressiveness of BRCA2-mutant tumors, we profiled the genomes and methylomes of localized prostate cancers from 14 germline BRCA2-mutation carriers and compared them to 200 sporadic prostate cancers. BRCA2-mutant prostate cancers had elevated genomic instability and global hypomethylation compared to sporadic tumors. In addition, some genomic features of BRCA2-mutant tumors more closely resembled metastatic than localized disease. Importantly, negative prognostic factors were enriched in BRCA2-mutant prostate cancers harboring IDC-P. Sequencing of macrodissected IDC-P and invasive carcinoma revealed that these two pathologies arise from a common tumor clone and diverge later in tumor evolution. In summary, this work demonstrates that IDC-P pathology and genomic instability are two high-risk features of localized BRCA2-mutant prostate cancers. Given the high prevalence of IDC-P in high-risk patient cohorts, including BRCA2-mutation carriers, IDC-P warrants greater recognition and reporting as this may improve patient risk stratification. Citation Format: Laura H. Porter, Mitchell G. Lawrence, Carmel Pezaro, Heather Thorne, Dragan Ilic, Melissa Papargiris, Michael Fraser, Julie Livingstone, Declan G. Murphy, Mark Frydenberg, Damien Bolton, Daniel Moon, David Clouston, Theo van der Kwast, Paul C. Boutros, Robert G. Bristow, Renea A. Taylor, Gail P. Risbridger. High-risk pathologic and genomic features of BRCA2-mutant prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr B100.

Abstract NG06: The clinico-genomics of localized, non-indolent prostate cancer: the CPC-GENE experience

Abstract NG06: The clinico-genomics of localized, non-indolent prostate cancer: the CPC-GENE experience

Abstract 2432: The genomic consequences of tumor hypoxia in human cancers

Abstract Introduction: Localized prostate cancers are classified into risk-groups using clinical measurements like grade and stage to inform treatment decisions. However, these groupings are imprecise: ~30% of intermediate-risk patients suffer relapse of their disease despite precision image-guided radiotherapy or radical prostatectomy. One reason for this variability in response to treatment is the underlying cellular and molecular heterogeneity of tumors. Prostate tumor cells exist within a microenvironment characterized by gradients of oxygen levels and prostate tumors with low levels of oxygen (hypoxia) have poor clinical outcomes. Methods and Results: To understand the correlates of hypoxia in cancer we conducted a pan-cancer analysis of copy number alterations (CNAs) and single nucleotide variants (SNVs) across 19 cancer types. We measured hypoxia using multiple mRNA-based signatures and discovered numerous CNAs and SNVs enriched or depleted in hypoxic tumors, highlighting the role of hypoxia in shaping the genomic landscape of multiple tumor types. Next, we examined 548 patients with localized prostate cancer and statistically assessed the association of hypoxia with CNAs, SNVs, genomic rearrangements, focal genomic events (i.e. kataegis, chromothripsis), telomere length, clinical indices (i.e. grade, stage) and subclonal architecture. Tumor hypoxia is associated with specific CNAs and SNVs in prostate cancer driver genes. To translate these findings into a biomarker for prostate cancer precision medicine, we integrated tumor microenvironmental data with genomic and pathological information to stratify patients into distinct prognostic groups. Impact: These data suggest that the aggressiveness of cancers is driven by the interplay of the tumor microenvironment and its genomic mutational profile. Citation Format: Vinayak Bhandari, Shadrielle M. Espiritu, Lydia Y. Liu, Emilie Lalonde, Takafumi N. Yamaguchi, Lawrence E. Heisler, Julie Livingstone, Vincent Huang, Yu-Jia Shiah, Veronica Y. Sabelnykova, Fouad Yousif, Melvin L. Chua, Michael Fraser, Theodorus van der Kwast, Paul C. Boutros, Robert G. Bristow. The genomic consequences of tumor hypoxia in human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2432.

MP12-01 CONSISTENT BIOPSY QUALITY AND GLEASON GRADING WITHIN THE GLOBAL ACTIVE SURVEILLANCE GLOBAL ACTION PLAN 3 INITIATIVE: A PREREQUISITE FOR FUTURE STUDIES

You have accessJournal of UrologyProstate Cancer: Localized: Active Surveillance I1 Apr 2018MP12-01 CONSISTENT BIOPSY QUALITY AND GLEASON GRADING WITHIN THE GLOBAL ACTIVE SURVEILLANCE GLOBAL ACTION PLAN 3 INITIATIVE: A PREREQUISITE FOR FUTURE STUDIES Theo van der Kwast, Sophie Bruinsma, Daan Nieboer, Jozien Helleman, Monigue Roobol, and The Movember Foundation’s GAP3 consortium Theo van der KwastTheo van der Kwast More articles by this author , Sophie BruinsmaSophie Bruinsma More articles by this author , Daan NieboerDaan Nieboer More articles by this author , Jozien HellemanJozien Helleman More articles by this author , Monigue RoobolMonigue Roobol More articles by this author , and The Movember Foundation’s GAP3 consortium More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2018.02.388AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Within the Movember Foundation′s Global Action Plan focused on Prostate Cancer Active Surveillance (GAP3), 25 centers across the globe collaborate to reach consensus on inclusion criteria, surveillance schedules and intervention thresholds for active surveillance (AS) of men with low risk prostate cancer (PCa). To this end, a centralized PCa AS database was created comprising data on more than 15,000 patients worldwide. Here comparability of the histopathology from different cohorts in terms of biopsy quality and Gleason grading was assessed. METHODS A centralized pathology review of 445 biopsies (5-10% randomly selected biopsies from 15 of the GAP3 centers) was performed by an experienced pathologist. These biopsies were reported over a timespan of more than 20 years. ISUP grade groups (GG), cribriform and/or intraductal carcinoma (CR/IDC) and biopsy core lengths measured on the glass slides were recorded. RESULTS Discrepant biopsy GG at review were found in 48 cases (11%), which is comparable to rates between 10-20% previously reported in literature. Frequency of discrepant GG was below 20% for 11 of the 15 centers (Figure 1a). Upgrading from GG1 to GG≥2 occurred in 20 biopsies and downgrading from GG≥2 to GG1 in 28 biopsies. The average biopsy core length was similar among the analyzed cohorts (Figure 1b). We observed CR/IDC in 7/377 biopsies originally reported as GG1 (1.8%), which is slightly more often than seen in contemporary GG1 biopsies according to literature (0.8%)1. CR/IDC was observed in 16 of 445 assessed biopsies (3.6%). Upgrading at review from GG1 to GG≥2 occurred in 5/16 biopsies showing CR/IDC (31%) and downgrading from GG≥2 to GG1 in 1 biopsy (6%). CONCLUSIONS This centralized pathology review of prostate biopsies from the multi center GAP3 initiative revealed an acceptable discrepancy rate for GG and similar overall biopsy core quality among the 15 GAP3 centers. The increased frequency of CR/IDC in GG1 biopsies may be attributed to modifications in Gleason grading over time, since in reviewed GG1 biopsies CR/IDC frequency was at the same low level as published in literature. The observed consistency in biopsy quality and grading will enable further data analyses without correction towards uniform global guidelines for active surveillance of men with low risk prostate cancer. © 2018FiguresReferencesRelatedDetails Volume 199Issue 4SApril 2018Page: e135 Advertisement Copyright & Permissions© 2018MetricsAuthor Information Theo van der Kwast More articles by this author Sophie Bruinsma More articles by this author Daan Nieboer More articles by this author Jozien Helleman More articles by this author Monigue Roobol More articles by this author The Movember Foundation’s GAP3 consortium More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Abstract 5860: Genomic architecture of prostate cancer at recurrence following radiotherapy

Abstract Aim: Spatial intra-tumoural heterogeneity of prostate cancer is secondary to differential genomics and multi-clonality, even for tumours with the same Gleason grade. These unique features promote resistance to treatment. Here, we investigated if clonal selection or adaptation of new clones dominates in prostate cancer at the time of recurrence following high dose precision radiotherapy. Methods: We identified 11 patients with biopsy-proven multi-focal recurrent prostate cancer following definitive image-guided radiotherapy/brachytherapy. Copy number aberration (CNA) profiling was performed on 33 anatomically distinct tumour foci with 11 matched-normals in the radio-resistant cohort. To assess clonality, 4 cases had matched pre-radiotherapy tumours for copy number profiling. We evaluated for recurrent driver amplifications and deletions, and genomic instability as measured by percent genome aberration (PGA). We also compared these genomic indices against 373 comprehensively profiled sporadic prostate cancers from the Canadian Prostate Cancer Gene Network [Fraser, et al., Nature, 2016]. Results: Independent of Gleason grade, we observed large intra-patient (COV of 0.66-1.13) and inter-patient heterogeneity (p &amp;lt;0.001, one-way ANOVA) in the levels of genomic instability, as judged by PGA scores, among the radioresistant tumours. Interestingly, although total CNA counts did not differ between the radioresistant and sporadic (CPC-GENE) cohorts (median CNAs of 40, radioresistant vs 33, sporadic, p = 0.20], we observed a trend for increased genomic instability in the radioresistant cohort (median PGA of 8.8 vs 4.9, p = 0.059). This concurs with the findings on intra-tumoural spatial CNA analyses, which revealed the acquisition of CNAs that were both common and non-recurrent in the multi-focal radioresistant tumours, thus suggesting a common origin with subsequent divergent evolution. Importantly, we observed a mixture of CNAs, including known drivers of aggressive prostate cancer, namely NKX3-1, PTEN, TP53, CDKN1B, and CDH1, that was shared between pre-radiotherapy and radioresistant tumours, supporting a clonal selection process. We also discovered a novel deleted region on Chr3p, consisting of RAD18 and FANCD2, which was unique only in the radioresistant tumours. Conclusions: Our novel observations in a small cohort of radioresistant prostate cancers favour the model of selection of radioresistant clones, as opposed to new-onset tumours. These results support the current approach of discovering biomarkers a priori, and molecular therapeutic targets for these radioresistant clones, so as to improve the therapeutic ratio of precision radiotherapy. Citation Format: Melvin L.K. Chua, Erle Holgersen, Veronica Sabelnykova, Adriana Salcedo, Alice Meng, Michael Fraser, Theodorus van der Kwast, Paul C. Boutros, Robert G. Bristow. Genomic architecture of prostate cancer at recurrence following radiotherapy [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 5860. doi:10.1158/1538-7445.AM2017-5860

Abstract A28: Mutational landscape of TP53 in localized prostate cancer

Abstract Background: We performed a comprehensive interrogation of the mutational landscape of TP53 in the context of localized prostate cancer using a large clinical/molecular-paired dataset from the Canadian Prostate Cancer Gene Network (CPC-GENE). We further test the associations of TP53 mutations with outcomes post-image-guided radiotherapy (IGRT) or radical prostatectomy (RadP). Methods: Copy number status (N = 284), single nucleotide variants (SNV) (N = 123), methylation status (N = 117), and mRNA abundance profiling (N = 115) were assessed using the Affymetrix Oncoscan FFPE express v3.0 assay, whole genome sequencing (up to 100-200x), Illumina 450K methylation array, and Affymetrix HuGene 2.0 array, respectively. Patient cohort comprised of NCCN-defined intermediate-risk prostate cancer who underwent either IGRT (N = 146) or RadP (N = 137). Biochemical-relapse free rate (bRFR) was assessed as the primary clinical end-point. Results: We identified 65 cases (22.9%) with mono-/bi-allelic copy number alteration (CNA) of TP53, and 7 cases (5.7%; 6 non-synonymous and 1 splice variant) with TP53 SNV in our cohort, which was comparable with the TCGA (30% CNA, 7% SNV) and MSKCC (17% CNA, 2.9% SNV) cohorts of low to high-risk localized prostate cancers. Epigenomic profiling revealed specific sites of DNA hypermethylation (β-value &amp;gt;0.7) within the body and 5' UTR gene-regions, while the TSS gene-region was unaffected. Genomic mutations (CNA and/or SNV) of TP53 were associated with global genomic instability (percent genome aberration of 9.5 vs 6.4, p = 0.001) and reduced mRNA levels (mRNA abundance Z-Score: -0.58 vs 0.22, p-value = 0.0011), but methylation status had no consequence on these indices. Neither TP53 genomic mutations (HR = 1.35, 95% CI 0.91-2.00, Wald's p = 0.14) nor mRNA abundance (HR = 1.39, 95% CI 0.71-2.75, Wald's p = 0.34) was associated with bRFR on multivariable analyses. However, stratification by combinatorial genomic and mRNA abundance indices identified an unfavorable subgroup that was associated with poorer bRFR on multivariable analysis (HR = 2.95, 95% CI 1.42-6.12, Wald's p = 0.004). Conclusions: This is the first comprehensive interrogation of the mutational landscape of TP53 in localized prostate cancer. Our findings suggest that functional TP53 loss at both the copy number and transcription level accounts for a subset of non-indolent localized prostate cancer. Citation Format: Osman Mahamud, Melvin L.K Chua, Stephane Supiot, Emilie Lalonde, Alan Dal Pra, Alejandro Berlin, Michèle Orain, Valerie Picard, Helene Hovington, Alain Bergeron, Yves Fradet, Bernard Têtu, Gaetano Zafarana, Alice Meng, Julie Livingstone, Melania Pintilie, Michael Fraser, Theodorus van der Kwast, Paul C. Boutros, Bristow G. Robert. Mutational landscape of TP53 in localized prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr A28.

Abstract 4339: Prognostic significance of copy number alteration burden in unfavorable intermediate-risk prostate cancers harboring intraductal carcinoma and cribriform architecture

Abstract Aim: Men with intermediate-risk prostate cancer represent a heterogeneous group of patients with varying prognoses. Intraductal carcinoma (IDC), cribriform architecture (CA), and high copy number alteration burden are novel pathological and genomic indices that predict aggressive disease and inferior clinical outcomes in patients with localised prostate cancer. We aimed to test the independent prognostic effect of these indices in a cohort of intermediate-risk prostate cancers. Experimental methods: We defined a set of clinical and genomic indices to test for their prognostic significance in a cohort of individuals with NCCN-defined intermediate-risk prostate cancer, who were treated with radical prostatectomy (RadP) or radiotherapy (RT) (N = 173, RadP; N = 358, RT). Clinical indices include primary T-category, pre-treatment PSA level, Gleason's score and pattern, and presence of IDC and/or CA. Pathological features were reviewed centrally by two expert pathologists. Copy number alteration burden was assessed in 215 tumours of the cohort using SNP array profiling (Affymetrix Oncoscan), and reported as percent genome aberration (PGA). Our primary endpoint was to test if a model incorporating IDC/CA and PGA stratifies patients with intermediate-risk disease for risk of biochemical relapse after primary treatment. Results: Biochemical relapse was associated with PGA on univariable and multivariable analysis for the sub-cohort of 215 patients (HR of High vs Low PGA defined by median = 1.61, 95% CI = 1.04-2.49, Wald's p = 0.033). Based on modelling of the clinical indices, presence of IDC/CA was associated with biochemical relapse-free rate (bRFR) on univariable and multivariable analyses (HR = 1.90, 95% CI = 1.34-2.69, p = 0.00034), along with PSA level. Risk stratification considering both IDC/CA and PGA indicated an additive prognostic effect of IDC/CA to PGA for early biochemical relapse, with 18-month bRFR of 83% in High PGA, present IDC/CA vs 94% in Low PGA, absent IDC/CA subgroups (HR = 2.55, 95% CI = 1.49-4.39, p = 0.00069). A comparison of risk stratification models revealed that inclusion of PGA to IDC/CA yielded the strongest model for predicting 18-month bRFR in patients with intermediate-risk prostate cancer following treatment (area under the curve, AUC = 0.580, 95% CI = 0.456-0.675 [T-category, PSA, and IDC/CA] vs 0.649, 95% CI = 0.476-0.776 [T-category, PSA, IDC/CA, and PGA]). Conclusions: We herein demonstrate for the first time a novel risk stratification model integrating pathological (IDC/CA) and genomic (PGA) indices to identify patients with unfavourable intermediate-risk prostate cancer, who may benefit from intensification to conventional definitive treatment. Citation Format: Melvin Lee Kiang Chua, Jure Murgic, Melania Pintilie, Emilie Lalonde, Charlotte Kweldam, Winnie Lo, Alejandro Berlin, Alan Dal Pra, Michele Orain, Valerie Picard, Helene Hovington, Alain Begeron, Yves Fradet, Bernard Tetu, Julie Livingstone, Alice Meng, Jun Yan Zhang, Gaetano Zafarana, Neil Fleshner, Mike Fraser, Paul Boutros, Robert Bristow, Theodorus van der Kwast. Prognostic significance of copy number alteration burden in unfavorable intermediate-risk prostate cancers harboring intraductal carcinoma and cribriform architecture. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4339.

Abstract 118: A comprehensive profile of the genomic architecture of curable prostate cancer

Abstract There is an urgent need to develop novel biomarkers of treatment response for precision medicine in prostate cancer, particularly in the setting of localized, non-indolent disease, which represents the vast majority of cases at initial clinical presentation. The Canadian Prostate Cancer Genome Network (CPC-GENE) - a member of the International Cancer Genome Consortium - aims to identify multi-modal prognostic and predictive signatures of therapeutic outcome based on intrinsic tumour genomics, transcriptomics, and epigenomics, which are being incorporated into novel clinical trials of treatment escalation/de-escalation for image-guided radiotherapy and/or radical prostatectomy. Herein we report the results of the largest prostate cancer whole-genome sequencing study to date, consisting of 194 patients and whole-exome sequencing of 479 patients with localized, potentially curable disease; a sample size that allows for saturating discovery of genes mutated at ≥1% frequency. We show that tumours treated by curative local therapy have a paucity of clinically-actionable mutations relative to high-risk localized or metastatic disease, but instead harbor a significant number of recurrent non-coding aberrations and genomic rearrangements, including a novel inversion - and an associated reduction in gene expression - of the PTEN tumour suppressor gene on chromosome 10. The median tumour contains three distinct driver mutations, with &amp;gt;86% of tumours possessing at least one known driver. Importantly, multiple driver aberrations are associated with patient outcome, including copy number aberrations and methylation events, but notably excluding well-described recurrent events such as TMPRSS2:ERG fusions and SPOP point mutations. Localized hypermutation events (e.g. kataegis) were detected in &amp;gt;20% of tumours, and were strongly enriched for aggressive disease. Taken together, these data provide a comprehensive analysis of the genomic landscape of localized, non-indolent prostate cancer. Moreover, our results strongly suggest that specific molecular aberrations may serve as useful biomarkers for improved pre-treatment stratification of patients with localized, low/intermediate risk disease into escalation/de-escalation protocols, and support the development of clinical trials to assess this hypothesis, based on patient-specific molecular profiles. Citation Format: Michael E. Fraser, Theodorus van der Kwast, John McPherson, Colin C. Collins, Yves Fradet, Bernard Tetu, Alain Bergeron, Rob G. Bristow, Paul C. Boutros. A comprehensive profile of the genomic architecture of curable prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 118.

Abstract 98: The somatic mutational landscape of the mitochondrial genome in prostate cancer: evaluation of clinical impact

Abstract Prostate cancer remains the most prevalent and second most lethal non-skin cancer in men. Whole genome studies have provided important insights into specific driver genes, however most of these studies have not assessed one key portion of the genome: the mitochondrial genome. To gain a complete understanding of the most commonly-diagnosed sub-groups of prostate cancer: low- and intermediate-risk localized disease, we surveyed the mitochondrial genomes from next-generation sequencing (NGS) data of over 300 tumour samples from prostate cancer patients. These samples were mainly from prostate cancer patients with clinical Gleason Scores of 3+3, 3+4 and 4+3. All had at least 5 years of follow-up data (median &amp;gt; 8 years), allowing identification of clinical associations with identified somatic mutations via Cox Proportional Hazards modeling and machine-learning. Recurrent somatic mutations in mtDNA were identified, and these were associated with clinical outcomes. One third of patients were found to have a somatic mtDNA mutation. These mutations appear to be associated with age of patient. The mtDNA region with the majority of mutations was the regulatory D-loop region, although certain proteins had high numbers of mutations. Those somatic mutations occurring within the coding regions in general were nonsynonymous. Specific identified candidate somatic mutations were validated via Sanger sequencing. Clinical associations between somatic were also integrated with existing copy-number alteration (CNA) biomarkers using machine learning methods to evaluate performance. mtDNA mutations were also compared to identified aberrations (CNA, PGA, SNVs) within the nuclear genome to determine correlations between the two genomes, in addition to other somatic mutations or altered-expression in nuclear-encoded mitochondrial proteins. Taken together, these data demonstrate a key role for mitochondrial mutations in driving prostate cancer. Citation Format: Julia F. Hopkins, Veronica Y. Sabelnykova, John Watson, Lawrence E. Heisler, Junyan Zhang, Michael Fraser, Theodorus van der Kwast, Robert G. Bristow, Paul C. Boutros. The somatic mutational landscape of the mitochondrial genome in prostate cancer: evaluation of clinical impact. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 98.

MP79-05 VALIDATION OF THE NOVEL 5-GROUP GLEASON GRADING SYSTEM: 3+5 DISEASE RISK MAY BE OVERESTIMATED

You have accessJournal of UrologyProstate Cancer: Staging II1 Apr 2016MP79-05 VALIDATION OF THE NOVEL 5-GROUP GLEASON GRADING SYSTEM: 3+5 DISEASE RISK MAY BE OVERESTIMATED Roderick van den Bergh, Theo van der Kwast, Jeroen de Jong, Homi Zargar, Declan Murphy, and Henk van der Poel Roderick van den BerghRoderick van den Bergh More articles by this author , Theo van der KwastTheo van der Kwast More articles by this author , Jeroen de JongJeroen de Jong More articles by this author , Homi ZargarHomi Zargar More articles by this author , Declan MurphyDeclan Murphy More articles by this author , and Henk van der PoelHenk van der Poel More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2016.02.2003AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES The International Society of Urological Pathology after a 2014 consensus meeting, suggested to change the classical Gleason grading system to 5 prognostic grade groups (1: 3+3, 2: 3+4, 3: 4+3, 4: Gleason score 8, and 5: Gleason score 9-10). We compared the predictive value for biochemical recurrence (BCR) after surgery of the classical grading system to the new risk group system. METHODS The radical prostatectomy database from a single referral centre was used (N=1,384). BCR was defined as a post-operative PSA of >=0.2 ng/ml and rising. The classical 9-group system (3+3, 3+4, 3+5, 4+3, 4+4, 5+3, 4+5, 5+4, and 5+5) was compared to the novel 5-group system. Separate analyses were performed for biopsy Gleason score and for prostatectomy Gleason score. Kaplan-Meier curves with Log-Rank test for comparisons between curves were used. P-values of <0.05 were considered statistically significant. RESULTS Prostatectomy Gleason score patient numbers were: 3+3: 479, 3+4: 474, 4+3: 142, 3+5: 52, 4+4: 46, 5+3: 13, 4+5: 44, 5+4: 13, 5+5: 7. For biopsy, the classical grading showed overlap between different subgroups of Gleason 7 and 8 and between 8 and 9 (all p>0.05). The new risk group 2 overlapped with 3 (p=0.282), and 3 with 4 (p=0.161), other group comparisons were significantly different. For prostatectomy, the classical grading showed overlap between different Gleason 9 subgroups and 10 (all p>0.05). The new risk group 3 overlapped with 4 (p=0.893), other group comparisons were significantly different. Within risk group 4, 3+5 patients (3-year BCR-free 65%) had more favorable (p<0.01) BCR than 4+4 patients (18%) and were even similar (p=0.524) to 3+4 (73%) [Figure]. No corrections for margin or lymph node status were made. Limitations include the use of a single database, the intermediate endpoint BCR, and limited patient numbers for some subgroups. CONCLUSIONS Condensing the classical 9-group Gleason system to the suggested 5-group system resulted in less overlap between BCR rates, suggesting increased prognostic stratification. However, in the new grading system, prognostic stratification value between some higher risk disease patients may be lost. Most markedly, the risk of prostatectomy Gleason 3+5 patients (new risk group 4) may be overestimated, as the BCR resembles that of Gleason 3+4 (new risk group 2) patients. © 2016FiguresReferencesRelatedDetails Volume 195Issue 4SApril 2016Page: e1036 Advertisement Copyright & Permissions© 2016MetricsAuthor Information Roderick van den Bergh More articles by this author Theo van der Kwast More articles by this author Jeroen de Jong More articles by this author Homi Zargar More articles by this author Declan Murphy More articles by this author Henk van der Poel More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Abstract B1-32: Genome-wide integrative analysis correlating locus-specific DNA methylation and hydroxymethylation to gene expression in normal prostate cells

Abstract Aberrant epigenetic modification in the form of regional hypermethylation and global hypomethylation has been implicated in the dysregulation of gene expression in various cancers, including prostate cancer (PCa). Recently discovered 5-hydroxymethylated marks (5hmC), considered to be key intermediates in the process of DNA demethylation, have also been shown to exhibit significant global loss in solid tumors as compared to normal tissue. Similar to cytosine base methylation (5mC), 5hmC may also play a key role in the regulation of gene expression and, consequently, gene function in PCa. We hypothesize that dynamic interplay between 5mC and 5hmC enrichment in promoter, CpG island, and intragenic regions shows specific association patterns with gene expression. A systematic investigation of these methylation marks may provide novel insights into epigenomic architecture by elucidating novel pathways and candidate genes in prostate tumorigenesis. Using Next Generation Sequencing (NGS), we characterized genome-wide 5mC and 5hmC marks and RNA expression data in a normal prostate tissue-derived representative cell line (RWPE-1). We have completed NGS following methyl-binding protein capture (MBD-seq) and hydroxymethyl-selective chemical labeling (hMe-Seal), and have performed integrative analysis correlating enriched genes stratified by region (intergenic regions proximal to DNase I hypersensitivity sites, as well as promoter, CpG island, and intragenic regions) to expression data obtained from RNA-seq and also validated using publicly available microarray expression data (GEO Accession Number: GSM375783) We divided expression data into equal tiers representing genes with no expression, low expression, and high expression, and have performed pathway-based analysis on genes significantly enriched for either 5mC or 5hmC marks for each tier stratified by gene region. We found gene expression to exhibit a strong positive correlation with core promoter and CpG island hydroxymethylation, with a corresponding negative correlation to methylation of these regions. In contrast, gene expression was found to be positively correlated with both methylation and hydroxymethylation in both intragenic regions and intergenic regions proximal to ENCODE DNase I hypersensitivity sites (GEO Accession Number: GSM1008595), which are associated with open chromatin and may play a role in downstream gene regulation. Interestingly, pathway-based analysis of these stratified tiers, grouped via the Molecular Complex Detection algorithm (MCODE) to identify pathway clusters with high biological significance, showed 5hmC and 5mC enrichment of the same pathways in each expression tier, suggesting a possible co-operative role for intragenic co-expression of these marks in regulating biological pathways. Clustered pathways co-enriched in intragenic 5mC and 5hmC showed strong enrichment in Gene Ontology terms related to core cellular functions within each expression tier, such as ion channel and transport regulation, primary metabolic processes, and protein and RNA binding. Currently, we are investigating these pathways to identify key candidate genes regulated by 5hmC and 5mC marks in normal prostate. This is the first study to correlate locus-specific global 5hmC enrichment to expression in normal prostate cells. Our preliminary analysis has shown correlation between 5hmC and 5mC enrichment in genic, promoter, CpG island, and upstream DNase I hypersensitivity site-proximal regions and expression in RWPE-1 cells. Insights from this model will subsequently be explored via whole-genome differential analysis between normal prostate and PCa to determine the effect of epigenetic alterations in cancer on gene expression. Subsequently, our characterization of key cellular pathways exhibiting dynamic enrichment patterns for 5hmC or 5mC marks will potentially allow us to identify differentially epigenetically modified target genes implicated in prostate cancer tumorigenesis. Citation Format: Shivani N. Kamdar, Linh T. Ho, Ruth Isserlin, Ken J. Kron, Theodorus van der Kwast, Alexandre R. Zlotta, Neil E. Fleshner, Gary Bader, Bharati Bapat. Genome-wide integrative analysis correlating locus-specific DNA methylation and hydroxymethylation to gene expression in normal prostate cells. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-32.

MP68-06 TISSUE-BASED DNA METHYLATION PROFILING ESTABLISHES A NOVEL PANEL OF BIOMARKERS FOR DISCRIMINATION OF HIGH-GRADE VERSUS LOW-GRADE BLADDER CANCER

You have accessJournal of UrologyBladder Cancer: Basic Research IV1 Apr 2015MP68-06 TISSUE-BASED DNA METHYLATION PROFILING ESTABLISHES A NOVEL PANEL OF BIOMARKERS FOR DISCRIMINATION OF HIGH-GRADE VERSUS LOW-GRADE BLADDER CANCER Andrea Savio, Ekaterina Olkhov-Mitsel, Ken Kron, Thomas Hermanns, Bas van Rhijn, Alexandre Zlotta, Theodorus van der Kwast, and Bharati Bapat Andrea SavioAndrea Savio More articles by this author , Ekaterina Olkhov-MitselEkaterina Olkhov-Mitsel More articles by this author , Ken KronKen Kron More articles by this author , Thomas HermannsThomas Hermanns More articles by this author , Bas van RhijnBas van Rhijn More articles by this author , Alexandre ZlottaAlexandre Zlotta More articles by this author , Theodorus van der KwastTheodorus van der Kwast More articles by this author , and Bharati BapatBharati Bapat More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2015.02.2468AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Epigenetic changes, including promoter CpG island hypermethylation, occur frequently in bladder cancer (BC) and may be exploited as a means for BC detection and distinction between high-grade (HG) and low-grade (LG) disease. METHODS To determine epigenetic differences between LG and HG BC we performed genome-wide methylation analysis with Agilent Human CpG Island Microarrays on a panel of fresh frozen BC tissue samples. Using Linear Models for Microarray Data (LIMMA) and local-pooled-error (LPE) approaches and unsupervised hierarchical clustering we identified 990 probes comprising a 32-gene panel that completely distinguished LG from HG BC based on methylation status. We selected five representative differentially methylated genes (DMGs) from our 32-gene panel for methylation validation by real-time PCR-based MethyLight in a series of 40 LG cases age- and sex-matched to 40 HG cases. RESULTS Among the DMGs tested, including EOMES, GP5, PAX6, TCF4, and ZSCAN12, we identified that EOMES, GP5, and ZSCAN12 methylation significantly differs between normal, LG, and HG disease. GP5 and ZSCAN12, two novel methylated genes in BC, are significantly hypermethylated in HG versus LG BC (p=0.006 and 0.028, respectively). Pathway enrichment analysis and functional annotation determined the most frequently methylated pathways in HG BC were enriched for anterior/posterior pattern specification, embryonic skeletal system development, and neuron fate commitment. The molecular functions of the most enriched genes were involved in DNA binding and transcription factor activity. CONCLUSIONS These results indicate the ability to distinguish normal tissue from cancer, as well as LG from HG tumours, and reveal important pathways dysregulated in HG BC. Ultimately, the creation of a methylation panel able to distinguish between disease phenotypes will improve disease management and patient outcomes. © 2015 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 193Issue 4SApril 2015Page: e860 Advertisement Copyright & Permissions© 2015 by American Urological Association Education and Research, Inc.MetricsAuthor Information Andrea Savio More articles by this author Ekaterina Olkhov-Mitsel More articles by this author Ken Kron More articles by this author Thomas Hermanns More articles by this author Bas van Rhijn More articles by this author Alexandre Zlotta More articles by this author Theodorus van der Kwast More articles by this author Bharati Bapat More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

MP28-13 EXPRESSION ANALYSIS OF LOW AND HIGH-GRADE HUMAN BLADDER CANCER TUMOUR SAMPLES AND BLADDER CANCER CELL LINES WITH RNA-SEQ IDENTIFIES A NEW GROUP OF ENHANCER RNAS WITH POTENTIAL REGULATORY FUNCTION

You have accessJournal of UrologyBladder Cancer: Basic Research II1 Apr 2014MP28-13 EXPRESSION ANALYSIS OF LOW AND HIGH-GRADE HUMAN BLADDER CANCER TUMOUR SAMPLES AND BLADDER CANCER CELL LINES WITH RNA-SEQ IDENTIFIES A NEW GROUP OF ENHANCER RNAS WITH POTENTIAL REGULATORY FUNCTION Aidan P. Noon, Yu Liu, Thomas Hermanns, Girish S. Kulkarni, Theodorus H. van der Kwast, Azar Azad, Alexandre R. Zlotta, and Jeffrey L. Wrana Aidan P. NoonAidan P. Noon More articles by this author , Yu LiuYu Liu More articles by this author , Thomas HermannsThomas Hermanns More articles by this author , Girish S. KulkarniGirish S. Kulkarni More articles by this author , Theodorus H. van der KwastTheodorus H. van der Kwast More articles by this author , Azar AzadAzar Azad More articles by this author , Alexandre R. ZlottaAlexandre R. Zlotta More articles by this author , and Jeffrey L. WranaJeffrey L. Wrana More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2014.02.662AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Despite continuing improvement in our understanding of urothelial bladder cancer (UBC), the molecular traits that underpin indolent low grade (LG) versus aggressive high grade (HG) UBC remain to be fully elucidated. High-throughput RNA sequencing (RNA-Seq) provides new insights into transcriptome complexity in cancer, enabling the detection of novel transcripts in both coding and non-coding RNA. One new family member of non-coding RNAs is enhancer RNAs (eRNAs), which have tissue specific expression patterns and regulatory functions. Although many eRNAs may represent transcriptional noise, some of them are thought to exert regulatory functions on nearby genes on the same chromosome (cis) or at distance on other chromosomes (trans). We set out to identify eRNAs that might have a regulatory role in UBC, possibly driving a HG phenotype. METHODS We performed whole transcriptome RNA sequencing (Illumina HiSeq 2000) on a cohort of 49 archival, formalin fixed paraffin embedded (FFPE) LG (n = 27) and HG (n = 22) UBC samples. The predicted eRNA annotations from ENCODE were used in our analyses. Our wRNAseq platform is not strand specific; therefore, we only characterized intergenic eRNAs within 5 – 100kb of the transcription sites of differentially expressed genes (DEGs) between the LG and HG samples (false discovery rate <0.05, fold change >2). To validate these in-silica analyses and provide a model for functional study, the differentiated expression of candidate eRNAs were investigated in UBC cell lines of different grades and a non-UBC cell line using qPCR. RESULTS RNA-Seq revealed 9049 intergenic eRNAs in the whole UBC cohort and 369 strongly differentially expressed between the LG and HG tumours. Among these 369, 147 were identified associated with coding DEGs and we named them as intergenic bladder cancer – eRNAS (iBC-eRNAs). Network analysis of iBC-eRNAs and their associated DEGs identified three major functional clusters including cell cycle, histone complexes and morphogenic regulators. Analysis of BC cell lines confirmed expression of eRNAs (qPCR) and their associated DEGs (RNA-Seq & qPCR). CONCLUSIONS Our results identify for the first time a functional network of eRNAs in human UBC. Some eRNAs are adjacent to genes that are also differentially expressed between LG and HG tumours suggesting possible eRNA-dependent regulation. Analysis of iBC-eRNA in human BC cell lines has enabled us to validate and explore the functional role of iBC-eRNAs and their associated DEGs. Ontario Premier Summit Award - (JLW) © 2014FiguresReferencesRelatedDetails Volume 191Issue 4SApril 2014Page: e301 Advertisement Copyright & Permissions© 2014MetricsAuthor Information Aidan P. Noon More articles by this author Yu Liu More articles by this author Thomas Hermanns More articles by this author Girish S. Kulkarni More articles by this author Theodorus H. van der Kwast More articles by this author Azar Azad More articles by this author Alexandre R. Zlotta More articles by this author Jeffrey L. Wrana More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...