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

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.

BMJ Open
Authors
Margo E Pearce, Kate Jongbloed, Sherri Pooyak, Wenecwtsin M Christian, Maaxswxw Gibuu White Wolf Mary Teegee, Nadine R Caron, Victoria Thomas, Earl Henderson, David Zamar, Eric M Yoshida, Martin T Schechter, Patricia M Spittal
Publication Abstract

This study examined associations between childhood maltreatment, colonial harms and sex/drug-related risks for HIV and hepatitis C virus (HCV) infection among young Indigenous people who use drugs.

Frontiers in Oncology
Authors
Zainab A. Bazzi, Isabella T. Tai
Publication Abstract

Cyclin-dependent kinase 10 (CDK10) is a CDC2-related serine/threonine kinase involved in cellular processes including cell proliferation, transcription regulation and cell cycle regulation. CDK10 has been identified as both a candidate tumor suppressor in hepatocellular carcinoma, biliary tract cancers and gastric cancer, and a candidate oncogene in colorectal cancer (CRC). CDK10 has been shown to be specifically involved in modulating cancer cell proliferation, motility and chemosensitivity. Specifically, in CRC, it may represent a viable biomarker and target for chemoresistance. The development of therapeutics targeting CDK10 has been hindered by lack a specific small molecule inhibitor for CDK10 kinase activity, due to a lack of a high throughput screening assay. Recently, a novel CDK10 kinase activity assay has been developed, which will aid in the development of small molecule inhibitors targeting CDK10 activity. Discovery of a small molecular inhibitor for CDK10 would facilitate further exploration of its biological functions and affirm its candidacy as a therapeutic target, specifically for CRC.

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Canadian Urological Association Journal
Authors
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
Publication Abstract

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.

Nature
Authors
Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, Kieran R. Campbell, Tehmina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Hakwoo Lee, Jerome Ting, Allen W. Zhang, Hoa Tran, Ciara O’Flanagan, Fatemeh Dorri, Nicole Rusk, Teresa Ruiz de Algara, So Ra Lee, Brian Yu Chieh Cheng, Peter Eirew, Takako Kono, Jenifer Pham, Diljot Grewal, Daniel Lai, Richard Moore, Andrew J. Mungall, Marco A. Marra, IMAXT Consortium, Andrew McPherson, Alexandre Bouchard-Côté, Samuel Aparicio, Sohrab P. Shah
Publication Abstract

Progress in defining genomic fitness landscapes in cancer, especially those defined by copy number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of polyclonal populations and temporal statistical models. Here we generated 42,000 genomes from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright-Fisher population genetics model to infer clonal fitness, we found that TP53 mutation alters the fitness landscape, reproducibly distributing fitness over a larger number of clones associated with distinct CNAs. Furthermore, in TNBC PDX models with mutated TP53, inferred fitness coefficients from CNA-based genotypes accurately forecast experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDXs resulted in cisplatin-resistant clones emerging from low-fitness phylogenetic lineages in the untreated setting. Conversely, high-fitness clones from treatment-naive controls were eradicated, signalling an inversion of the fitness landscape. Finally, upon release of drug, selection pressure dynamics were reversed, indicating a fitness cost of treatment resistance. Together, our findings define clonal fitness linked to both CNA and therapeutic resistance in polyclonal tumours.

Clinical Cancer Research
Authors
Karen A Urtishak, Deborah S Ricci, Oliver Brendan Rooney, Angela Lopez-Gitlitz, Margaret K Yu, Alexander W Wyatt, Mark Li, Gerhardt Attard, Eric J Small.
Publication Abstract

Purpose: In the placebo-controlled SPARTAN study, apalutamide added to androgen-deprivation therapy (ADT) improved metastasis-free survival, second progression-free survival, and overall survival (OS) in patients with nonmetastatic castration-resistant prostate cancer (nmCRPC). Mechanisms of resistance to apalutamide in nmCRPC require evaluation.

Experimental design: In a subset of patients from SPARTAN, aberrations were assessed at baseline and end of study treatment (EOST) using targeted next-generation sequencing or quantitative reverse transcription PCR. Circulating tumor (ct)DNA levels were assessed qualitatively. Select aberrations in androgen receptor (AR) and other common PC-driving genes were detected and summarized by treatment group; genomic aberrations were summarized in ctDNA-positive samples. Association between detection of aberrations in all patients and outcomes was assessed using Cox proportional-hazards models and multivariate analysis.

Results: In 247 patients, the overall prevalence of ctDNA, AR aberrations, and TP53 inactivation increased from baseline (40.6%, 13.6%, 22.2%) to EOST (57.1%, 25.4%, 35.0%) and was comparable between treatment groups at EOST. In patients who received subsequent androgen signaling inhibition after study treatment, detectable biomarkers at EOST were significantly associated with poor outcomes: ctDNA with PFS2 or OS [HR = 2.01 or 2.17, respectively; P < 0.0001 for both], any AR aberration with PFS2 [1.74; P = 0.024], and TP53 or BRCA2 inactivation with OS [2.06; P = 0.003; or 3.1; P <0.0001].

Conclusions: Apalutamide plus ADT did not increase detectable AR/non-AR aberrations over ADT alone. Detectable ctDNA, AR aberrations, and TP53/BRCA2 inactivation at EOST were associated with poor outcomes in patients treated with first subsequent androgen signaling inhibitor.

Modern Pathology
Authors
Julia R Naso, Adrian B Levine, Hossein Farahani, Lucian R Chirieac, Sanja Dacic, Joanne L Wright, Chi Lai, Hui-Min Yang, Steven J M Jones, Ali Bashashati, Stephen Yip, Andrew Churg
Publication Abstract

Sarcomatoid mesothelioma is an aggressive malignancy that can be challenging to distinguish from benign spindle cell mesothelial proliferations based on biopsy, and this distinction is crucial to patient treatment and prognosis. A novel deep learning based classifier may be able to aid pathologists in making this critical diagnostic distinction. SpindleMesoNET was trained on cases of malignant sarcomatoid mesothelioma and benign spindle cell mesothelial proliferations. Performance was assessed through cross-validation on the training set, on an independent set of challenging cases referred for expert opinion ('referral' test set), and on an externally stained set from outside institutions ('externally stained' test set). SpindleMesoNET predicted the benign or malignant status of cases with AUC's of 0.932, 0.925, and 0.989 on the cross-validation, referral and external test sets, respectively. The accuracy of SpindleMesoNET on the referral set cases (92.5%) was comparable to the average accuracy of 3 experienced pathologists on the same slide set (91.7%). We conclude that SpindleMesoNET can accurately distinguish sarcomatoid mesothelioma from benign spindle cell mesothelial proliferations. A deep learning system of this type holds potential for future use as an ancillary test in diagnostic pathology.

Cancer Medicine
Authors
Deirdre Weymann, Samantha Pollard, Brandon Chan, Emma Titmuss, Alexandra Bohm, Janessa Laskin, Steven J M Jones, Erin Pleasance, Jessica Nelson, Alexandra Fok, Howard Lim, Aly Karsan, Daniel J Renouf, Kasmintan A Schrader, Sophie Sun, Stephen Yip, David F Schaeffer, Marco A Marra, Dean A Regier

Publication Abstract

Single-arm trials are common in precision oncology. Owing to the lack of randomized counterfactual, resultant data are not amenable to comparative outcomes analyses. Difference-in-difference (DID) methods present an opportunity to generate causal estimates of time-varying treatment outcomes. Using DID, our study estimates within-cohort effects of genomics-informed treatment versus standard care on clinical and cost outcomes.

F1000 Research
Authors
René L Warren, Inanc Birol
Publication Abstract

As the year 2020 came to a close, several new strains have been reported of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent responsible for the coronavirus disease 2019 (COVID-19) pandemic that has afflicted us all this past year. However, it is difficult to comprehend the scale, in sequence space, geographical location and time, at which SARS-CoV-2 mutates and evolves in its human hosts. To get an appreciation for the rapid evolution of the coronavirus, we built interactive scalable vector graphics maps that show daily nucleotide variations in genomes from the six most populated continents compared to that of the initial, ground-zero SARS-CoV-2 isolate sequenced at the beginning of the year.

Clinical Cancer Research
Authors
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
Publication Abstract

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.

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