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Genomic and clinical characterization of a familial GIST kindred intolerant to imatinib

12 hours 29 minutes ago
Familial gastrointestinal stromal tumors (GIST) are rare. We present a kindred with multiple family members affected with multifocal GIST who underwent whole genome sequencing of the germline and tumor. Affected individuals with GIST harbored a germline variant found within exon 13 of the KIT gene (c.1965T>G; p.Asn655Lys, p.N655K) and a variant in the MSR1 gene (c.877 C > T; p.Arg293*, pR293X). Multifocal GISTs in the proband and her mother were treated with preoperative imatinib, which resulted...
K M Ingley

Examining the longitudinal associations between activity limitations, instrumental supports and social participation in osteoarthritis: A CLSA population-based study

1 day 12 hours ago
CONCLUSIONS: With a goal of increasing social participation, findings suggest a focus on interventions to reduce activity limitations in OA is necessary. Findings additionally highlight an important role for perceived availability of instrumental supports in maintaining or improving social participation in OA, in addition to current social participation, particularly intensity, for future social participation status.
Anthony V Perruccio

The multimodality cell segmentation challenge: toward universal solutions

1 day 12 hours ago
Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multimodality cell segmentation benchmark, comprising more than 1,500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning...
Jun Ma

The HisRS-like domain of GCN2 is a pseudoenzyme that can bind uncharged tRNA

2 days 12 hours ago
GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2α to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated with tRNA aminoacylation, led to the hypothesis that eIF2α kinase activity is regulated by the direct binding of this domain to uncharged tRNA. Here we solved the structure of the HisRS-like domain in the context of full-length GCN2 by cryoEM....
Jay Z Yin

Oncogenic ETS fusions promote DNA damage and proinflammatory responses via pericentromeric RNAs in extracellular vesicles

2 days 12 hours ago
Aberrant expression of ETS transcription factors characterizes numerous human malignancies. Many of these proteins, including EWS::FLI1 and EWS::ERG fusions in Ewing sarcoma (EwS) and TMPRSS2::ERG in prostate cancer (PCa), drive oncogenic programs via binding to GGAA repeats. We report here that both EWS::FLI1 and ERG bind and transcriptionally activate GGAA-rich pericentromeric heterochromatin. The respective pathogen-like HSAT2 and HSAT3 RNAs, together with LINE, SINE, ERV and other repeat...
Peter Ruzanov

Measurement of the Centrality Dependence of the Dijet Yield in p+Pb Collisions at sqrt[s_{NN}]=8.16  TeV with the ATLAS Detector

6 days 12 hours ago
ATLAS measured the centrality dependence of the dijet yield using 165 nb^{-1} of p+Pb data collected at sqrt[s_{NN}]=8.16 TeV in 2016. The event centrality, which reflects the p+Pb impact parameter, is characterized by the total transverse energy registered in the Pb-going side of the forward calorimeter. The central-to-peripheral ratio of the scaled dijet yields, R_{CP}, is evaluated, and the results are presented as a function of variables that reflect the kinematics of the initial hard parton...
G Aad

Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring

6 days 12 hours ago
The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we...
Elena Kuzmin

Canadian COVID-19 host genetics cohort replicates known severity associations

6 days 12 hours ago
The HostSeq initiative recruited 10,059 Canadians infected with SARS-CoV-2 between March 2020 and March 2023, obtained clinical information on their disease experience and whole genome sequenced (WGS) their DNA. We analyzed the WGS data for genetic contributors to severe COVID-19 (considering 3,499 hospitalized cases and 4,975 non-hospitalized after quality control). We investigated the evidence for replication of loci reported by the International Host Genetics Initiative (HGI); analyzed the X...
Elika Garg

Childhood cancer mutagenesis caused by transposase-derived PGBD5

6 days 12 hours ago
Genomic rearrangements are a hallmark of most childhood tumors, including medulloblastoma, one of the most common brain tumors in children, but their causes remain largely unknown. Here, we show that PiggyBac transposable element derived 5 (Pgbd5) promotes tumor development in multiple developmentally accurate mouse models of Sonic Hedgehog (SHH) medulloblastoma. Most Pgbd5-deficient mice do not develop tumors, while maintaining normal cerebellar development. Ectopic activation of SHH signaling...
Makiko Yamada

Expanding TheCellVision.org: A Central Repository for Visualizing and Mining High-Content Cell Imaging Projects

6 days 12 hours ago
We previously constructed TheCellVision.org, a central repository for visualizing and mining data from yeast high-content imaging projects. At its inception, TheCellVision.org housed two high-content screening (HCS) projects providing genome-scale protein abundance and localization information for the budding yeast Saccharomyces cerevisiae, as well as a comprehensive analysis of the morphology of its endocytic compartments upon systematic genetic perturbation of each yeast gene. Here, we report...
Myra Paz David Masinas

Proteome-scale discovery of protein degradation and stabilization effectors

1 week ago
Targeted protein degradation and stabilization are promising therapeutic modalities because of their potency, versatility and their potential to expand the druggable target space^(1,2). However, only a few of the hundreds of E3 ligases and deubiquitinases in the human proteome have been harnessed for this purpose, which substantially limits the potential of the approach. Moreover, there may be other protein classes that could be exploited for protein stabilization or degradation^(3-5), but there...
Juline Poirson

scGREAT: Transformer-based deep-language model for gene regulatory network inference from single-cell transcriptomics

1 week ago
Gene regulatory networks (GRNs) involve complex and multi-layer regulatory interactions between regulators and their target genes. Precise knowledge of GRNs is important in understanding cellular processes and molecular functions. Recent breakthroughs in single-cell sequencing technology made it possible to infer GRNs at single-cell level. Existing methods, however, are limited by expensive computations, and sometimes simplistic assumptions. To overcome these obstacles, we propose scGREAT, a...
Yuchen Wang

<em>Tmod2</em> is a regulator of cocaine responses through control of striatal and cortical excitability, and drug-induced plasticity

1 week 1 day ago
Drugs of abuse induce neuroadaptations, including synaptic plasticity, that are critical for transition to addiction, and genes and pathways that regulate these neuroadaptations are potential therapeutic targets. Tropomodulin 2 (Tmod2) is an actin-regulating gene that plays an important role in synapse maturation and dendritic arborization and has been implicated in substance-abuse and intellectual disability in humans. Here we mine the KOMP2 data and find that Tmod2 knockout mice show...
Arojit Mitra

Using optically pumped magnetometers to replicate task-related responses in next generation magnetoencephalography

1 week 2 days ago
Optically pumped magnetometers (OPMs) offer a new wearable means to measure magnetoencephalography (MEG) signals, with many advantages compared to conventional systems. However, OPMs are an emerging technology, thus characterizing and replicating MEG recordings is essential. Using OPM-MEG and SQUID-MEG, this study investigated evoked responses, oscillatory power, and functional connectivity during emotion processing in 20 adults, to establish replicability across the two technologies. Five...
Kristina Safar

Systematic endoscopic staging of mediastinum to guide radiotherapy planning in patients with locally advanced non-small-cell lung cancer (SEISMIC): an international, multicentre, single-arm, clinical trial

1 week 6 days ago
BACKGROUND: Systematic mediastinal lymph node staging by endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) improves accuracy of staging in patients with early-stage non-small-cell lung cancer (NSCLC). However, patients with locally advanced NSCLC commonly undergo only selective lymph node sampling. This study aimed to determine the proportion of patients with locally advanced NSCLC in whom systematic endoscopic mediastinal staging identified PET-occult lymph node...
Daniel P Steinfort

Rigorous science demands support of transgender scientists

1 week 6 days ago
To build a just, equitable, and diverse academy, scientists and institutions must address systemic barriers that sex and gender minorities face. This Commentary summarizes (1) critical context informing the contemporary oppression of transgender people, (2) how this shapes extant research on sex and gender, and (3) actions to build an inclusive and rigorous academy for all.
Krisha Aghi

Target-locked: a mechanism for disaggregase binding to aggregated proteins

2 weeks ago
ClpG is a novel autonomous disaggregase found in Pseudomonas aeruginosa that confers resistance to lethal heat stress. The mechanism by which ClpG specifically targets protein aggregates for disaggregation is unknown. In their recent work published in JBC, Katikaridis et al. (2023) identify an avidity-based mechanism by which four or more ClpG subunits, through specific N-terminal hydrophobic residues located on an exposed β-sheet loop, interact with multiple hydrophobic patches on an aggregated...
Trevor M Morey

Aniline antioxidants in road dust, parking lot dust, and green-belt soil in Harbin, a megacity in China: Occurrence, profile, and seasonal variation

2 weeks 1 day ago
Aniline antioxidants (ANs) are widely used as industrial chemicals in products composed of rubber. ANs originate mainly from vehicles, where tire wear particles end up in dust and soil after being deposited on roads. Nowadays, limited information is available on the fate and seasonal variation of ANs in the road environment. In this study, we investigated the occurrence of 32 ANs in dust and soil from different road environments, including road dust, garage dust, parking lot dust, and green-belt...
Ye Zhang