Cold Spring Harbor molecular case studies, 2018
Authors
Ko, Jenny J, Grewal, Jasleen K, Ng, Tony, Lavoie, Jean-Michel, Thibodeau, My Linh, Shen, Yaoqing, Mungall, Andrew J, Taylor, Greg, Schrader, Kasmintan A, Jones, Steven J M, Kollmannsberger, Christian, Laskin, Janessa, Marra, Marco A
Publication Abstract
Thyroid-like follicular renal cell carcinoma (TLFRCC) is a rare cancer with few reports of metastatic disease. Little is known regarding genomic characteristics and therapeutic targets. We present the clinical, pathologic, genomic, and transcriptomic analyses of a case of a 27-yr-old male with TLFRCC who presented initially with bone metastases of unknown primary. Genomic DNA from peripheral blood and metastatic tumor samples were sequenced. A transcriptome of 280 million sequence reads was generated from the same tumor sample. Tumor somatic expression profiles were analyzed to detect aberrant expression. Genomic and transcriptomic data sets were integrated to reveal dysregulation in pathways and identify potential therapeutic targets. Integrative genomic analysis with The Cancer Genome Atlas (TCGA) data set revealed the following outliers in gene expression profiles: (81st percentile), (99th percentile), (100th percentile), and (99th and 100th percentiles, respectively), and (86th percentile). The patient received first-line sunitinib to target PDGFRA and PDGFRB and had stable disease for >6 mo, followed by nivolumab upon progression. To the authors' knowledge, this is the first reported case of comprehensive somatic genomic analyses in a patient with metastatic TLFRCC. Somatic analyses provided molecular confirmation of the primary site of cancer and potential therapeutic strategies in a rare disease with little evidence of efficacy on systemic therapy.

Cell stem cell, 2018
Authors
Giambra, Vincenzo, Gusscott, Samuel, Gracias, Deanne, Song, Raymond, Lam, Sonya H, Panelli, Patrizio, Tyshchenko, Kateryna, Jenkins, Catherine E, Hoofd, Catherine, Lorzadeh, Alireza, Carles, Annaick, Hirst, Martin, Eaves, Connie J, Weng, Andrew P
Publication Abstract
Acute leukemias are aggressive malignancies of developmentally arrested hematopoietic progenitors. We sought here to explore the possibility that changes in hematopoietic stem/progenitor cells during development might alter the biology of leukemias arising from this tissue compartment. Using a mouse model of acute T cell leukemia, we found that leukemias generated from fetal liver (FL) and adult bone marrow (BM) differed dramatically in their leukemia stem cell activity with FL leukemias showing markedly reduced serial transplantability as compared to BM leukemias. We present evidence that this difference is due to NOTCH1-driven autocrine IGF1 signaling, which is active in FL cells but restrained in BM cells by EZH2-dependent H3K27 trimethylation. Further, we confirmed this mechanism is operative in human disease and show that enforced IGF1 signaling effectively limits leukemia stem cell activity. These findings demonstrate that resurrecting dormant fetal programs in adult cells may represent an alternate therapeutic approach in human cancer.

Genes, 2018
Authors
Taylor, Gregory A, Kirk, Heather, Coombe, Lauren, Jackman, Shaun D, Chu, Justin, Tse, Kane, Cheng, Dean, Chuah, Eric, Pandoh, Pawan, Carlsen, Rebecca, Zhao, Yongjun, Mungall, Andrew J, Moore, Richard, Birol, Inanc, Franke, Maria, Marra, Marco A, Dutton, Christopher, Jones, Steven J M
Publication Abstract
The grizzly bear ( ssp. ) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was 2.33 Gb with a scaffold N50 of 36.7 Mb, and the genome is of comparable size to that of its close relative the polar bear (2.30 Gb). An analysis using 4104 highly conserved mammalian genes indicated that 96.1% were found to be complete within the assembly. An automated annotation of the genome identified 19,848 protein coding genes. Our study shows that the combination of the two sequencing modalities that we used is sufficient for the construction of highly contiguous reference quality mammalian genomes. The assembled genome sequence and the supporting raw sequence reads are available from the NCBI (National Center for Biotechnology Information) under the bioproject identifier PRJNA493656, and the assembly described in this paper is version QXTK01000000.

BMC bioinformatics, 2018
Authors
Jackman, Shaun D, Coombe, Lauren, Chu, Justin, Warren, Rene L, Vandervalk, Benjamin P, Yeo, Sarah, Xue, Zhuyi, Mohamadi, Hamid, Bohlmann, Joerg, Jones, Steven J M, Birol, Inanc
Publication Abstract
Genome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficult due to gaps and errors in the sequencing data, repetitive sequence in the underlying genome, and heterozygosity. As a result, assembly errors are common. In the absence of a reference genome, these misassemblies may be identified by comparing the sequencing data to the assembly and looking for discrepancies between the two. Once identified, these misassemblies may be corrected, improving the quality of the assembled sequence. Although tools exist to identify and correct misassemblies using Illumina paired-end and mate-pair sequencing, no such tool yet exists that makes use of the long distance information of the large molecules provided by linked reads, such as those offered by the 10x Genomics Chromium platform. We have developed the tool Tigmint to address this gap.

Nature communications, 2018
Authors
Arthur, Sarah E, Jiang, Aixiang, Grande, Bruno M, Alcaide, Miguel, Cojocaru, Razvan, Rushton, Christopher K, Mottok, Anja, Hilton, Laura K, Lat, Prince Kumar, Zhao, Eric Y, Culibrk, Luka, Ennishi, Daisuke, Jessa, Selin, Chong, Lauren, Thomas, Nicole, Pararajalingam, Prasath, Meissner, Barbara, Boyle, Merrill, Davidson, Jordan, Bushell, Kevin R, Lai, Daniel, Farinha, Pedro, Slack, Graham W, Morin, Gregg B, Shah, Sohrab, Sen, Dipankar, Jones, Steven J M, Mungall, Andrew J, Gascoyne, Randy D, Audas, Timothy E, Unrau, Peter, Marra, Marco A, Connors, Joseph M, Steidl, Christian, Scott, David W, Morin, Ryan D
Publication Abstract
Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3' UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-κB pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fcγ receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics.

Canadian journal of surgery. Journal canadien de chirurgie, 2018
Authors
Bonneau, Christopher, Caron, Nadine R., Hussain, Mohamad A., Kayssi, Ahmed, Verma, Subodh, Al-Omran, Mohammed
Publication Abstract
Indigenous Canadians experience a disproportionate burden of chronic atherosclerotic diseases, including peripheral artery disease (PAD). Despite an estimated prevalence of 800 000 patients with PAD in Canada, the burden of the disease among Indigenous Canadians is unclear. Available evidence suggests that this population has a higher prevalence of several major risk factors associated with PAD (diabetes, smoking and kidney disease). Unique socioeconomic, geographic and systemic obstacles affecting Indigenous Canadians’ health and health care access may worsen chronic disease outcomes. Little is known about the cardiovascular and limb outcomes of Indigenous peoples with PAD. A novel approach via multidisciplinary vascular health teams engaging Indigenous communities in a culturally competent manner may potentially provide optimal vascular care to this population. Further research into the prevalence and outcomes of PAD among Indigenous Canadians is necessary to define the problem and allow development of more ffective initiatives to alleviate the disease burden in this marginalized group.

BMC medical genomics, 2018
Authors
Chiu, Readman, Nip, Ka Ming, Chu, Justin, Birol, Inanc
Publication Abstract
RNA-seq is a powerful and cost-effective technology for molecular diagnostics of cancer and other diseases, and it can reach its full potential when coupled with validated clinical-grade informatics tools. Despite recent advances in long-read sequencing, transcriptome assembly of short reads remains a useful and cost-effective methodology for unveiling transcript-level rearrangements and novel isoforms. One of the major concerns for adopting the proven de novo assembly approach for RNA-seq data in clinical settings has been the analysis turnaround time. To address this concern, we have developed a targeted approach to expedite assembly and analysis of RNA-seq data.

Journal of cell science, 2018
Authors
Xu, Jing, Camfield, Robert, Gorski, Sharon M
Publication Abstract
The eukaryotic endomembrane system is a complex series of interconnected membranous organelles that play important roles in responding to stress and maintaining cell homeostasis during health and disease. Two components of this system, exosome biogenesis and autophagy, are linked by the endolysosomal pathway. Exosomes are cargo-laden extracellular vesicles that arise from endosome-derived multivesicular bodies, and autophagy is a lysosomal-dependent degradation and recycling pathway. Recent studies have revealed shared molecular machinery between exosome biogenesis and autophagy, as well as substantial crosstalk between these two processes. In this Review, we first describe the classic view of exosome biogenesis and autophagy, including their links to the endolysosomal pathway. We then present the evidence for autophagy-related proteins in exosome biogenesis, the emerging roles of amphisomes and the evolving models of exosome-autophagy pathway interactions. Finally, we discuss the implications of exosome and autophagy interplay in the context of neurodegeneration and cancer.

Experimental hematology, 2018
Authors
Jenkins, Catherine E, Gusscott, Samuel, Wong, Rachel J, Shevchuk, Olena O, Rana, Gurneet, Giambra, Vincenzo, Tyshchenko, Kateryna, Islam, Rashedul, Hirst, Martin, Weng, Andrew P
Publication Abstract
RUNX1 is frequently mutated in T-cell acute lymphoblastic leukemia (T-ALL). The spectrum of RUNX1 mutations has led to the notion that it acts as a tumor suppressor in this context; however, other studies have placed RUNX1, along with transcription factors TAL1 and NOTCH1, as core drivers of an oncogenic transcriptional program. To reconcile these divergent roles, we knocked down RUNX1 in human T-ALL cell lines and deleted Runx1 or Cbfb in primary mouse T-cell leukemias. RUNX1 depletion consistently resulted in reduced cell proliferation and increased apoptosis. RUNX1 upregulated variable sets of target genes in each cell line, but consistently included a core set of oncogenic effectors including insulin-like growth factor 1 receptor (IGF1R) and NRAS. Our results support the conclusion that RUNX1 has a net positive effect on cell growth in the context of established T-ALL.

Stem cell reports, 2018
Authors
Hui, Tony, Cao, Qi, Wegrzyn-Woltosz, Joanna, O'Neill, Kieran, Hammond, Colin A, Knapp, David J H F, Laks, Emma, Moksa, Michelle, Aparicio, Samuel, Eaves, Connie J, Karsan, Aly, Hirst, Martin
Publication Abstract
Increasing evidence of functional and transcriptional heterogeneity in phenotypically similar cells examined individually has prompted interest in obtaining parallel methylome data. We describe the development and application of such a protocol to index-sorted murine and human hematopoietic cells that are highly enriched in their content of functionally defined stem cells. Utilizing an optimized single-cell bisulfite sequencing protocol, we obtained quantitative DNA methylation measurements of up to 5.7 million CpGs in single hematopoietic cells. In parallel, we developed an analytical strategy (PDclust) to define single-cell DNA methylation states through pairwise comparisons of single-CpG methylation measurements. PDclust revealed that a single-cell epigenetic state can be described by a small (<1%) stochastically sampled fraction of CpGs and that these states are reflective of cell identity and state. Using relationships revealed by PDclust, we derive near complete methylomes for epigenetically distinct subpopulations of hematopoietic cells enriched for functional stem cell content.
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