bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inherently reduced expression of ASC restricts caspase-1 processing in hepatocytes and promotesPlasmodiuminfection
Authors: Marques-da-Silva Camila , Baptista Rodrigo P. , Kurup Samarchith P. 
Published: July 2023

AbstractInflammasome-mediated caspase-1 activation facilitates innate immune control ofPlasmodiumin the liver, thereby limiting the incidence and severity of clinical malaria. However, caspase-1 processing occurs incompletely in the hepatocytes and precludes the generation of mature IL-1β or IL-18, unlike in other cells. Why this is so, or how it impactsPlasmodiumcontrol in the liver has remained unknown. We show that an inherently reduced expression of the inflammasome adaptor molecule ASC (apoptosis-associated speck-like protein containing CARD) is responsible for the incomplete proteolytic processing of caspase-1 in hepatocytes. Transgenically enhancing ASC expression in hepatocytes enabled complete caspase-1 processing, enhanced pyroptotic cell-death, maturation of the proinflammatory cytokines IL-1β and IL-18 that was otherwise absent, and resulted in better overall control ofPlasmodiuminfection in the liver mice. This however impeded the protection offered by live-attenuated anti-malarial vaccination. Tempering ASC expression in macrophages on the other hand resulted in incomplete processing of caspase-1. Our work shows how caspase-1 activation and function in host cells are fundamentally defined by ASC expression and offers a potential new pathway to create better disease and vaccination outcomes by modifying the latter.
NOTCH3 drives meningioma tumorigenesis and resistance to radiotherapy
Authors: Choudhury Abrar , Cady Martha A. , Lucas Calixto-Hope G. , Najem Hinda , Phillips Joanna J. , Palikuqi Brisa , Zakimi Naomi , Joseph Tara , Birrueta Janeth Ochoa , Chen William C. , Bush Nancy Ann Oberheim , Hervey-Jumper Shawn L. , Klein Ophir D. , Toedebusch Christine M. , Horbinski Craig M. , Magill Stephen T. , Bhaduri Aparna , Perry Arie , Dickinson Peter J. , Heimberger Amy B. , Ashworth Alan , Crouch Elizabeth E. , Raleigh David R. 
Published: July 2023

SummaryMeningiomas are the most common primary intracranial tumors1–3. Treatments for patients with meningiomas are limited to surgery and radiotherapy, and systemic therapies remain ineffective or experimental4,5. Resistance to radiotherapy is common in high-grade meningiomas6, and the cell types and signaling mechanisms driving meningioma tumorigenesis or resistance to radiotherapy are incompletely understood. Here we report NOTCH3 drives meningioma tumorigenesis and resistance to radiotherapy and find NOTCH3+ meningioma mural cells are conserved across meningiomas from humans, dogs, and mice. NOTCH3+ cells are restricted to the perivascular niche during meningeal development and homeostasis and in low-grade meningiomas but are expressed throughout high-grade meningiomas that are resistant to radiotherapy. Integrating single-cell transcriptomics with lineage tracing and imaging approaches across mouse genetic and xenograft models, we show NOTCH3 drives tumor initiating capacity, cell proliferation, angiogenesis, and resistance to radiotherapy to increase meningioma growth and reduce survival. An antibody stabilizing the extracellular negative regulatory region of NOTCH37,8blocks meningioma tumorigenesis and sensitizes meningiomas to radiotherapy, reducing tumor growth and improving survival in preclinical models. In summary, our results identify a conserved cell type and signaling mechanism that underlie meningioma tumorigenesis and resistance to radiotherapy, revealing a new therapeutic vulnerability to treat meningiomas that are resistant to standard interventions.
Genomic Surveillance of SARS-CoV-2 Using Long-Range PCR Primers
Authors: Kandel Sangam , Hartzell Susanna L. , Ingold Ashton K. , Turner Grace A. , Kennedy Joshua L. , Ussery David W. 
Published: July 2023

AbstractWhole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence the ∼30,000 nucleotide SARS-CoV-2 genome that use a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight primers and ARTIC V4.1 primers are the most popular primer schemes that can amplify segments of SARS-CoV-2 (400 bp and 1200 bp, respectively) tiled across the viral RNA genome. Mutations within primer binding sites and primer-primer interactions can result in amplicon dropouts and coverage bias, yielding low-quality genomes with ‘Ns’ inserted in the missing amplicon regions, causing inaccurate lineage assignments, and making it challenging to monitor lineage-specific mutations in Variants of Concern (VoCs). This study uses seven long-range PCR primers with an amplicon size of ∼4500 bp to tile across the complete SARS-CoV-2 genome. One of these regions includes the full-length S-gene by using a set of flanking primers. Using a small set of long-range primers to sequence SARS-CoV-2 genomes reduces the possibility of amplicon dropout and coverage bias.
Handling difficult cryo-ET samples: A study with primary neurons fromDrosophila melanogaster
Authors: Kim Joseph Y. , Yang Jie E. , Mitchell Josephine W. , English Lauren A. , Yang Sihui Z. , Tenpas Tanner , Dent Erik W. , Wildonger Jill , Wright Elizabeth R. 
Published: July 2023

ABSTRACTCellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rdinstarDrosophila melanogasterlarval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishingDrosophilaneurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
Expression status transition ofNOTCH1accompanies chromatin remodeling in human early retinal progenitor cells
Authors: Watabe Yoshitoku , Kobayashi Sakurako , Nakayama Takahiro , Takahashi Satoru , Yoshihara Masaharu 
Published: July 2023

AbstractObjectiveThe regulation of receptor expression is crucial for fine-tuned signal transduction. Notch signaling is a key signaling pathway involved in retinal development. Although the involvement of this signaling pathway in the differentiation of retinal ganglion cells has been documented, less is known about its involvement in earlier stages of retinal progenitor cell differentiation. To clarify the timing of Notch receptor expression in undifferentiated retinal progenitor cells and elucidate the possible involvement of chromatin remodeling in the regulation of Notch receptor expressions, we re-analyzed publicly available human fetal retina single-cell RNA-seq and ATAC-seq data.ResultsOn days 59, 74, and 78, we observedNOTCH1mRNA expression in early retinal progenitor cells, which diminished at later stages of differentiation. Integration of single-cell RNA-seq and ATAC-seq revealed that chromatin remodeling in part of theNOTCH1locus was accompanied by transitions in its mRNA expression. Importantly, chromatin accessibility in the region upstream ofNOTCH1depended on the differentiated cell types. These results suggest that chromatin remodeling may be involved in the differential expression ofNOTCH1, although another type of Notch mRNA expression regulation may exist.
Impact of genetic counselling strategy on diagnostic yield and workload for genome sequencing-based tumour diagnostics
Authors: Koster Roelof , Schipper Luuk J. , Giesbertz Noor A. A. , van Beek Daphne , Mendeville Matías , Samsom Kris G. , Rosenberg Efraim H. , Hogervorst Frans B.L. , Roepman Paul , Boelens Mirjam C. , Bosch Linda J.W. , van den Berg Jose G. , Meijer Gerrit A. , Voest Emile E. , Cuppen Edwin , Ruijs Marielle W.G. , van Wezel Tom , van der Kolk Lizet , Monkhorst Kim 
Published: July 2023

AbstractPurposeGenome sequencing (GS) enables comprehensive molecular analysis of tumours and identification of hereditary cancer predisposition. According to guidelines, directly determining pathogenic germline variants (PGVs) requires pre-test genetic counselling, which is cost-ineffective. Referral for genetic counselling based on tumour variants alone could miss relevant PGVs and/or result in unnecessary referrals.MethodsWe validated GS for detection of germline variants and simulated three strategies using paired tumour-normal genome sequencing data of 937 metastatic patients. In strategy-1 genetic counselling prior to tumour testing allowed direct PGV analysis. In strategy-2 and -3, germline testing and referral for post-test genetic counselling is based on tumour variants using Dutch (strategy-2) or ESMO-PMWG (strategy-3) guidelines.ResultsIn strategy-1, PGVs would be detected in 50 patients (number-needed-to counsel; NTC=18.7). In strategy-2, 86 patients would have been referred for genetic counselling and 43 would have PGVs (NTC=2). In strategy-3, 94 patients would have been referred for genetic counselling and 32 would have PGVs (NTC=2.9). Hence, 43 and 62 patients, respectively, were unnecessarily referred based on a somatic variant.ConclusionBoth post-tumour test counselling strategies (2 and 3) had significantly lower NTC, and strategy-2 had the highest PGV yield. Combining pre-tumour test mainstreaming and post-tumour test counselling may maximize the clinically relevant PGV yield and minimize unnecessary referrals.
Understanding Health Service Utilisation Patterns for Care Home Residents During the COVID-19 Pandemic using Routinely Collected Healthcare Data
Authors: Garner Alex , Preston Nancy , Caiado Camila , Stubington Emma , Hanratty Barbara , Limb James , Mason Suzanne , Knight Jo 
Published: July 2023

AbstractBackgroundHealthcare in care homes during the COVID-19 pandemic required a balance, providing treatment while minimising exposure risk. Policy for how residents should receive care changed rapidly throughout the pandemic. A lack of accessible data on care home residents over this time meant policy decisions were difficult to make and verify. This study investigates common patterns of healthcare utilisation for care home residents in relation to COVID-19 testing events, and associations between utilisation patterns and resident characteristics.MethodsLinked datasets including secondary care, community care and a care home telehealth app are used to define daily healthcare utilisation sequences for care home residents. We derive four 10-day sets of sequences related to Pillar 1 COVID-19 testing; before [1] and after [2] a resident’s first positive test and before [3] and after [4] a resident’s first test. These sequences are clustered, grouping residents with similar healthcare patterns in each set. Association of individual characteristics (e.g. health conditions such as diabetes and dementia) with healthcare patterns are investigated.ResultsWe demonstrate how routinely collected health data can be used to produce longitudinal descriptions of patient care. Clustered sequences [1,2,3,4] are produced for 3,471 care home residents tested between 01/03/2020–01/09/2021. Clusters characterised by higher levels of utilisation were significantly associated with higher prevalence of diabetes. Dementia is associated with higher levels of care after a testing event, and appears to be correlated with a hospital discharge after a first test. Residents discharged from inpatient care within 10 days of their first test had the same mortality rate as those who stayed in hospital.ConclusionWe provide longitudinal, resident-level data on care home resident healthcare during the COVID-19 pandemic. We find that vulnerable residents were associated with higher levels of healthcare usage despite the additional risks. Implications of findings are limited by the challenges of routinely collected data. However, this study demonstrates the potential for further research into healthcare pathways using linked, routinely collected datasets.
Genomic characterization ofPseudomonas syringaepv.syringaefrom Callery pear and the efficiency of associated phages in disease protection
Authors: Holtappels D. , Abelson S.A. , Nouth S.C. , Rickus G.E.J. , Giller J.P. , Koskella B. 
Published: July 2023

AbstractPseudomonas syringaeis a heterogeneous species complex of plant pathogenic bacteria associated with a wide distribution of plant species. Advances in genomics are revealing the complex evolutionary history of this species complex and the wide array of genetic adaptations underpinning their diverse lifestyles. Here, we genomically characterize twoP. syringaeisolates collected from diseased Callery pears (Pyrus calleryana) in Berkeley, California in 2019 and 2022. We also isolated a lytic bacteriophage, which we characterized and evaluated for biocontrol efficiency. Using a multilocus sequence analysis and core genome alignment, we classified theP. syringaeisolates as members of phylogroup two, related to other strains previously isolated fromPyrusandPrunus. An analysis of effector proteins demonstrated an evolutionary conservation of effectoromes across isolates classified in PG2, and yet uncovered unique effector profiles for each, including the two newly identified isolates. Whole genome sequencing of the associated phage uncovered a novel phage genus related to Psa phage PHB09 and theFlaundravirusgenus. Finally, using in planta infection assays, we demonstrate that the phage was equally useful in symptom mitigation of immature pear fruit regardless of the Pss strain tested. Overall, this study demonstrates the diversity ofP. syringaeand their viruses associated with ornamental pear trees, posing spill-over risks to commercial pear trees and the possibility of using phages as biocontrol agents to reduce the impact of disease.
Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells
Authors: Yamaguchi Kosuke , Chen Xiaoying , Rodgers Brianna , Miura Fumihito , Bashtrykov Pavel , Ferry Laure , Kirsh Olivier , Laisné Marthe , Bonhomme Frédéric , Salinas-Luypaert Catalina , Scelfo Andrea , Ugur Enes , Arimondo Paola B. , Leonhardt Heinrich , Kanemaki Masato T. , Fachinetti Daniele , Jeltsch Albert , Ito Takashi , Defossez Pierre-Antoine 
Published: July 2023

AbstractDNA methylation is an essential epigenetic chromatin modification, and its maintenance in mammals requires the protein UHRF1. It is yet unclear if UHRF1 functions solely by stimulating DNA methylation maintenance by DNMT1, or if it has important additional functions. Using degron alleles, we show that UHRF1 depletion causes a much greater loss of DNA methylation than DNMT1 depletion. This is not caused by passive demethylation as UHRF1-depleted cells proliferate more slowly than DNMT1-depleted cells. Instead, bioinformatics, proteomics and genetics experiments establish that UHRF1, besides activating DNMT1, interacts with DNMT3A and DNMT3B and promotes their activity. In addition, we show that UHRF1 antagonizes active DNA demethylation by TET2. Therefore, UHRF1 has non-canonical roles that contribute importantly to DNA methylation homeostasis; these findings have practical implications for epigenetics in health and disease.
Treatment with furosemide indirectly increases inhibitory transmission in the developing hippocampus
Authors: Peerboom C. , Wijne T. , Wierenga C.J. 
Published: July 2023

AbstractDuring the first two postnatal weeks intraneuronal chloride concentrations in rodents gradually decrease, causing a shift from depolarizing to hyperpolarizing γ-aminobutyric acid (GABA) responses. GABAergic depolarization in the immature brain is crucial for the formation and maturation of excitatory synapses, but when GABAergic signaling becomes inhibitory it no longer promotes synapse formation. Here we examined the role of chloride transporters in developing postnatal hippocampal neurons using furosemide, an inhibitor of the chloride importer NKCC1 and chloride exporter KCC2 with reported anticonvulsant effects. We treated organotypic hippocampal cultures made from 6 to 7-day old mice with 200 μM furosemide from DIV1 to DIV8. Using perforated patch clamp recordings we observed that the GABA reversal potential was depolarized after acute furosemide application, but after a week of furosemide treatment the GABA reversal potential but was more hyperpolarized compared to control. Expression levels of the chloride cotransporters were unaffected after one week furosemide treatment. This suggests that furosemide inhibited KCC2 acutely, while prolonged treatment resulted in (additional) inhibition of NKCC1, but we cannot exclude changes in HCO3-. We assessed the effects of accelerating the GABA shift by furosemide treatment on inhibitory synapses onto CA1 pyramidal cells. Directly after cessation of furosemide treatment at DIV9, inhibitory synapses were not affected. However at DIV21, two weeks after ending the treatment, we found that the frequency of inhibitory currents was increased, and VGAT puncta density instratum Radiatumwas increased. In addition, cell capacitance of CA1 pyramidal neurons was reduced in furosemide-treated slices at DIV21 in an activity-dependent manner. Our results suggest that furosemide treatment indirectly promoted inhibitory transmission, possibly by increasing activity-independent GABA release.
FAST: a fast and scalable factor analysis for spatially aware dimension reduction of multi-section spatial transcriptomics data
Authors: Liu Wei , Zhang Xiao , Chai Xiaoran , Fan Zhenqian , Lin Huazhen , Chen Jinmiao , Sun Lei , Yu Tianwei , Yeong Joe , Liu Jin 
Published: July 2023

AbstractBiological techniques for spatially resolved transcriptomics (SRT) have advanced rapidly in both throughput and spatial resolution for a single spatial location. This progress necessitates the development of efficient and scalable spatial dimension reduction methods that can handle large-scale SRT data from multiple sections. Here, we developed FAST as a fast and efficient generalized probabilistic factor analysis for spatially aware dimension reduction, which simultaneously accounts for the count nature of SRT data and extracts a low-dimensional representation of SRT data across multiple sections, while preserving biological effects with consideration of spatial smoothness among nearby locations. Compared with existing methods, FAST uniquely models the count data across multiple sections while using a local spatial dependence with scalable computational complexity. Using both simulated and real datasets, we demonstrated the improved correlation between FAST estimated embeddings and annotated cell/domain types. Furthermore, FAST exhibits remarkable speed, with only FAST being applicable to analyze a mouse embryo Stereo-seq dataset with >2.3 million locations in only 2 hours. More importantly, FAST identified the differential activities of immune-related transcription factors between tumor and non-tumor clusters and also predicted a carcinogenesis factorCCNHas the upstream regulator of differentially expressed genes in a breast cancer Xenium dataset.
Low concentrations of ethylene bisdithiocarbamate pesticides maneb and mancozeb impair manganese and zinc homeostasis to induce oxidative stress and caspase-dependent apoptosis in human hepatocytes
Authors: Petitjean Kilian , Verres Yann , Bristeau Sébastien , Ribault Catherine , Aninat Caroline , Olivier Christophe , Leroyer Patricia , Ropert Martine , Loreal Olivier , Herault Olivier , Amalric Laurence , Baran Nicole , Fromenty Bernard , Corlu Anne , Loyer Pascal 
Published: July 2023

ABSTRACTThe worldwide and intensive use of phytosanitary compounds results in environmental and food contamination by chemical residues. Human exposure to multiple pesticide residues is a major health issue. Considering that the liver is not only the main organ for metabolizing pesticides but also a major target of toxicities induced by xenobiotics, we studied the effects of a mixture of 7 pesticides (chlorpyrifos-ethyl, dimethoate, diazinon, iprodione, imazalil, maneb, mancozeb) often detected in food samples. Effects of the mixture was investigated using metabolically competent HepaRG cells and human hepatocytes in primary culture. We report the strong cytotoxicity of the pesticide mixture towards hepatocytes-like HepaRG cells and human hepatocytes upon acute and chronic exposures at low concentrations extrapolated from the Acceptable Daily Intake (ADI) of each compound. Unexpectedly, we demonstrated that the manganese (Mn)-containing dithiocarbamates (DTCs) maneb and mancozeb were solely responsible for the cytotoxicity induced by the mixture. The mechanism of cell death involved the induction of oxidative stress, which led to cell death by intrinsic apoptosis involving caspases 3 and 9. Importantly, this cytotoxic effect was found only in cells metabolizing these pesticides. Herein, we unveil a novel mechanism of toxicity of the Mn-containing DTCs maneb and mancozeb through their metabolization in hepatocytes generating the main metabolite ethylene thiourea (ETU) and the release of Mn leading to intracellular Mn overload and depletion in zinc (Zn). Alteration of the Mn and Zn homeostasis provokes the oxidative stress and the induction of apoptosis, which can be prevented by Zn supplementation. Our data demonstrate the hepatotoxicity of Mn-containing fungicides at very low doses and unveil their adverse effect in disrupting Mn and Zn homeostasis and triggering oxidative stress in human hepatocytes.