Molecular Genetics & Genomic Medicine, 2020
Authors
Deirdre Weymann, Janessa Laskin, Steven J M Jones, Howard Lim, Daniel J Renouf, Robyn Roscoe, Kasmintan A Schrader, Sophie Sun, Stephen Yip, Marco A Marra, Dean A Regier
Publication Abstract

Randomized controlled trials (RCTs) are uncommon in precision oncology. We provide an introduction and illustrative example of matching methods for evaluating precision oncology in the absence of RCTs. We focus on British Columbia's Personalized OncoGenomics (POG) program, which applies whole-genome and transcriptome analysis (WGTA) to inform advanced cancer care.

Scientific Reports, 2020
Authors
Sylvain Lefort, Sneha Balani, Davide Pellacani, Boris Guyot, Sharon M Gorski, Véronique Maguer-Satta, Connie J Eaves
Publication Abstract

Assessment of autophagy activity has historically been limited to investigations of fixed tissue or bulk cell populations. To address questions of heterogeneity and relate measurements to functional properties of viable cells isolated from primary tissue, we created a lentiviral (RFP-GFP-MAP1LC3B) vector that allows the autophagosome and autolysosome content of transduced cells to be monitored at the single-cell level. Use of this strategy to analyze purified subsets of normal human mammary cells showed that both the luminal progenitor-containing (LP) subset and the basal cells (BCs) display highly variable but overall similar autophagic flux activity despite differences suggested by measurements of the proteins responsible (i.e., LC3B, ATG7 and BECLIN1) in bulk lysates. Autophagosome content was also highly variable in the clonogenic cells within both the LPs and BCs, but the proliferative response of the BCs was more sensitive to autophagy inhibition. In addition, use of this vector showed cells with the lowest autophagosome content elicited the fastest tumor growth in 2 different models of human mammary tumorigenesis. These results illustrate the utility of this vector to define differences in the autophagy properties of individual cells in primary tissue and couple these with their responses to proliferative and oncogenic stimuli.

Brain, 2020
Authors
Katayoun Ayasoufi, Christian K Pfaller, Laura Evgin, Roman H Khadka, Zachariah P Tritz, Emma N Goddery, Cori E Fain, Lila T Yokanovich, Benjamin T Himes, Fang Jin, Jiaying Zheng, Matthew R Schuelke, Michael J Hansen, Wesley Tung, Ian F Parney, Larry R Pease, Richard G Vile, Aaron J Johnson
Publication Abstract

Immunosuppression of unknown aetiology is a hallmark feature of glioblastoma and is characterized by decreased CD4 T-cell counts and downregulation of major histocompatibility complex class II expression on peripheral blood monocytes in patients. This immunosuppression is a critical barrier to the successful development of immunotherapies for glioblastoma. We recapitulated the immunosuppression observed in glioblastoma patients in the C57BL/6 mouse and investigated the aetiology of low CD4 T-cell counts. We determined that thymic involution was a hallmark feature of immunosuppression in three distinct models of brain cancer, including mice harbouring GL261 glioma, B16 melanoma, and in a spontaneous model of diffuse intrinsic pontine glioma. In addition to thymic involution, we determined that tumour growth in the brain induced significant splenic involution, reductions in peripheral T cells, reduced MHC II expression on blood leucocytes, and a modest increase in bone marrow resident CD4 T cells. Using parabiosis we report that thymic involution, declines in peripheral T-cell counts, and reduced major histocompatibility complex class II expression levels were mediated through circulating blood-derived factors. Conversely, T-cell sequestration in the bone marrow was not governed through circulating factors. Serum isolated from glioma-bearing mice potently inhibited proliferation and functions of T cells both in vitro and in vivo. Interestingly, the factor responsible for immunosuppression in serum is non-steroidal and of high molecular weight. Through further analysis of neurological disease models, we determined that the immunosuppression was not unique to cancer itself, but rather occurs in response to brain injury. Non-cancerous acute neurological insults also induced significant thymic involution and rendered serum immunosuppressive. Both thymic involution and serum-derived immunosuppression were reversible upon clearance of brain insults. These findings demonstrate that brain cancers cause multifaceted immunosuppression and pinpoint circulating factors as a target of intervention to restore immunity.

Frontiers in Immunology, 2020
Authors
Nicola Principe, Joel Kidman, Siting Goh, Caitlin M Tilsed, Scott A Fisher, Vanessa S Fear, Catherine A Forbes, Rachael M Zemek, Abha Chopra, Mark Watson, Ian M Dick, Louis Boon, Robert A Holt, Richard A Lake, Anna K Nowak, Willem Joost Lesterhuis, Alison M McDonnell, Jonathan Chee
Publication Abstract

Immune checkpoint therapy (ICT) results in durable responses in individuals with some cancers, but not all patients respond to treatment. ICT improves CD8+ cytotoxic T lymphocyte (CTL) function, but changes in tumor antigen-specific CTLs post-ICT that correlate with successful responses have not been well characterized. Here, we studied murine tumor models with dichotomous responses to ICT. We tracked tumor antigen-specific CTL frequencies and phenotype before and after ICT in responding and non-responding animals. Tumor antigen-specific CTLs increased within tumor and draining lymph nodes after ICT, and exhibited an effector memory-like phenotype, expressing IL-7R (CD127), KLRG1, T-bet, and granzyme B. Responding tumors exhibited higher infiltration of effector memory tumor antigen-specific CTLs, but lower frequencies of regulatory T cells compared to non-responders. Tumor antigen-specific CTLs persisted in responding animals and formed memory responses against tumor antigens. Our results suggest that increased effector memory tumor antigen-specific CTLs, in the presence of reduced immunosuppression within tumors is part of a successful ICT response. Temporal and nuanced analysis of T cell subsets provides a potential new source of immune based biomarkers for response to ICT.

Case Reports In Gastrointestinal Medicine
Authors
Chris Shamatutu, Daljeet Chahal, Isabella T Tai, Peter Kwan
Publication Abstract

Colonoscopy is widely used for the diagnosis and management of colorectal disease and requires adequate bowel preparation. Ischemic colitis is a form of intestinal ischemia that presents with abdominal pain, diarrhea, and hematochezia. Risk factors include advanced age, cardiovascular disease, and diabetes. Both colonoscopy and bisacodyl bowel preparation have been described as rare causes of ischemic colitis with less than 35 cases collectively in the literature. Our review found that of these cases, there exists significant heterogeneity within individual patient characteristics. The majority of the cases are managed conservatively without complications or sequela. Due to the risk of ischemic colitis, the FDA has withdrawn bisacodyl bowel preparations from use in the USA. Bisacodyl bowel preparations are still used in Canada.

Authors
Yi-Jye Chern, Isabella T Tai
Publication Abstract

Despite advances in cancer therapeutics and the integration of personalized medicine, the development of chemoresistance in many patients remains a significant contributing factor to cancer mortality. Upon treatment with chemotherapeutics, the disruption of homeostasis in cancer cells triggers the adaptive response which has emerged as a key resistance mechanism. In this review, we summarize the mechanistic studies investigating the three major components of the adaptive response, autophagy, endoplasmic reticulum (ER) stress signaling, and senescence, in response to cancer chemotherapy. We will discuss the development of potential cancer therapeutic strategies in the context of these adaptive resistance mechanisms, with the goal of stimulating research that may facilitate the development of effective cancer therapy.

Gynecologic Oncology, 2020
Authors
Allyson C Banville, Maartje C A Wouters, Ann L Oberg, Krista M Goergen, Matthew J Maurer, Katy Milne, Jahanshah Ashkani, Emma Field, Chanel Ghesquiere, Steven J M Jones, Matthew S Block, Brad H Nelson
Publication Abstract

Objective: Chimeric antigen receptor (CAR)-T cell strategies ideally target a surface antigen that is exclusively and uniformly expressed by tumors; however, no such antigen is known for high-grade serous ovarian carcinoma (HGSC). A potential solution involves combinatorial antigen targeting with AND or OR logic-gating. Therefore, we investigated co-expression of CA125, Mesothelin (MSLN) and Folate Receptor alpha (FOLRA) on individual tumor cells in HGSC.

Methods: RNA expression of CA125, MSLN, and FOLR1 was assessed using TCGA (HGSC) and GTEx (healthy tissues) databases. Antigen expression profiles and CD3+, CD8+ and CD20+ tumor-infiltrating lymphocyte (TIL) patterns were assessed in primary and recurrent HGSC by multiplex immunofluorescence and immunohistochemistry.

Results: At the transcriptional level, each antigen was overexpressed in >90% of cases; however, MSLN and FOLR1 showed substantial expression in healthy tissues. At the protein level, CA125 was expressed by the highest proportion of cases and tumor cells per case, followed by MSLN and FOLRA. The most promising pairwise combination was CA125 and/or MSLN (OR gate), with 51.9% of cases containing ≥90% of tumor cells expressing one or both antigens. In contrast, only 5.8% of cases contained ≥90% of tumor cells co-expressing CA125 and MSLN (AND gate). Antigen expression patterns showed modest correlations with TIL. Recurrent tumors retained expression of all three antigens and showed increased TIL densities.

Conclusions: An OR-gated CAR-T cell strategy against CA125 and MSLN would target the majority of tumor cells in most cases. Antigen expression and T-cell infiltration patterns are favorable for this strategy in primary and recurrent disease.

Keywords: Antigens; Chimeric antigen receptor (CAR)-T cell therapy; High-grade serous ovarian carcinoma; Immunotherapy; Ovarian cancer; Tumor-infiltrating lymphocytes.

Frontiers in Genetics, 2020
Authors
Richard D Corbett, Robert Eveleigh, Joe Whitney, Namrata Barai, Mathieu Bourgey, Eric Chuah, Joanne Johnson, Richard A Moore, Neda Moradin, Karen L Mungall, Sergio Pereira, Miriam S Reuter, Bhooma Thiruvahindrapuram, Richard F Wintle, Jiannis Ragoussis, Lisa J Strug, Jo-Anne Herbrick, Naveed Aziz, Steven J M Jones, Mark Lathrop, Stephen W Scherer, Alfredo Staffa, Andrew J Mungall
Publication Abstract

Population sequencing often requires collaboration across a distributed network of sequencing centers for the timely processing of thousands of samples. In such massive efforts, it is important that participating scientists can be confident that the accuracy of the sequence data produced is not affected by which center generates the data. A study was conducted across three established sequencing centers, located in Montreal, Toronto, and Vancouver, constituting Canada's Genomics Enterprise (www.cgen.ca). Whole genome sequencing was performed at each center, on three genomic DNA replicates from three well-characterized cell lines. Secondary analysis pipelines employed by each site were applied to sequence data from each of the sites, resulting in three datasets for each of four variables (cell line, replicate, sequencing center, and analysis pipeline), for a total of 81 datasets. These datasets were each assessed according to multiple quality metrics including concordance with benchmark variant truth sets to assess consistent quality across all three conditions for each variable. Three-way concordance analysis of variants across conditions for each variable was performed. Our results showed that the variant concordance between datasets differing only by sequencing center was similar to the concordance for datasets differing only by replicate, using the same analysis pipeline. We also showed that the statistically significant differences between datasets result from the analysis pipeline used, which can be unified and updated as new approaches become available. We conclude that genome sequencing projects can rely on the quality and reproducibility of aggregate data generated across a network of distributed sites.

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.

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