Oncotarget, 2020
Authors
Kelly Yi Ping Liu, Sarah Yuqi Zhu, Denise Brooks, Reanne Bowlby, J Scott Durham, Yussanne Ma, Richard A Moore, Andrew J Mungall, Steven Jones, Catherine F Poh
Publication Abstract

Neck lymph node metastasis (LN+) is one of the most significant prognostic factors affecting 1-in-2 patients diagnosed with oral squamous cell carcinoma (OSCC). The different LN outcomes between clinico-pathologically similar primary tumors suggest underlying molecular signatures that could be associated with the risk of nodal disease development. MicroRNAs (miRNAs)are short non-coding molecules that regulate the expression of their target genes to maintain the balance of cellular processes. A plethora of evidence has indicated that aberrantly expressed miRNAs are involved in cancers with either an antitumor or oncogenic role. In this study, we characterized miRNA expression among OSCC fresh-frozen tumors with known outcomes of nodal disease (82 LN+, 76 LN0). We identified 49 differentially expressed miRNAs in tumors of the LN+ group. Using penalized lasso Cox regression, we identified a group of 10 miRNAs of which expression levels were highly associated with nodal-disease free survival. We further reported a 4-miRNA panel (miR-21-5p, miR-107, miR-1247-3p, and miR-181b-3p) with high accuracy in discriminating LN status, suggesting their potential application as prognostic biomarkers for nodal disease.

Clinical Cancer Research, 2020
Authors
Jenny E Chu, Benny Johnson, Laveniya Kugathasan, Van K Morris, Kanwal Raghav, Lucas Swanson, Howard Lim, Daniel J Renouf, Sharlene Gill, Robert Wolber, Aly Karsan, Scott Kopetz, David F Schaeffer, Jonathan M Loree
Publication Abstract

PURPOSE BRAFV600E mutations portend poor prognosis in metastatic colorectal cancer (mCRC); however, the true prevalence and prognosis are unknown, as unwell patients may not undergo BRAF sequencing. PATIENTS AND METHODS We reviewed a population-based cohort of 1898 patients with CRC that underwent reflexive immunohistochemistry (IHC) mismatch repair (MMR) & BRAFV600E testing. Outcomes among IHC detected BRAFV600E mCRC (BRAFIHC) were compared to patients with next generation sequencing identified BRAFV600E mutated mCRC from two institutions (BRAFNGS) with patients spanning from 2004-2018. RESULTS All-stage population prevalence of BRAFV600E was 12.5% (238/1898) and did not differ between early and metastatic stages (p=0.094). Prevalence among mCRC was 10.6% (61/575), of whom 51 (83.6%) were referred to oncology and 26 (42.6%) had NGS testing. BRAFIHC had worse median overall survival (mOS) than BRAFNGS (5.5 vs 20.4 months, hazard ratio (HR) 2.90, 95% confidence interval (CI) 1.89-4.45, p<0.0001) which persisted in multivariate analysis (p<0.0001). Across a combined NGS and IHC cohort, BRAFV600E tumors with deficient MMR showed worse mOS compared to MMR proficient tumors (8.9 vs 17.2 months, HR 1.46, 95% CI 0.96-2.27, p=0.043). In this combined cohort, first-line progression free survival was 5.9 months, with minimal differences between regimens. Within the population-based cohort, attrition between treatment lines was high with only 60.7% receiving first-line chemotherapy and 26.2% receiving second-line. CONCLUSION BRAFV600E mutated mCRC has a worse prognosis than previously suggested, potentially arising from referral bias for testing. High attrition between lines of therapy suggests efficacious therapies need to be prioritized early for patients to benefit.

Annals Of Translational Medicine, 2020
Authors
Cally J Ho, Sharon M Gorski

Journal Of Medical Genetics, 2020
Authors
Alexandra Roston, Dan Evans, Harinder Gill, Margaret McKinnon, Bertrand Isidor, Benjamin Cogné, Jill Mwenifumbo, Clara van Karnebeek, Jianghong An, Steven J M Jones, Matthew Farrer, Michelle Demos, Mary Connolly, William T Gibson
Publication Abstract

Dysfunction of histone methyltransferases and chromatin modifiers has been implicated in complex neurodevelopmental syndromes and cancers.

Genetics, 2020
Authors
Aleksandar Vujin, Steven J Jones, Monique Zetka
Publication Abstract

DNA double-strand breaks (DSBs) are a particularly lethal form of DNA damage that must be repaired to restore genomic integrity. Canonical non-homologous end joining (NHEJ), is the widely conserved pathway that detects and directly ligates the broken ends to repair the DSB. These events globally require the two proteins that form the Ku ring complex, Ku70 and Ku80, and the terminal ligase Lig4. While the NHEJ pathway in vertebrates is elaborated by more than a dozen factors of varying conservation and is similarly complex in other eukaryotes, the entire known NHEJ toolkit in

Nature Methods, 2020
Authors
Ottar N Bjørnstad, Katriona Shea, Martin Krzywinski, Naomi Altman

Clinical Lymphoma, Myeloma & Leukemia, 2020
Authors
Wasithep Limvorapitak, Jeremy Parker, Curtis Hughesman, Kelly McNeil, Lynda Foltz, Aly Karsan
Publication Abstract

JAK2 V617F mutation is one of the major criteria in the diagnosis of myeloproliferative neoplasms (MPN) and its variant allele fraction (VAF) determines the disease phenotype and outcomes. This study aimed to define characteristics and outcomes of patients with JAK2 V617F VAF < 2% compared to patients with VAF 2%-10%.

Frontiers In Veterinary Science, 2020
Authors
Lauren C Tindale, Waren Baticados, Jun Duan, Michelle Coombe, Agatha Jassem, Patrick Tang, Miguel Uyaguari-Diaz, Richard Moore, Chelsea Himsworth, William Hsiao, Natalie Prystajecky
Publication Abstract

Early virus detection and characterization is key to successful avian influenza virus (AIV) surveillance for the health of humans as well as domestic poultry. We explored a novel sampling approach and molecular strategy using sediment from wetlands and outdoor waterbodies on poultry farms as a population-level proxy of AIV activity in waterfowls. RNA was extracted using the MoBio RNA PowerSoil Total RNA isolation kit with additional chloroform extraction steps to reduce PCR inhibition. AIV matrix protein (MP) gene was detected in 42/345 (12.2%) samples by RT-qPCR; an additional 64 (18.6%) samples showed evidence of amplification below the threshold and were categorized as "suspect positive." Enrichment-based targeted resequencing (TR) identified AIV sequences in 79/345 (22.9%) samples. TR probes were designed for MP, hemagglutinin (HA), and neuraminidase (NA), however PB2 and PA were also identified. Although RT-qPCR and TR only had fair-moderate agreement, RT-qPCR positivity was predictive of TR-positivity both when using only strictly positive RT-qPCR samples (OR = 11.29) and when coding suspect positives as positive (OR = 7.56). This indicates that RT-qPCR could be used as a screening tool to select samples for virus characterization by TR and that future studies should consider RT-qPCR suspect positives to be positive samples for subsequent resequencing when avoiding false negatives is the priority, for instance in a diagnostic test, and to consider suspect positives to be negative samples when cost efficiency over a large number of samples is the priority, for instance in a surveillance program. A total of 13 HA (H1-7, H9-13, H16) and 9 NA (N1-9) subtypes were identified, with a maximum of 8 HA and 8 NA subtypes detected in a single sample. The optimized RNA extraction and targeted resequencing methods provided increased virus detection and subtyping characterization that could be implemented in an AIV surveillance system.

Autophagy, 2020
Authors
Cally J Ho, Gayathri Samarasekera, Katharina Rothe, Jing Xu, Kevin C Yang, Emily Leung, Michelle Chan, Xiaoyan Jiang, Sharon M Gorski.
Publication Abstract

Proteome profiling and global protein-interaction approaches have significantly improved our knowledge of the protein interactomes of autophagy and other cellular stress-response pathways. New discoveries regarding protein complexes, interaction partners, interaction domains, and biological roles of players that are part of these pathways are emerging. The fourth Vancouver Autophagy Symposium showcased research that expands our understanding of the protein interaction networks and molecular mechanisms underlying autophagy and other cellular stress responses in the context of distinct stressors. In the keynote presentation, Dr. Wade Harper described his team's recent discovery of a novel reticulophagy receptor for selective autophagic degradation of the endoplasmic reticulum, and discussed molecular mechanisms involved in ribophagy and non-autophagic ribosomal turnover. In other presentations, both omic and targeted approaches were used to reveal molecular players of other cellular stress responses including amyloid body and stress granule formation, anastasis, and extracellular vesicle biogenesis. Additional topics included the roles of autophagy in disease pathogenesis, autophagy regulatory mechanisms, and crosstalk between autophagy and cellular metabolism in anti-tumor immunity. The relationship between autophagy and other cell stress responses remains a relatively unexplored area in the field, with future investigations required to understand how the various processes are coordinated and connected in cells and tissues.

Haematologica, 2020
Authors
Ivan Sloma, Philip Beer, Christophe Desterke, Elizabeth Bulaeva, Misha Bilenky, Annaïck Carles, Michelle Moksa, Kamini Raghuram, Cedric Brimacombe, Karen Lambie, Ali G. Turhan, Orianne Wagner-Ballon, Philippe Gaulard, Keith Humphries, Martin Hirst, Connie J. Eaves.
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