Human Pathology, 2020
Authors
Evan Gibbard, Dawn R Cochrane, Jennifer Pors, Gian Luca Negri, Shane Colborne, Angela Cheng, Christine Chow, David Farnell, Basile Tessier-Cloutier, Jessica N McAlpine, Gregg B Morin, Dietmar Schmidt, Stefan Kommoss, Friedrich Kommoss, Jacqueline Keul, Blake Gilks, David G Huntsman, Lynn Hoang
Publication Abstract

Mesonephric carcinomas (ME) and female adnexal tumours of probable Wolffian origin (FATWO) are derived from embryologic remnants of Wolffian/mesonephric ducts. Mesonephric-like carcinomas (MLC) show identical morphology to ME of the cervix, but occur in the uterus and ovary without convincing mesonephric remnants. ME, MLC and FATWO are challenging to diagnose due to their morphologic similarities to Müllerian/paramesonephric tumours, contributing to a lack of evidence-based and tumour-specific treatments. We performed whole proteomic analysis on 9 ME/MLC and 56 endometrial carcinomas (EC) to identify potential diagnostic biomarkers. While there were no convincing differences between ME and MLC, 543 proteins showed increased expression in ME/MLC relative to EC. From these proteins, EHMT2, GSTM3, EEF1A2, and GSK3β were identified as putative biomarkers. Immunohistochemistry was performed on these candidates at GATA3 in 14 ME/MLC, 8 FATWO, 155 EC, and normal tissues. Of the candidates, only GATA3 and EHMT2 were highly expressed in mesonephric remnants and mesonephric-derived male tissues. GATA3 had the highest sensitivity and specificity for ME/MLC versus EC (93% and 99%), but was absent in FATWO. EHMT2 was 100% sensitive for ME/MLC & FATWO, but was not specific (65%). Similarly, EEF1A2 was reasonably sensitive to ME/MLC (92%) and FATWO (88%), but was the least specific (38%). GSTM3 performed intermediately (sensitivity for ME/MLC and FATWO: 83% and 38% respectively; specificity 67%). While GATA3 remained the best diagnostic biomarker for ME/MLC, we have identified EHMT2, EEF1A2, and GSTM3 as proteins of interest in these cancers. FATWO's cell-of-origin is uncertain and remains an area for future research.

Journal of Natural Products, 2020
Authors
Luping Yan, Carmen A Banuelos, Nasrin R Mawji, Brian O Patrick, Marianne D Sadar, Raymond J Andersen
Publication Abstract

Synthetic analogues of the marine natural product sintokamides have been prepared in order to investigate the structure-activity relationships for the androgen receptor N-terminal domain (AR NTD) antagonist activity of the sintokamide scaffold. An in vitro LNCaP cell-based transcriptional activity assay with an androgen-driven luciferase (Luc) reporter was used to monitor the potency of analogues. The data have shown that the chlorine atoms on the leucine side chains are essential for potent activity. Analogues missing the nonchlorinated methyl groups of the leucine side chains (C-1 and C-17) are just as active and in some cases more active than the natural products. Analogues with the natural R configuration at C-10 and the unnatural R configuration at C-4 are most potent. Replacing the natural propionamide N-terminus cap with the more sterically hindered pivaloylamide N-terminus cap leads to enhanced potency. The tetramic acid fragment and the methyl ether on the tetramic acid fragment are essential for activity. The SAR optimized analogue 76 is more selective, easier to synthesize, more potent, and presumed to be more resistant to proteolysis than the natural sintokamides.

Blood, 2020
Authors
Brett J Collinge, Susana Ben-Neriah, Lauren C Chong, Merrill Boyle, Aixiang Jiang, Tomoko Miyata-Takata, Pedro Farinha, Jeffrey W Craig, Graham W Slack, Daisuke Ennishi, Anja Mottok, Barbara Meissner, Elizabeth A Chavez, Alina S Gerrie, Diego Villa, Ciara L Freeman, Kerry J Savage, Laurie H Sehn, Ryan D Morin, Andrew J Mungall, Randy D Gascoyne, Marco A Marra, Joseph M Connors, Christian Steidl, David W Scott
Publication Abstract

When the WHO defined high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/TH) as a clinical category, rearrangements were the only structural variant (SV) incorporated. An "atypical double-hit" entity has been proposed, encompassing tumors with concurrent MYC and BCL2 SVs other than co-occurring translocations - i.e. copy number variations (CNVs). While the identification of a gene expression signature (DHITsig) shared among tumors harboring MYC and BCL2 rearrangements (HGBL-DH/TH-BCL2) has confirmed a shared underlying biology, the biological implication of MYC and BCL2 CNVs requires further elucidation. We performed a comprehensive analysis of MYC and BCL2 SVs, as determined by fluorescent in situ hybridization (FISH), in a cohort of 802 de novo tumors with diffuse large B-cell lymphoma (DLBCL) morphology. While BCL2 CNVs were associated with increased expression, MYC CNVs were not. Furthermore, MYC and BCL2 CNVs, in the context of atypical double-hit, did not confer a similar gene expression profile as HGBL-DH/TH-BCL2. Finally, while MYC IHC has been proposed as a screening tool for FISH testing, two mechanisms were observed that uncoupled MYC rearrangement from IHC positivity. 1) low MYC mRNA expression and 2) false-negative immunohistochemistry (IHC) staining mediated by a single nucleotide polymorphism resulting in an asparagine to serine substitution at the 11th amino acid residue of MYC (MYC-N11S). Taken together, these results support the current exclusion of MYC and BCL2 CNVs from HGBL-DH/TH and highlight the ability of a molecular based classification system to identify tumors with shared biology that FISH and IHC fail to fully capture.

BMC Biology, 2020
Authors
Derek Wong, Lisa Sogerer, Samantha S Lee, Victor Wong, Amy Lum, Adrian B Levine, Marco A Marra, Stephen Yip
Publication Abstract

Aberrations in Capicua (CIC) have recently been implicated as a negative prognostic factor in a multitude of cancer types through the derepression of targets downstream of the mitogen-activated protein kinase (MAPK) signaling cascade, such as oncogenic E26 transformation-specific (ETS) transcription factors. The Ataxin-family protein ATXN1L has previously been reported to interact with CIC in both developmental and disease contexts to facilitate the repression of CIC target genes and promote the post-translational stability of CIC. However, little is known about the mechanisms at the base of ATXN1L-mediated CIC post-translational stability.

Frontiers in Public Health, 2020
Authors
Meck Chongo, Josée G Lavoie, Javier Mignone, Nadine R Caron, Henry G Harder, Rob Chase.
Publication Abstract

Introduction: Indigenous peoples in Canada have endured and continue to experience the impact of colonization by European settlers. The deleterious manifestations of intergenerational historic trauma (HT) are evidenced in the high HIV/AIDS epidemic-related premature mortality rates among Indigenous men, despite the availability of novel highly active antiretroviral therapies (HAARTs). Aim: The aims of this study were to explore the impact of historic trauma (HT) on treatment adherence and health promoting practices among Indigenous men living with HIV, and how resilience was both expressed and mediated by survivor status. Methods: This interpretive description study incorporated a cultural safety lens. Through partnership with the Vancouver Native Health Society, 36 male HT survivors were recruited using purposive and theoretical sampling. They told their lived experiences and health promoting practices with respect to HAART adherence through interviews and a focus group. Results: Two broad categories (findings) emerged: (1) resilience as facilitator of HAART adherence; and (2) differential views on HT's impact. Resilience was expressed through nine concepts. Conclusion: Most Indigenous men in this study demonstrate health promoting behavior, stay on HAART and have better health and well-being even if the environments they live in are marginalized or heavily stigmatizing. This study shows that areas of strength and adaptation, including factors promoting resilience can be harnessed to foster HAART adherence. With a consideration of these areas of strength and adaptation, this study offers implications for research and recommendations to improve treatment-adherent behavior, fostering healing from HT, and reducing HIV/AIDS-related deaths.

Research Involvement and Engagement, 2020
Authors
Madison Foster, Dean A Fergusson, Terry Hawrysh, Justin Presseau, Natasha Kekre, Stuart Schwartz, Gisell Castillo, Sarah Asad, Grace Fox, Harold Atkins, Kednapa Thavorn, Joshua Montroy, Robert A Holt, Zarah Monfaredi, Manoj M Lalu
Publication Abstract

Aim: Though patient engagement in clinical research is growing, recent reports suggest few clinical trials report on such activities. To address this gap, we describe our approach to patient engagement in the development of a clinical trial protocol to assess a new immunotherapy for blood cancer (chimeric antigen receptor T-cell therapy, CAR-T cell therapy).

Methods: Our team developed a clinical trial protocol by working with patient partners from inception. Two patient partners with lived blood cancer experience were identified through referrals from our team's professional network and patient organization contacts. Our patient partners were onboarded to the team and engaged in several studies conducted to develop the clinical trial protocol, including a systematic review of the existing literature on the therapy, patient interviews and a survey to obtain perspectives on barriers and enablers to participating in the trial, an early economic analysis, and a retrospective cohort study.

Results: Engaging patient partners enhanced our research in ways that would not have otherwise occurred. By selecting patient important outcomes for data collection, our partners helped flag that quality of life and health utility measures have not been reported in previous CAR-T cell therapy trials for blood cancer. Our partners also co-developed a non-technical summary of the systematic review that summarized results in an accessible manner. Our patient partners reviewed interview and survey questions, to improve the language and appropriateness; provided recruitment suggestions; and provided a patient perspective on the results, thereby confirming the importance of findings. Input was also obtained on costs for the early economic analysis. Our patient partners identified costs that may be a burden to both patients and caregivers during a trial and helped to confirm that the overall structure of the economic model reflected the patient care pathway. Our patient partners also shared their diagnosis and treatment stories, which helped to provide the research team with insight into this experience.

Conclusions: Contributions by our patient partners were invaluable to each component study, as well as the overall development of the trial protocol. We plan to use this approach in the future in order to meaningfully engage patients in the development of other clinical trials; we also hope that by reporting our methods this will help other research teams to do the same.

Clinical Cancer Research, 2020
Authors
James T Topham, Joanna M Karasinska, Michael Kuan-Ching Lee, Veronika Csizmok, Laura M Williamson, Gun Ho Jang, Robert E Denroche, Erica S Tsang, Steve E Kalloger, Hui-Li Wong, Grainne M O'Kane, Richard A Moore, Andrew J Mungall, Faiyaz Notta, Jonathan M Loree, Julie M Wilson, Oliver F Bathe, Patricia A Tang, Rachel A Goodwin, Jennifer J Knox, Steven Gallinger, Janessa Laskin, Marco A Marra, Steven JM Jones, Daniel J Renouf, David F Schaeffer.
Publication Abstract

Background RNA-sequencing-based subtyping of pancreatic ductal adenocarcinoma (PDAC) has been reported by multiple research groups, each using different methodologies and patient cohorts. 'Classical' and 'basal-like' PDAC subtypes are associated with survival differences, with basal-like tumors associated with worse prognosis. We amalgamated various PDAC subtyping tools to evaluate the potential of such tools to be reliable in clinical practice. Methods Sequencing data for 574 PDAC tumors was obtained from prospective trials and retrospective public databases. Six published PDAC subtyping strategies (Moffitt regression tools, clustering-based Moffitt, Collisson, Bailey, and Karasinska subtypes) were employed on each sample, and results were tested for subtype call consistency and association with survival. Results Basal-like and classical subtype calls were concordant in 88% of patient samples, and survival outcomes were significantly different (p<0.05) between prognostic subtypes. 12% of tumors had subtype-discordant calls across the different methods, showing intermediate survival in univariate and multivariate survival analyses. Transcriptional profiles compatible with that of a hybrid subtype signature were observed for subtype-discordant tumors, in which classical and basal-like genes were concomitantly expressed. Subtype-discordant tumors showed intermediate molecular characteristics, including subtyping gene expression (p<0.0001) and mutant KRAS allelic imbalance (p<0.001). Conclusions Nearly one in six patients with PDAC have tumors that fail to reliably fall into the classical or basal-like PDAC subtype categories, based on two regression tools aimed towards clinical practice. Rather, these patient tumors show intermediate prognostic and molecular traits. We propose close consideration of the non-binary nature of PDAC subtypes for future incorporation of subtyping into clinical practice.

Clinical Cancer Research, 2020
Authors
Alexandra Pender, Emma Titmuss, Erin D Pleasance, Kevin Y Fan, Hillary Pearson, Scott D Brown, Cameron J Grisdale, James T Topham, Yaoqing Shen, Melika Bonakdar, Greg Taylor, Laura M Williamson, Karen L Mungall, Eric Chuah, Andrew J Mungall, Richard A Moore, Jean-Michel Lavoie, Stephen Yip, Howard Lim, Daniel J Renouf, Sophie Sun, Robert A Holt, Steven JM Jones, Marco A Marra, Janessa Laskin
Publication Abstract

Purpose: Immune checkpoint inhibitors (ICIs) have revolutionised the treatment of solid tumours with dramatic and durable responses seen across multiple tumour types. However, identifying patients who will respond to these drugs remains challenging, particularly in the context of advanced and previously treated cancers.

Experimental design: We characterised fresh tumour biopsies from a heterogeneous pan-cancer cohort of 98 patients with metastatic predominantly pre-treated disease through the Personalized OncoGenomics (POG) program at BC Cancer using whole genome and transcriptome analysis (WGTA). Baseline characteristics and follow up data were collected retrospectively.

Results: We found that tumour mutation burden (TMB), independent of mismatch repair status, was the most predictive marker of time to progression (TTP, p=0.007), but immune related CD8+ T cell and M1-M2 macrophage ratio scores were more predictive for overall survival (OS) (p=0.0014 and 0.0012 respectively). While CD274 (PD-L1) gene expression is comparable to protein levels detected by immunohistochemistry (IHC), we did not observe a clinical benefit for patients with this marker. We demonstrate that a combination of markers based on WGTA provides the best stratification of patients (p=0.00071, OS), and also present a case study of possible acquired resistance to pembrolizumab in a non-small cell lung cancer (NSCLC) patient.

Conclusions: Interpreting the tumour-immune interface to predict ICI efficacy remains challenging. WGTA allows for identification of multiple biomarkers simultaneously that in combination may help to identify responders, particularly in the context of a heterogeneous population of advanced and previously treated cancers, thus precluding tumour type-specific testing.

Journal of Oncology Pharmacy Practice, 2020
Authors
Jolene Guenter, Shirin Abadi, Howard Lim, Stephen Chia, Ryan Woods, Martin Jones, Nevena Rebic, Daniel J Renouf, Janessa Laskin, Marco Marra
Publication Abstract

Introduction: Carcinogenesis is driven by an array of complex genomic patterns; these patterns can render an individual resistant or sensitive to certain chemotherapy agents. The Personalized Oncogenomics (POG) project at BC Cancer has performed integrative genomic analysis of whole tumour genomes and transcriptomes for over 700 patients with advanced cancers, with an aim to predict therapeutic sensitivities. The aim of this study was to utilize the POG genomic data to evaluate a discrete set of biomarkers associated with chemo-sensitivity or-resistance in advanced stage breast and colorectal cancer POG patients.

Methods: This was a retrospective multi-centre analysis across all BC CANCER sites. All breast and colorectal cancer patients enrolled in the POG program between July 1, 2012 and November 30, 2016 were eligible for inclusion. Within the breast cancer population, those treated with capecitabine, paclitaxel, and everolimus were analyzed, and for the colorectal cancer patients, those treated with capecitabine, bevacizumab, irinotecan, and oxaliplatin were analyzed. The expression levels of the selected biomarkers of interest (EPHB4, FIGF, CD133, DICER1, DPYD, TYMP, TYMS, TAP1, TOP1, CKDN1A, ERCC1, GSTP1, BRCA1, PTEN, ABCB1, TLE3, and TXNDC17) were reported as mRNA percentiles.

Results: For the breast cancer population, there were 32 patients in the capecitabine cohort, 15 in the everolimus cohort, and 12 in the paclitaxel cohort. For the colorectal cancer population, there were 29 patients in the bevacizumab cohort, 12 in the oxaliplatin cohort, 29 in the irinotecan cohort, and 6 in the capecitabine cohort. Of the biomarkers evaluated, the strongest associations were found between Bevacizumab-based therapy and DICER1 (P = 0.0445); and between capecitabine therapy and TYMP (P = 0.0553).

Conclusions: Among breast cancer patients, higher TYMP expression was associated with sensitivity to capecitabine. Among colorectal cancer patients, higher DICER1 expression was associated with sensitivity to bevacizumab-based therapy. This study supports further assessment of the potential predictive value of mRNA expression of these genomic biomarkers.

Nature Communications, 2020
Authors
Astrid De Boeck, Bo Young Ahn, Charlotte D'Mello, Xueqing Lun, Shyam V Menon, Mana M Alshehri, Frank Szulzewsky, Yaoqing Shen, Lubaba Khan, Ngoc Ha Dang, Elliott Reichardt, Kimberly-Ann Goring, Jennifer King, Cameron J Grisdale, Natalie Grinshtein, Dolores Hambardzumyan, Karlyne M Reilly, Michael D Blough, J Gregory Cairncross, V Wee Yong, Marco A Marra, Steven J M Jones, David R Kaplan, Kathy D McCoy, Eric C Holland, Pinaki Bose, Jennifer A Chan, Stephen M Robbins, Donna L Senger
Publication Abstract

Despite a deeper molecular understanding, human glioblastoma remains one of the most treatment refractory and fatal cancers. It is known that the presence of macrophages and microglia impact glioblastoma tumorigenesis and prevent durable response. Herein we identify the dual function cytokine IL-33 as an orchestrator of the glioblastoma microenvironment that contributes to tumorigenesis. We find that IL-33 expression in a large subset of human glioma specimens and murine models correlates with increased tumor-associated macrophages/monocytes/microglia. In addition, nuclear and secreted functions of IL-33 regulate chemokines that collectively recruit and activate circulating and resident innate immune cells creating a pro-tumorigenic environment. Conversely, loss of nuclear IL-33 cripples recruitment, dramatically suppresses glioma growth, and increases survival. Our data supports the paradigm that recruitment and activation of immune cells, when instructed appropriately, offer a therapeutic strategy that switches the focus from the cancer cell alone to one that includes the normal host environment.

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