Gigascience, 2020
Authors
Saber Hafezqorani, Chen Yang, Theodora Lo, Ka Ming Nip, René L Warren, Inanc Birol
Publication Abstract

Background: Compared with second-generation sequencing technologies, third-generation single-molecule RNA sequencing has unprecedented advantages; the long reads it generates facilitate isoform-level transcript characterization. In particular, the Oxford Nanopore Technology sequencing platforms have become more popular in recent years owing to their relatively high affordability and portability compared with other third-generation sequencing technologies. To aid the development of analytical tools that leverage the power of this technology, simulated data provide a cost-effective solution with ground truth. However, a nanopore sequence simulator targeting transcriptomic data is not available yet.

Findings: We introduce Trans-NanoSim, a tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-sequncing data. We comprehensively benchmarked Trans-NanoSim on direct RNA and complementary DNA datasets describing human and mouse transcriptomes. Through comparison against other nanopore read simulators, we show the unique advantage and robustness of Trans-NanoSim in capturing the characteristics of nanopore complementary DNA and direct RNA reads.

Conclusions: As a cost-effective alternative to sequencing real transcriptomes, Trans-NanoSim will facilitate the rapid development of analytical tools for nanopore RNA-sequencing data. Trans-NanoSim and its pre-trained models are freely accessible at https://github.com/bcgsc/NanoSim.

Nature Neuroscience, 2020
Authors
Alexandra Garancher, Hiromichi Suzuki, Svasti Haricharan, Lianne Q. Chau, Meher Beigi Masihi, Jessica M. Rusert, Paula S. Norris, Florent Carrette, Megan M. Romero, Sorana A. Morrissy, Patryk Skowron, Florence M. G. Cavalli, Hamza Farooq, Vijay Ramaswamy, Steven J. M. Jones, Richard A. Moore, Andrew J. Mungall, Yussanne Ma, Nina Thiessen, Yisu Li, Alaide Morcavallo, Lin Qi, Mari Kogiso, Yuchen Du, Patricia Baxter, Jacob J. Henderson, John R. Crawford, Michael L. Levy, James M. Olson, Yoon-Jae Cho, Aniruddha J. Deshpande, Xiao-Nan Li, Louis Chesler, Marco A. Marra, Harald Wajant, Oren J. Becher, Linda M. Bradley, Carl F. Ware, Michael D. Taylor & Robert J. Wechsler-Reya
Publication Abstract

Many immunotherapies act by enhancing the ability of cytotoxic T cells to kill tumor cells. Killing depends on T cell recognition of antigens presented by class I major histocompatibility complex (MHC-I) proteins on tumor cells. In this study, we showed that medulloblastomas lacking the p53 tumor suppressor do not express surface MHC-I and are therefore resistant to immune rejection. Mechanistically, this is because p53 regulates expression of the peptide transporter Tap1 and the aminopeptidase Erap1, which are required for MHC-I trafficking to the cell surface. In vitro, tumor necrosis factor (TNF) or lymphotoxin-β receptor agonist can rescue expression of Erap1, Tap1 and MHC-I on p53-mutant tumor cells. In vivo, low doses of TNF prolong survival and synergize with immune checkpoint inhibitors to promote tumor rejection. These studies identified p53 as a key regulator of immune evasion and suggest that TNF could be used to enhance sensitivity of tumors to immunotherapy.

Genome Biology and Evolution, 2020
Authors
Shaun D Jackman, Lauren Coombe, René L Warren, Heather Kirk, Eva Trinh, Tina MacLeod, Stephen Pleasance, Pawan Pandoh, Yongjun Zhao, Robin J Coope, Jean Bousquet, Joerg Bohlmann, Steven J M Jones, Inanc Birol
Publication Abstract

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5 Mbp mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168 kbp circular segment of DNA, and a larger 5.4 Mbp single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

Clinical Cancer Research, 2020
Authors
Jennifer X Ji, Dawn R Cochrane, Basile Tessier-Cloutier, Shary Yuting Chen, Germain Ho, Khyatiben V Pathak, Isabel N Alcazar, David Farnell, Samuel Leung, Angela Cheng, Christine Chow, Shane Colborne, Gian Luca Negri, Friedrich Kommoss, Anthony Karnezis, Gregg B Morin, Jessica N McAlpine, Blake Gilks, Bernard E Weissman, Jeffrey M Trent, Lynn Hoang, Patrick Pirrotte, Yemin Wang, David G Huntsman.
Publication Abstract

Purpose: Many rare ovarian cancer subtypes such as small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) have poor prognosis due to their aggressive nature and resistance to standard platinum and taxane based chemotherapy. The development of effective therapeutics has been hindered by the rarity of such tumors. We sought to identify targetable vulnerabilities in rare ovarian cancer subtypes.

Experimental design: We compared the global proteomic landscape of six cases each of endometrioid ovarian cancer (ENOC), clear cell ovarian cancer (CCOC), and SCCOHT to the most common subtype high grade serous ovarian cancer (HGSC) to identify potential therapeutic targets. Immunohistochemistry of tissue microarrays were used as validation of ASS1 deficiency. The efficacy of arginine-depriving therapeutic ADI-PEG20 was assessed in-vitro using cell lines and patient derived xenograft mouse models representing SCCOHT.

Results: Global proteomic analysis identified low ASS1 expression in ENOC, CCOC, and SCCOHT compared to HGSC. Low ASS1 levels were validated through IHC in large patient cohorts. The lowest levels of ASS1 were observed in SCCOHT, where ASS1 was absent in 12/31 cases, and expressed in less than 5% of the tumor cells in 9/31 cases. ASS1 deficient ovarian cancer cells were sensitive to ADI-PEG20 treatment regardless of subtype in-vitro Furthermore, in two cell line mouse xenograft models and one patient derived mouse xenograft model of SCCOHT, once a week treatment of ADI-PEG20 (30mg/kg and 15mg/kg) inhibited tumor growth in-vivo Conclusions: Preclinical in-vitro and in-vivo studies identified ADI-PEG20 as a potential therapy for patients with rare ovarian cancers including SCCOHT.

Electrophoresis, 2020
Authors
Lingyu Wang, Jianhui Cheng, Julie E McNutt, Gregg B Morin, David D Y Chen.
Publication Abstract

Dynamic pH barrage junction focusing in CE enables effective signal enhancement, quantitative capture efficiencies, and straightforward optimization. The method is a technical variant of dynamic pH junction focusing. CE separation with dynamic pH barrage junction focusing is compatible with both optical and mass spectrometric detection. We developed a CE-MS/MS method using hydrophilic polyethyleneimine-coated capillaries and validated it for the qualitative analysis of amino acids, peptides, and tryptic peptides of digested monoclonal antibodies. The S/N of extracted ion electropherograms of zwitterionic analytes were enhanced by approximately two orders of magnitude with a tradeoff of a shortened separation window. Online focusing improved the MS signal intensity of a diluted antibody digest, enabling more precursor ions to be analyzed with subsequent tandem mass spectrometric identification. It also broadened the concentration range of protein digest samples for which adequate sequence coverage data can be obtained. With only 0.9 ng of digested infliximab sample loaded into the capillary, 76% and 100% sequence coverage was realized for antibody heavy and light chains, respectively, after online focusing. Full coverage was achieved with 9 ng of injected digest.

Blood, 2020
Authors
Ryan D Morin, David W Scott

Cancer Cell, 2020
Authors
Jian Carrot-Zhang, Nyasha Chambwe, Jeffrey S Damrauer, Theo A Knijnenburg, A Gordon Robertson, Christina Yau, Wanding Zhou, Ashton C Berger, Kuan-Lin Huang, Justin Y Newberg, R Jay Mashl, Alessandro Romanel, Rosalyn W Sayaman, Francesca Demichelis, Ina Felau, Garrett M Frampton, Seunghun Han, Katherine A Hoadley, Anab Kemal, Peter W Laird, Alexander J Lazar, Xiuning Le, Ninad Oak, Hui Shen, Christopher K Wong, Jean C Zenklusen, Elad Ziv, Andrew D Cherniack, Rameen Beroukhim
Publication Abstract

We evaluated ancestry effects on mutation rates, DNA methylation, and mRNA and miRNA expression among 10,678 patients across 33 cancer types from The Cancer Genome Atlas. We demonstrated that cancer subtypes and ancestry-related technical artifacts are important confounders that have been insufficiently accounted for. Once accounted for, ancestry-associated differences spanned all molecular features and hundreds of genes. Biologically significant differences were usually tissue specific but not specific to cancer. However, admixture and pathway analyses suggested some of these differences are causally related to cancer. Specific findings included increased FBXW7 mutations in patients of African origin, decreased VHL and PBRM1 mutations in renal cancer patients of African origin, and decreased immune activity in bladder cancer patients of East Asian origin.

Blood, 2020
Authors
Jennifer Margaret Grants, Joanna Wegrzyn-Woltosz, Tony Hui, Kieran O'Neill, Marion Shadbolt, David J H F Knapp, Jeremy Dk Parker, Deborah Deng, Aparna Gopal, T Roderick Docking, Megan Fuller, Jenny Li, Mark Boldin, Connie J Eaves, Martin Hirst, Aly Karsan
Publication Abstract

Aging is associated with significant changes in the hematopoietic system, including increased inflammation, impaired hematopoietic stem cell (HSC) function, and increased incidence of myeloid malignancy. Inflammation of aging ("inflammaging") has been proposed as a driver of age-related changes in HSC function and myeloid malignancy, but mechanisms linking these phenomena remain poorly defined. Here, we identify loss of miR-146a as driving aging-associated inflammation in AML patients. miR-146a expression declined in old wild-type mice, and loss of miR-146a promoted premature HSC aging and inflammation in young miR-146a-null mice, preceding development of aging-associated myeloid malignancy. Using single-cell assays of HSC quiescence, stemness, differentiation potential, and epigenetic state to probe HSC function and population structure, we found that loss of miR-146a depleted a subpopulation of primitive, quiescent HSCs. DNA methylation and transcriptome profiling implicated NF-κB, IL6, and TNF as potential drivers of HSC dysfunction, activating an inflammatory signaling relay promoting IL6 and TNF secretion from mature miR-146a-/- myeloid and lymphoid cells. Reducing inflammation by targeting Il6 or Tnf was sufficient to restore single-cell measures of miR-146a-/-HSC function and subpopulation structure, and reduced the incidence of hematological malignancy in miR‑146a-/-mice. miR-146a-/- HSCs exhibited enhanced sensitivity to IL6 stimulation, indicating that loss of miR-146a affects HSC function via both cell-extrinsic inflammatory signals and increased cell-intrinsic sensitivity to inflammation. Thus, loss of miR‑146a regulates cell-extrinsic and -intrinsic mechanisms linking HSC inflammaging to the development of myeloid malignancy.

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Nature Cancer, 2020
Authors
Erin Pleasance, Emma Titmuss, Laura Williamson, Harwood Kwan, Luka Culibrk, Eric Y. Zhao, Katherine Dixon, Kevin Fan, Reanne Bowlby, Martin R. Jones, Yaoqing Shen, Jasleen K. Grewal, Jahanshah Ashkani, Kathleen Wee, Cameron J. Grisdale, My Linh Thibodeau, Zoltan Bozoky, Hillary Pearson, Elisa Majounie, Tariq Vira, Reva Shenwai, Karen L. Mungall, Eric Chuah, Anna Davies, Mya Warren, Caralyn Reisle, Melika Bonakdar, Gregory A. Taylor, Veronika Csizmok, Simon K. Chan, Zusheng Zong, Steve Bilobram, Amir Muhammadzadeh, Darryl D’Souza, Richard D. Corbett, Daniel MacMillan, Marcus Carreira, Caleb Choo, Dustin Bleile, Sara Sadeghi, Wei Zhang, Tina Wong, Dean Cheng, Scott D. Brown, Robert A. Holt, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Jessica Nelson, Alexandra Fok, Yussanne Ma, Michael K. C. Lee, Jean-Michel Lavoie, Shehara Mendis, Joanna M. Karasinska, Balvir Deol, Ana Fisic, David F. Schaeffer, Stephen Yip, Kasmintan Schrader, Dean A. Regier, Deirdre Weymann, Stephen Chia, Karen Gelmon, Anna Tinker, Sophie Sun, Howard Lim, Daniel J. Renouf, Janessa Laskin, Steven J. M. Jones & Marco A. Marra
Publication Abstract

Advanced and metastatic tumors with complex treatment histories drive cancer mortality. Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and clinical dataset, amenable for exploration of the impacts of therapies on genomic landscapes. Previous exposure to DNA-damaging chemotherapies and mutations affecting DNA repair genes, including POLQ and genes encoding Polζ, were associated with genome-wide, therapy-induced mutagenesis. Exposure to platinum therapies coincided with signatures SBS31 and DSB5 and, when combined with DNA synthesis inhibitors, signature SBS17b. Alterations in ESR1, EGFR, CTNNB1, FGFR1, VEGFA and DPYD were consistent with drug resistance and sensitivity. Recurrent noncoding events were found in regulatory region hotspots of genes including TERT, PLEKHS1, AP2A1 and ADGRG6. Mutation burden and immune signatures corresponded with overall survival and response to immunotherapy. Our data offer a rich resource for investigation of advanced cancers and interpretation of whole-genome and transcriptome sequencing in the context of a cancer clinic.

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Bioinformatics, 2020
Authors
Lauren Coombe , Vladimir Nikolić, Justin Chu, Inanc Birol, René L Warren
Publication Abstract

Summary: The ability to generate high-quality genome sequences is cornerstone to modern biological research. Even with recent advancements in sequencing technologies, many genome assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between a draft assembly and reference sequence(s) to contiguate and correct the former with respect to the latter. Instead of alignments, ntJoin uses a lightweight mapping approach based on a graph data structure generated from ordered minimizer sketches. The tool can be used in a variety of different applications, including improving a draft assembly with a reference-grade genome, a short read assembly with a draft long read assembly, and a draft assembly with an assembly from a closely-related species. When scaffolding a human short read assembly using the reference human genome or a long read assembly, ntJoin improves the NGA50 length 23- and 13-fold, respectively, in under 13 m, using less than 11 GB of RAM. Compared to existing reference-guided scaffolders, ntJoin generates highly contiguous assemblies faster and using less memory.

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