Dr. Wyatt’s research is focused on metastatic genitourinary cancers, including prostate and bladder cancer. To enable genomic profiling of these cancers, his team has pioneered methods for circulating tumour DNA analysis of prostate cancer from minimally invasive blood samples,  developed targeted sequencing approaches, built custom bioinformatic software and amassed important clinical data from men with metastatic prostate cancer, enabling comparison of genomic alterations with treatment outcomes.

Dr. Wyatt designed the circulating tumour DNA screening strategy and directs the molecular tumour board for the Canadian Cancer Trials Group (CCTG) Phase II precision oncology umbrella trial for metastatic prostate cancer. The Canada-wide trial matches patients with treatments based on analysis of their circulating tumour DNA and has enrolled more than 350 patients to date. His laboratory is also working to bring his research to the clinic by creating a panel-based circulating tumour DNA test that could be used as part of routine clinical practice.

Learn more about Dr. Wyatt’s research here.

Selected Publications

Somatic Features of Response and Relapse in Non-muscle-invasive Bladder Cancer Treated with Bacillus Calmette-Guérin Immunotherapy

European Urology Oncology
Jack VW Bacon, David C Müller, Elie Ritch, Matti Annala, Sarah G Dugas, Cameron Herberts, Gillian Vandekerkhove, Helge Seifert, Tobias Zellweger, Peter C Black, Lukas Bubendorf, Alexander W Wyatt, Cyrill A Rentsch

Background: High-risk non-muscle-invasive bladder cancer (NMIBC) is treated with bacillus Calmette-Guérin (BCG), but relapse is common. Improvement of patient outcomes requires better understanding of links between BCG resistance and genomic driver alterations.

Objective: To validate the prognostic impact of common genomic alterations in NMIBC pretreatment and define somatic changes present in post-BCG relapses.

Design, setting, and participants: We retrieved tumour tissues and outcomes for 90 patients with BCG-naive NMIBC initiating BCG monotherapy. Post-BCG tissue was available from 34 patients. All tissues underwent targeted sequencing of tumour and matched normal.

Outcome measurements and statistical analysis: Associations between clinical outcomes and genomics were determined using Cox proportional hazard models.

Results and limitations: Of the patients, 58% were relapse free at data cut-off, 24% had NMIBC recurrence, and 18% experienced muscle-invasive progression. The risk of relapse was associated with ARID1A mutation (hazard ratio [HR] = 2.00; p = 0.04) and CCNE1 amplification (HR = 2.61; p = 0.02). Pre- and post-BCG tumours shared truncal driver alterations, with mutations in TERT and chromatin remodelling genes particularly conserved. However, shifts in somatic profiles were common and clinically relevant alterations in FGFR3, PIK3CA, TSC1, and TP53 were temporally variable, despite apparent clonal prevalence at one time point. Limitations include the difficulty of resolving the relative impact of BCG therapy versus surgery on genomics at relapse and biopsy bias.

Conclusions: Somatic hypermutation and alterations in CCNE1 and ARID1A should be incorporated into future models predicting NMIBC BCG outcomes. Changes in tumour genomics over time highlight the importance of recent biopsy when considering targeted therapies, and suggest that relapse after BCG is due to persisting and evolving precursor populations.

Patient summary: Changes in key cancer genes can predict bladder cancer relapse after treatment with bacillus Calmette-Guérin. Relapses after treatment can be driven by large-scale genetic changes within the cancer. These genetic changes help us understand how superficial bladder cancer can progress to be treatment resistant.

Considerations on the identification and management of metastatic prostate cancer patients with DNA repair gene alterations in the Canadian context

Canadian Urological Association Journal
Michael P Kolinsky, Karen Y Niederhoffer, Edmond M Kwan, Sebastien J Hotte, Zineb Hamilou, Steven M Yip, Kim N Chi, Alexander W Wyatt, Fred Saad

Olaparib is the first Health Canadaapproved agent in metastatic prostate cancer to use a companion diagnostic to identify alterations in BRCA1, BRCA2, or ATM. As olaparib is introduced, clinicians must learn to access and interpret germline and somatic next-generation sequencing (NGS) results, and how to manage affected patients who appear to have distinct clinical features. The traditional model of referring patients to a hereditary cancer clinic (HCC) for germline testing is likely impractical in this disease, as the metastatic prostate cancer patient population would be overwhelming. Alternate approaches to this are clinician-ordered genetic testing (so-called "mainstreaming"), out-of-pocket payment for third-party private company genetic testing, or germline testing done in conjunction with somatic testing, particularly cell free circulating tumor DNA (ctDNA).Germline testing alone is not sufficient for identifying Olaparib-eligible patients, as less than half of BRCA1, BRCA2, or ATM alterations are germline in origin, but it is critically important to identify family members who are carriers so that risk-reduction measures can be undertaken. Somatic testing is not widely available in Canada, but some patients can access it through research protocols or by paying out-of-pocket. Somatic testing can be performed on archival or fresh solid tissue biopsy samples, or through whole blood samples to access plasma-derived circulating tumor DNA (ctDNA). Both testing approaches have relative advantages and disadvantages, but neither may be informative in all patients and, therefore, ideal somatic NGS pathways should provide options for both tissue and ctDNA testing.We advocate that clinicians begin discussions with their provincial lab formularies, HCC, and molecular pathology labs to highlight the importance of germline and somatic testing in this population and identify pathways for patient access. While olaparib has approval for use in BRCA1, BRCA2, and ATM-altered mCRPC, emerging evidence suggests that PARP inhibitors have variable activity in these three genes, with BRCA2 alterations appearing to be the most responsive. Retrospective and prospective series have reported varying outcomes to standard of care therapies, such as ARATs and taxane-based chemotherapy, in metastatic castration-resistant prostate cancer (mCRPC) patients with DNA damage repair (DDR) gene alterations, such as BRCA2. In the absence of high-level evidence showing a lack of benefit, we believe this patient population should still be considered for these treatments.In addition, platinum-based chemotherapy appears to have activity in DDR gene-altered mCRPC and should be considered another option when access to olaparib is not possible.At present, there is no evidence to support an optimal treatment sequence in this patient population, therefore, physician and patient preferences will need to be taken into consideration when selecting therapies. As olaparib and other PARP inhibitors are tested in different disease states and in combination with other therapies, we will likely see a more refined approach to use of these agents and management of this new biomarker-defined patient population.

Tissue- and Blood-derived Genomic Biomarkers for Metastatic Hormone-sensitive Prostate Cancer: A Systematic Review

European Urology Oncology
Kim Van der Eecken, Jan Vanwelkenhuyzen, Matthew P Deek, Phuoc T Tran, Evan Warner, Alexander W Wyatt, Edmond M Kwan, Sofie Verbeke, Jo Van Dorpe, Valérie Fonteyne, Nicolaas Lumen, Bram De Laere, Piet Ost

Context: Multiple studies have reported on the genomic characteristics of metastatic hormone-sensitive prostate cancer (mHSPC). The impact of these findings on prognostication, treatment selection, and clinical trial design remains unclear.

Objective: To summarise genomic alteration prevalences in liquid and/or tissue biopsies, infer their clinical implications, and compare genomic alteration frequencies across different disease states and clinical phenotypes.

Evidence acquisition: The PubMed and Web of Knowledge databases were systematically searched up to January 2021. Quality assessment was performed using the Joanna Briggs Institute Critical Appraisal tools.

Evidence synthesis: In total, 11 studies encompassing 1682 mHSPC patients were included. High-volume disease was associated with more frequent alterations in TP53, DNA damage repair, and Wnt pathways. Tumours from patients with de novo mHSPC were enriched for alterations in TP53 and CDK12 compared with recurrent disease. Alterations in AR, TP53, cell cycle signalling, and MYC were associated with a poorer clinical outcome. A comparative analysis of gene alteration frequencies across disease states revealed a relative increase from localised to castration-resistant tumours, with noteworthy enrichment of CTNNB1 alterations in mHSPC (5%), which warrants further investigation. This study was limited by variability in methodology and definitions used among the eligible studies, including differences in sequencing methods, analytes (being either tissue or liquid), alteration calling thresholds, and target patient populations with a relative under-representation of recurrent metastatic disease.

Conclusions: Several genomic alterations are associated with differential prognosis and clinical phenotypes in mHSPC. We urge that emerging data on these potential predictive biomarkers must be validated in biomarker-driven randomised controlled trials before any clinical implementation. Alignment of the assay methodology and reporting will be critical for ensuring rapid scalability.

Patient summary: We reviewed current data on genomic alterations of metastatic hormone-sensitive prostate cancer, and summarised key genomic subtypes that associate with specific clinical phenotypes and treatment outcomes.

A marrow-minded look at immune checkpoint blockade resistance in metastatic castration resistant prostate cancer

Translational Andrology and Urology
Nicolette M Fonseca, Morgan E Roberts, Alexander W Wyatt

Prostate cancer is the second most common malignancy diagnosed in men and the sixth highest contributor to cancer-related mortality worldwide (1). Advanced prostate cancer initially responds to androgen deprivation therapy before progression to an incurable state termed metastatic castration resistant prostate cancer (mCRPC). mCRPC is typically treated with taxanes or androgen receptor (AR) pathway inhibitors, but the survival benefit is variable and often brief (2). In recent years, focus has turned to the development of therapies outside of the AR signaling pathway. PARP inhibitors and pembrolizumab are effective in the subset of mCRPC with homologous recombination repair and mismatch repair defects, respectively (3,4). Further agents including PSMA-lutetium-177, DNA peptide-based vaccines, and oncolytic viruses are in various stages of clinical development (3). While single agent immune checkpoint blockade (ICB) has proved relatively ineffective in unselected mCRPC, in this commentary, we highlight its potential for eliciting potent anti-tumor responses when combined with agents that target the uniquely immunosuppressive tumor microenvironment (TME) of mCRPC.

Prospective Evaluation of Clinical Outcomes Using a Multiplex Liquid Biopsy Targeting Diverse Resistance Mechanisms in Metastatic Prostate Cancer

Journal of Clinical Oncology
Jamie M Sperger, Hamid Emamekhoo, Rana R McKay, Charlotte N Stahlfeld, Anupama Singh, Xinyi E Chen, Lucia Kwak, Cole S Gilsdorf, Serena K Wolfe, Xiao X Wei, Rebecca Silver, Zhenwei Zhang, Michael J Morris, Glenn Bubley, Felix Y Feng, Howard I Scher, Dana Rathkopf, Scott M Dehm, Toni K Choueiri, Susan Halabi, Andrew J Armstrong, Alexander W Wyatt, Mary-Ellen Taplin, Shuang G Zhao, Joshua M Lang

PURPOSE

Nearly all men with prostate cancer treated with androgen receptor (AR) signaling inhibitors (ARSIs) develop resistance via diverse mechanisms including constitutive activation of the AR pathway, driven by AR genomic structural alterations, expression of AR splice variants (AR-Vs), or loss of AR dependence and lineage plasticity termed neuroendocrine prostate cancer. Understanding these de novo acquired ARSI resistance mechanisms is critical for optimizing therapy.

MATERIALS AND METHODS

A novel liquid biopsy technology was used to collect mRNA from circulating tumor cells (CTCs) to measure expression of AR-Vs, AR targets, and neuroendocrine prostate cancer markers. An institutional review board–approved prospective cohort (N = 99) was used to identify patterns of gene expression. Two prospective multicenter phase II clinical trials of ARSIs for men with castration-resistant prostate cancer (ClinicalTrials.gov: NCT01942837 [enzalutamide, N = 21] and NCT02025010 [abiraterone, N = 27]) were used to further validate these findings.

RESULTS

Hierarchical clustering of CTC transcripts identified two distinct clusters. Cluster 2 (C2) exhibited increased expression of AR-regulated genes and was associated with worse overall survival (median 8.6 v 22.4 months; P < .01; hazard ratio [HR] = 3.45 [1.9 to 6.14]). In multivariable analysis, C2 was prognostic independent of other clinicopathologic variables. AR-V status was not significant when accounting for C2. Upon further validation in pooled multicenter phase II trials, C2 was associated with worse overall survival (15.2 months v not reached; P < .01; HR = 8.43 [2.74 to 25.92]), prostate-specific antigen progression-free survival (3.6 v 12 months; P < .01; HR = 4.64 [1.53 to 14.11]), and radiographic progression-free survival (2.7 v 40.6 months; P < .01; HR = 4.64 [1.82 to 17.41]).

CONCLUSION

We demonstrate that a transcriptional profile detectable in CTCs obtained from liquid biopsies can serve as an independent prognostic marker beyond AR-V7 in patients with metastatic prostate cancer and can be used to identify the emergence of multiple ARSI resistance mechanisms. This is currently being investigated in additional prospective trials.

Development of secondary urothelial carcinoma following complete response to immune checkpoint inhibitors.

Urology Case Reports
Jean-Michel Lavoie, Gillian Vandekerkhove, Andrew J Murtha, Gang Wang, Alexander W Wyatt, Bernhard J Eigl

The management of metastatic urothelial cancer is rapidly evolving since immune checkpoint inhibitors were introduced. We present the case of a patient with metastatic upper tract urothelial cancer who had a complete response to durvalumab and tremelimumab. This patient then developed multiple non-invasive papillary bladder tumours. Next-generation sequencing revealed that the tumours shared ancestry with the upper tract cancer, although there were key differences, most notably the presence of a TP53 missense mutation in the upper tract disease that was absent in the bladder tumours. This illustrates an important practice point in the management of exceptional responders to checkpoint inhibitors.

The evolving role of germline genetic testing and management in prostate cancer: Report from the Princess Margaret Cancer Centre International Retreat

Canadian Urological Association Journal
Roderick Clark, Miran Kenk, Kristen McAlpine, Emily Thain, Kirsten M Farncombe, Colin C Pritchard, Robert Nussbaum, Alexander W Wyatt, Johann de Bono, Danny Vesprini, Yvonne Bombard, Justin Lorentz, Steven Narod, Raymond Kim, Neil Fleshner

Prostate cancer is a significant cause of cancer mortality. It has been well-established that certain germline pathogenic variants confer both an increased risk of being diagnosed with prostate cancer and dying of prostate cancer.1 There are exciting developments in both the availability of genetic testing and opportunities for improved treatment of patients. On August 19, 2020, the Princess Margaret Cancer Centre in Toronto, Ontario, hosted a virtual retreat, bringing together international experts in urology, medical oncology, radiation oncology, medical genetics, and translational research, as well as a patient representative. We are pleased to provide this manuscript as a review of those proceedings for Canadian clinicians.

Technical and biological constraints on ctDNA-based genotyping

Trends in Cancer
Cameron Herberts, Alexander W Wyatt

Circulating tumor DNA (ctDNA) enables real-time genomic profiling of cancer without the need for tissue biopsy. ctDNA-based technology is seeing rapid uptake in clinical practice due to the potential to inform patient management from diagnosis to advanced disease. In metastatic disease, ctDNA can identify somatic mutations, copy-number variants (CNVs), and structural rearrangements that are predictive of therapy response. However, the ctDNA fraction (ctDNA%) is unpredictable and confounds variant detection strategies, undermining confidence in liquid biopsy results. Assay design also influences which types of genomic alterations are identifiable. Here, we describe the relationships between ctDNA%, methodology, and sensitivity–specificity for major classes of genomic alterations in prostate cancer. We provide recommendations to navigate the technical complexities that constrain the detection of clinically relevant genomic alterations in ctDNA.

Cabazitaxel versus abiraterone or enzalutamide in poor prognosis metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase II trial

Annals of Oncology
M Annala, S Fu, JVW Bacon, J Sipola, N Iqbal, C Ferrario, M Ong, D Wadhwa, SJ Hotte, G Lo, B Tran, LA Wood, JR Gingerich, SA North, CJ Pezaro, JD Ruether, SS Sridhar, HML Kallio, DJ Khalaf, A Wong, K Beja, E Schönlau, S Taavitsainen, M Nykter, G Vandekerkhove, AA Azad, AW Wyatt, KN Chi,

Background: Treatment of poor prognosis metastatic castration-resistant prostate cancer (mCRPC) includes taxane chemotherapy and androgen receptor pathway inhibitors (ARPI). We sought to determine optimal treatment in this setting.

Patients and methods: This multicentre, randomised, open-label, phase II trial recruited patients with ARPI-naive mCRPC and poor prognosis features (presence of liver metastases, progression to mCRPC after <12 months of androgen deprivation therapy, or ≥4 of 6 clinical criteria). Patients were randomly assigned 1 : 1 to receive cabazitaxel plus prednisone (group A) or physician's choice of enzalutamide or abiraterone plus prednisone (group B) at standard doses. Patients could cross over at progression. The primary endpoint was clinical benefit rate for first-line treatment (defined as prostate-specific antigen response ≥50%, radiographic response, or stable disease ≥12 weeks).

Results: Ninety-five patients were accrued (median follow-up 21.9 months). First-line clinical benefit rate was greater in group A versus group B (80% versus 62%, P = 0.039). Overall survival was not different between groups A and B (median 37.0 versus 15.5 months, hazard ratio (HR) = 0.58, P = 0.073) nor was time to progression (median 5.3 versus 2.8 months, HR = 0.87, P = 0.52). The most common first-line treatment-related grade ≥3 adverse events were neutropenia (cabazitaxel 32% versus ARPI 0%), diarrhoea (9% versus 0%), infection (9% versus 0%), and fatigue (7% versus 5%). Baseline circulating tumour DNA (ctDNA) fraction above the cohort median and on-treatment ctDNA increase were associated with shorter time to progression (HR = 2.38, P < 0.001; HR = 4.03, P < 0.001). Patients with >30% ctDNA fraction at baseline had markedly shorter overall survival than those with undetectable ctDNA (HR = 38.22, P < 0.001).

Conclusions: Cabazitaxel was associated with a higher clinical benefit rate in patients with ARPI-naive poor prognosis mCRPC. ctDNA abundance was prognostic independent of clinical features, and holds promise as a stratification biomarker.

Trial registration: ClinicalTrials.gov NCT02254785.

Evolution of castration-resistant prostate cancer in ctDNA during sequential androgen receptor pathway inhibition

Clinical Cancer Research
Matti Annala, Sinja Taavitsainen, Daniel J Khalaf, Gillian Vandekerkhove, Kevin Beja, Joonatan Sipola, Evan W Warner, Cameron Herberts, Amanda Wong, Simon Fu, Daygen L Finch, Conrad D Oja, Joanna Vergidis, Muhammad Zulfiqar, Bernhard J Eigl, Christian K Kollmansberger, Matti Nykter, Martin E Gleave, Kim N Chi, Alexander W Wyatt

Cross-resistance renders multiple lines of androgen receptor (AR) signaling inhibitors increasingly futile in metastatic castration-resistant prostate cancer (mCRPC). We sought to determine acquired genomic contributors to cross-resistance.

Paternally expressed gene 10 (PEG10) promotes growth, invasion, and survival of bladder cancer

Molecular Cancer Therapeutics
Yoshihisa Kawai, Kenjiro Imada, Shusuke Akamatsu, Fan Zhang, Roland Seiler, Tetsutaro Hayashi, Jeffrey Leong, Eliana Beraldi, Neetu Saxena, Alexander Kretschmer, Htoo Zarni Oo, Alberto Contreras-Sanz, Hideyasu Matsuyama, Dong Lin, Ladan Fazli, Colin C Collins, Alexander W Wyatt, Peter C Black, Martin E Gleave

Paternally expressed gene 10 (PEG10) has been associated with neuroendocrine muscle-invasive bladder cancer (MIBC), a subtype of the disease with the poorest survival. In this work, we further characterized the expression pattern of PEG10 in The Cancer Genome Atlas database of 412 patients with MIBC, and found that, compared with other subtypes, PEG10 mRNA level was enhanced in neuroendocrine-like MIBC and highly correlated with other neuroendocrine markers. PEG10 protein level also associated with neuroendocrine markers in a tissue microarray of 82 cases. In bladder cancer cell lines, PEG10 expression was induced in drug-resistant compared with parental cells, and knocking down of PEG10 resensitized cells to chemotherapy. Loss of PEG10 increased protein levels of cell-cycle regulators p21 and p27 and delayed G1–S-phase transition, while overexpression of PEG10 enhanced cancer cell proliferation. PEG10 silencing also lowered levels of SLUG and SNAIL, leading to reduced invasion and migration. In an orthotopic bladder cancer model, systemic treatment with PEG10 antisense oligonucleotide delayed progression of T24 xenografts. In summary, elevated expression of PEG10 in MIBC may contribute to the disease progression by promoting survival, proliferation, and metastasis. Targeting PEG10 is a novel potential therapeutic approach for a subset of bladder cancers.

HSD3B1 (1245A>C) germline variant and clinical outcomes in metastatic castration-resistant prostate cancer patients treated with abiraterone and enzalutamide: results from two prospective studies

Annals of Oncology
Isabel Aragon, Daniel J Khalaf, Rebeca Lozano, Matti Annala, Sinja Taavitsainen, David Lorente, Daygen L Finch, Nuria Romero-Laorden, Joanna Vergidis, Ylenia Cendon, Conrad D Oja, Maria I Pacheco, Muhammad Zulfiqar, Martin Gleave, Alexander W Wyatt, David Olmos, Elena Castro, Kim N Chi

Background: A common polymorphism (1245A>C) in the HSD3B1 gene is associated with increased de novo synthesis of androgens and worse outcomes in men treated with androgen-deprivation therapy for metastatic castration-sensitive prostate cancer. The objective of the study was to determine whether this polymorphism is associated with outcomes for metastatic castration-resistant prostate cancer (mCRPC) treated with abiraterone or enzalutamide.

Patients and methods: A total of 547 patients treated with abiraterone or enzalutamide from two prospective cohorts were evaluated. The HSD3B1 genotype was determined by targeted sequencing and/or TaqMan single-nucleotide polymorphism genotyping. In cohort 1, patients were randomized to receive abiraterone + prednisone or enzalutamide. In cohort 2, patients received either agent according to investigator's choice. Prostate-specific antigen (PSA) response rate, time to PSA progression (TTPP), time to progression (TTP) and overall survival were determined. Associations between HSD3B1 genotypes and outcomes were evaluated via univariate Cox regression. Multivariable Cox model was used to determine the independent association of each covariate.

Results: The HSD3B1 variant genotype (CC) was present in 15% of patients and was associated with worse TTP [hazard ratio (HR) 1.31, 95% confidence interval (CI) 1.02-1.67, P = 0.032] and PSA response rates (48% for CC versus 62% and 65% for AA and AC, respectively [P = 0.019]), with no significant difference in TTPP (HR 1.28, 95% CI 0.99-1.66, P = 0.064). The effect of genotype was similar for treatment with abiraterone or enzalutamide with a negative test for interaction for TTPP (P = 0.997) and TTP (P = 0.749). Multivariable analysis did not show a significant association between genotype and TTP or TTPP.

Conclusions: The HSD3B1 (CC) genotype was associated with shorter TTP and lower PSA response rate in patients with mCRPC treated with abiraterone or enzalutamide. However, the CC genotype did not provide prognostic information beyond that conferred by standard clinical variables, suggesting that it may not be a suitable stand-alone biomarker in mCRPC.

The DNA methylation landscape of advanced prostate cancer

Nature Genetics
Shuang G Zhao, William S Chen, Haolong Li, Adam Foye, Meng Zhang, Martin Sjöström, Rahul Aggarwal, Denise Playdle, Arnold Liao, Joshi J Alumkal, Rajdeep Das, Jonathan Chou, Junjie T Hua, Travis J Barnard, Adina M Bailey, Eric D Chow, Marc D Perry, Ha X Dang, Rendong Yang, Ruhollah Moussavi-Baygi, Li Zhang, Mohammed Alshalalfa, S Laura Chang, Kathleen E Houlahan, Yu-Jia Shiah, Tomasz M Beer, George Thomas, Kim N Chi, Martin Gleave, Amina Zoubeidi, Robert E Reiter, Matthew B Rettig, Owen Witte, M Yvonne Kim, Lawrence Fong, Daniel E Spratt, Todd M Morgan, Rohit Bose, Franklin W Huang, Hui Li, Lisa Chesner, Tanushree Shenoy, Hani Goodarzi, Irfan A Asangani, Shahneen Sandhu, Joshua M Lang, Nupam P Mahajan, Primo N Lara, Christopher P Evans, Phillip Febbo, Serafim Batzoglou, Karen E Knudsen, Housheng H He, Jiaoti Huang, Wilbert Zwart, Joseph F Costello, Jianhua Luo, Scott A Tomlins, Alexander W Wyatt, Scott M Dehm, Alan Ashworth, Luke A Gilbert, Paul C Boutros, Kyle Farh, Arul M Chinnaiyan, Christopher A Maher, Eric J Small, David A Quigley, Felix Y Feng

Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes that were detectable only with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hypermethylation and somatic mutations in TET2DNMT3BIDH1 and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes ARMYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer that provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.

Activating AKT1 and PIK3CA mutations in metastatic castration-Rresistant prostate cancer

European Urology
Cameron Herberts, Andrew J Murthaa, Simon Fu, Gang Wang, Elena Schönlau, Hui Xue, Dong Lin, Anna Gleave, Steven Yip, Arkhjamil Angeles, Sebastien Hotte, Ben Tran, Scott North, Sinja Taavitsainen, Kevin Beja, Gillian Vandekerkhove, Elie Ritch, Evan Warner, Fred Saad, Nayyer Iqbal, Matti Nykter, Martin E Gleave, Yuzhuo Wang, Matti Annala, Kim N Chia, Alexander W Wyatt

Background

Activating mutations in AKT1 and PIK3CA are undercharacterised in metastatic castration-resistant prostate cancer (mCRPC), but are linked to activation of phosphatidylinositol 3-kinase (PI3K) signalling and sensitivity to pathway inhibitors in other cancers.

Objective

To determine the prevalence, genomic context, and clinical associations of AKT1/PIK3CA activating mutations in mCRPC.

Design, setting, and participants

We analysed targeted cell-free DNA (cfDNA) sequencing data from 599 metastatic prostate cancer patients with circulating tumour DNA (ctDNA) content above 2%.

Outcome measurements and statistical analysis

In patients with AKT1/PIK3CA mutations, cfDNA was subjected to PTEN intron sequencing and matched diagnostic tumour tissue was analysed when possible.

Results and limitations

Of the patients, 6.0% (36/599) harboured somatic clonal activating mutation(s) in AKT1 or PIK3CA. Mutant allele-specific imbalance was common. Clonal mutations in mCRPC ctDNA were typically detected in pretreatment primary tissue and were consistent across serial ctDNA collections. AKT1/PIK3CA-mutant mCRPC had fewer androgen receptor (AR) gene copies than AKT1/PIK3CA wild-type mCRPC (median 4.7 vs 10.3, p =  0.003). AKT1 mutations were mutually exclusive with PTEN alterations. Patients with and without AKT1/PIK3CA mutations showed similar clinical outcomes with standard of care treatments. A heavily pretreated mCRPC patient with an AKT1 mutation experienced a 50% decline in prostate-specific antigen with Akt inhibitor (ipatasertib) monotherapy. Ipatasertib also had a marked antitumour effect in a patient-derived xenograft harbouring an AKT1 mutation. Limitations include the inability to assess AKT1/PIK3CA correlatives in ctDNA-negative patients.

Conclusions

AKT1/PIK3CA activating mutations are relatively common and delineate a distinct mCRPC molecular subtype with low-level AR copy gain. Clonal prevalence and evidence of mutant allele selection propose PI3K pathway dependency in selected patients. The use of cfDNA screening enables prospective clinical trials to test PI3K pathway inhibitors in this population.

Patient summary

Of advanced prostate cancer cases, 6% have activating mutations in the genes AKT1 or PIK3CA. These mutations can be identified using a blood test and may help select patients suitable for clinical trials of phosphatidylinositol 3-kinase inhibitors.

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Concurrent germline and somatic pathogenic BAP1 variants in a patient with metastatic bladder cancer

NPJ Genomic Medicine
Megan E Tesch, Justin A Pater, Gillian Vandekerkhove, Gang Wang, Kristin Binnington, Alan I So, Alexander W Wyatt, Bernhard J Eigl

Germline pathogenic variants in the BRCA1-associated protein-1 (BAP1) gene cause the BAP1 tumor predisposition syndrome (TPDS). BAP1 TPDS is associated with an increased risk of uveal and cutaneous melanoma, mesothelioma, renal cell carcinoma, and several other cancer subtypes. Here, we report a germline nonsense BAP1 variant (c.850G>T, p.Glu284Ter) in a patient with bladder cancer and a strong family history of malignancy. Concurrently, we identified a somatic frameshift BAP1 variant, and as expected, immunostaining validated the loss of BAP1 protein in patient-derived tumor specimens. Together, these data provide strong evidence of pathogenicity in this case. With the addition of bladder cancer to the tumor types reported with germline BAP1 mutations, our understanding of the BAP1 TPDS continues to evolve, and may affect future screening and surveillance guidelines.

Clinical outcomes in cyclin-dependent kinase 12 mutant advanced prostate cancer

European Urology
Melissa A Reimers, Steven M Yip, Li Zhang, Marcin Cieslik, Mallika Dhawan, Bruce Montgomery, Alexander W Wyatt, Kim N Chi, Eric J Small, Arul M Chinnaiyan, Ajjai S Alva, Felix Y Feng, Jonathan Chou

Background: Cyclin-dependent kinase 12 (CDK12) loss occurs in 3-7% of metastatic prostate cancer patients and is characterized by a genomic instability signature, but the clinical implications of CDK12 loss are not well established.

Objective: To determine the clinical course of patients with CDK12 mutant advanced prostate cancer compared with other genomic subtypes.

Design, setting, and participants: A retrospective analysis of data from three academic medical centers, including 317 patients with advanced prostate cancer and prior next-generation sequencing from tumor tissue (n = 172) or circulating tumor DNA (n = 145), was performed. Forty-six patients had CDK12 mutations; 34 had biallelic CDK12 loss (79%).

Outcome measurements and statistical analysis: Patients were stratified by mutation status (CDK12, homologous recombination deficiency [HRD; BRCA1/2 and ATM], TP53, and other cohort). The Kaplan-Meier method was used to evaluate time to event outcomes: time to development of metastatic disease, time to development of castration resistance, and time to prostate-specific antigen (PSA) progression after first-line androgen receptor pathway inhibitor (ARPI) therapy in a patient subset.

Results and limitations: The median follow-up was 66.6 mo. Patients with CDK12 mutant prostate cancer exhibited shorter time to metastasis (median = 34.9 mo, p = 0.004) and development of castration-resistant disease (median = 32.7 mo, p < 0.001), compared with other genomic subtypes, with shorter time to PSA progression on first-line ARPI treatment of metastatic castration-resistant disease (median = 3.6 mo, p = 0.0219). CDK12 mutant patients did not have overall shorter time on treatment compared with other mutation subgroups, and CDK12 status did not demonstrate statistical significance in multivariate analysis. Limitations include variable center-dependent practice patterns and heterogeneity due to combining tumor and liquid biopsy data.

Conclusions: Our data suggest that advanced prostate cancers harboring CDK12 mutations display aggressive clinical behavior, underscoring the need to fully delineate the molecular and clinical characteristics, and appropriate therapeutic approaches for distinct subtypes of advanced prostate cancers.

Patient summary: In this report, we evaluate the clinical characteristics and outcomes of patients with prostate cancer and CDK12 mutation in their tumors. These patients seem to have more aggressive disease, with more high-grade Gleason ≥8 cancers and shorter time to developing metastatic cancer. Cases of advanced CDK12-mutated prostate cancer may warrant consideration of therapy intensification or combination approaches.

Plasma Circulating Tumor DNA and Clonal Hematopoiesis in Metastatic Renal Cell Carcinoma

Clinical Genitourinary Cancer
Jack VW Bacon, Matti Annala, Maryam Soleimani, Jean-Michel Lavoie, Alan So, Martin E Gleave, Ladan Fazli, Gang Wang, Kim N Chi, Christian K Kollmannsberger, Alexander W Wyatt, Lucia Nappi

Background: There is a lack of molecularly-informed biomarkers for patients with metastatic renal cell carcinoma (RCC). Plasma cell-free DNA (cfDNA) sequencing is a minimally-invasive alternative to tissue for profiling the genome in other cancers but relevance in metastatic RCC remains unclear.

Materials and methods: Whole blood was collected from 55 patients with metastatic RCC. Plasma cfDNA and leukocyte DNA were subjected to targeted sequencing across 981 cancer genes. Matched tumor tissue from 14 patients was analyzed.

Results: Thirty-three percent of patients had evidence for RCC-derived circulating tumor DNA (ctDNA), significantly lower than patients with metastatic prostate or bladder cancer analyzed using the same approach. Among ctDNA-positive patients, ctDNA fraction averaged only 3.9% and showed no strong association with clinical variables. In these patients, the most commonly mutated genes were VHL, BAP1, and PBRM1, and matched tissue concordance was 77%. Evidence of somatic expansions unrelated to RCC, such as clonal hematopoiesis of indeterminate potential, were detected in 43% of patients. Pathogenic germline mutations in DNA repair genes were detected in 11% of patients. CtDNA-positive patients had shorter overall survival and progression-free survival on first-line therapy. Patients with evidence of clonal hematopoiesis of indeterminate potential had an intermediate prognosis compared with ctDNA-positive and -negative patients.

Conclusions: CfDNA sequencing enables straightforward characterization of the somatic RCC genome in a minority of patients with metastatic RCC. Owing to low ctDNA abundance, and the presence of non-RCC derived somatic clones in circulation, cfDNA sequencing may not be a simple pan-patient alternative to tissue biopsy in metastatic RCC.

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