bluuebunny/crossref_metadata_2025 huggingface dataset:
REAL-TIME MECHANISTIC BAYESIAN FORECASTS OF COVID-19 MORTALITY
Authors: Gibson Graham C. , Reich Nicholas G. , Sheldon Daniel
Published: December 2020

Abstract

The COVID-19 pandemic emerged in late December 2019. In the first six months of the global outbreak, the US reported more cases and deaths than any other country in the world. Effective modeling of the course of the pandemic can help assist with public health resource planning, intervention efforts, and vaccine clinical trials. However, building applied forecasting models presents unique challenges during a pandemic. First, case data available to models in real-time represent a non-stationary fraction of the true case incidence due to changes in available diagnostic tests and test-seeking behavior. Second, interventions varied across time and geography leading to large changes in transmissibility over the course of the pandemic. We propose a mechanistic Bayesian model (MechBayes) that builds upon the classic compartmental susceptible-exposed-infected-recovered (SEIR) model to operationalize COVID-19 forecasting in real time. This framework includes non-parametric modeling of varying transmission rates, non-parametric modeling of case and death discrepancies due to testing and reporting issues, and a joint observation likelihood on new case counts and new deaths; it is implemented in a probabilistic programming language to automate the use of Bayesian reasoning for quantifying uncertainty in probabilistic forecasts. The model has been used to submit forecasts to the US Centers for Disease Control, through the COVID-19 Forecast Hub. We examine the performance relative to a baseline model as well as alternate models submitted to the Forecast Hub. Additionally, we include an ablation test of our extensions to the classic SEIR model. We demonstrate a significant gain in both point and probabilistic forecast scoring measures using MechBayes when compared to a baseline model and show that MechBayes ranks as one of the top 2 models out of 10 submitted to the COVID-19 Forecast Hub. Finally, we demonstrate that MechBayes performs significantly better than the classical SEIR model.
Improving on estimates of the potential relative harm to health from using modern ENDS (vaping) compared to tobacco smoking
Authors: Wilson Nick , Summers Jennifer A , Ait Ouakrim Driss , Hoek Janet , Edwards Richard , Blakely Tony
Published: December 2020

Background

Although the harm to health from electronic nicotine delivery systems (ENDS) compared to smoked tobacco remains highly uncertain, society and governments still need to know the likely range of the relative harm to inform regulatory policies for ENDS and smoking.

Methods

We identified biomarkers with specificity of association with different disease groupings e.g., volatile organic compound (VOCs) for chronic obstructive pulmonary disease; and tobacco-specific N’-nitrosamines (TSNAs) and polycyclic aromatic hydrocarbons (PAHs) for all cancers. We conducted a review of recent studies (post January 2017) that compared these biomarkers between people exclusively using ENDS and those exclusively smoking tobacco. The percentage differences in these biomarkers, weighted by study size and adjusted for acrolein from other sources, were used as a proxy for the assumed percentage difference in disease harm between ENDS and smoking. These relative differences were applied to previously modelled estimates of smoking-related health loss (in health-adjusted life-years; HALYs).

Results

The respective relative biomarker levels (ENDS vs smoking) were: 28% for respiratory diseases (five results, three studies); 42% for cancers (five results, four studies); and 35% for cardiovascular (seven results, four studies). When integrated with the HALY impacts by disease, the overall harm to health from ENDS was estimated to be 33% that of smoking.

Conclusions

This analysis, suggests that the use of modern ENDS devices (vaping) could be a third as harmful to health as smoking in a high-income country setting. But this estimate is based on a limited number of biomarker studies and is best be considered a likely upper level of ENDS risk given potential biases in our method (i.e., the biomarkers used being correlated with more unaccounted for toxicants in smoking compared to with using ENDS).
Unravelling the early warning capability of wastewater surveillance for COVID-19: A temporal study on SARS-CoV-2 RNA detection and need for the escalation
Authors: Kumar Manish , Joshi Madhvi , Patel Arbind Kumar , Joshi Chaitanya G
Published: December 2020

Wastewater-based Epidemiological (WBE) surveillance offers a promising approach to assess the pandemic situation covering pre-symptomatic and asymptomatic cases in highly populated area under limited clinical tests. In the present study, we analysed SARS-CoV-2 RNA in the influent wastewater samples (n = 43) from four wastewater treatment plants (WWTPs) in Gandhinagar, India, during August 7th to September 30th, 2020. A total of 40 samples out of 43 were found positive i.e. having at least two genes of SARS-CoV-2. The average Ct values for S, N, and ORF 1ab genes were 32.66, 33.03, and 33.95, respectively. Monthly variation depicted a substantial rise in the average copies of N (∼120%) and ORF 1ab (∼38%) genes in the month of September as compared to August, while S-gene copies declined by 58% in September 2020. The SARS-CoV-2 genome concentration was higher in the month of September (∼924.5 copies/ L) than August (∼897.5 copies/ L), corresponding to a ∼ 2.2-fold rise in the number of confirmed cases during the study period. Further, the percentage change in genome concentration level on a particular date was found in the lead of 1-2 weeks of time with respect to the official confirmed cases registered based on clinical tests on a temporal scale. The results profoundly unravel the potential of WBE surveillance to predict the fluctuation of COVID-19 cases to provide an early warning. Our study explicitly suggests that it is the need of hour that the wastewater surveillance must be included as an integral part of COVID-19 pandemic monitoring which can not only help the water authorities to identify the hotspots within a city but can provide up to 2 weeks of time lead for better tuning the management interventions.

HIGHLIGHTS

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Study unravels the early warning potential of wastewater based surveillance of COVID-19.

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Adequate SARS-CoV-2 RNA were detected despite of limited reported case in the vicinity.

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Up to 2 weeks of lead is possible from a regular wastewater based COVID-19 surveillance.

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SARS-CoV-2 RNA was higher in September than August in response to a ∼ 2.2-fold rise in COVID-19 active cases.

Graphical Abstract
Response of human liver tissue to innate immune stimuli
Authors: Wu Xia , Roberto Jessica B. , Knupp Allison , Greninger Alexander L. , Truong Camtu D. , Hollingshead Nicole , Kenerson Heidi L. , Tuefferd Marianne , Chen Antony , Horton Helen , Jerome Keith R. , Polyak Stephen J. , Yeung Raymond S. , Crispe Ian N.
Published: December 2020

Precision-cut human liver slice cultures (PCLS) has become an important alternative immunological platform in preclinical testing. To further evaluate the capacity of PCLS, we investigated the innate immune response to TLR3 agonist (poly-I:C) and TLR4 agonist (LPS) with the normal and pathological liver tissue. Pathological liver tissue was obtained from patients with active chronic HCV infection, and patients with former chronic HCV infection cured by recent Direct-Acting Antiviral (DAA) drug therapy. We found that hepatic innate immunity was not suppressed but enhanced in the HCV-infected tissue, compared with the healthy controls. Furthermore, despite recent HCV elimination, DAA-cured liver tissue manifested ongoing abnormalities in liver immunity. Sustained abnormal immune gene expression in DAA-cured samples were identified from direct ex vivo measurements and with TLR3 and TLR4 stimulation assays. Those genes that were up-regulated in chronic HCV-infected liver tissue were enriched in expression in the liver non-parenchymal cell compartment. These results demonstrated the utility of PCLS in studying the liver pathology and innate immunity.
Host Cell Proteases Drive Early or Late SARS-CoV-2 Penetration
Authors: Koch Jana , Uckeley Zina M , Doldan Patricio , Stanifer Megan , Boulant Steeve , Lozach Pierre-Yves
Published: December 2020

SARS-CoV-2 is a newly emerged coronavirus (CoV) that spread through human populations worldwide in early 2020. CoVs rely on host cell proteases for activation and infection. The trypsin-like protease TMPRSS2 at the cell surface, cathepsin L in endolysosomes, and furin in the Golgi have all been implicated in the SARS-CoV-2 proteolytic processing. Whether SARS-CoV-2 depends on endocytosis internalization and vacuolar acidification for infectious entry remains unclear. Here, we examined the dynamics of SARS-CoV-2 activation during the cell entry process in tissue culture. Using four cell lines representative of lung, colon, and kidney epithelial tissues, we found that TMPRSS2 determines the SARS-CoV-2 entry pathways. In TMPRSS2-positive cells, infection was sensitive to aprotinin, a TMPRSS2 inhibitor, but not to SB412515, a drug that impairs cathepsin L. Infectious penetration was marginally dependent on endosomal acidification, and the virus passed the protease-sensitive step within 10 min. In a marked contrast, in TMPRSS2-negative cells cathepsin L and low pH were required for SARS-CoV-2 entry. The cathepsin L-activated penetration occurred within 40-60 min after internalization and required intact endolysosomal functions. Importantly, pre-activation of the virus allowed it to bypass the need for endosomal acidification for viral fusion and productive entry. Overall, our results indicate that SARS-CoV-2 shares with other CoVs a strategy of differential use of host cell proteases for activation and infectious penetration. This study also highlights the importance of TMPRSS2 in dictating the entry pathway used by SARS-CoV-2.

Significance

Preventing SARS-CoV-2 spread requires approaches affecting early virus-host cell interactions before the virus enters and infects target cells. Host cell proteases are critical for coronavirus activation and infectious entry. Here, we reconcile apparent contradictory observations from recent reports on endosomal acidification and the role of furin, TMPRSS2, and cathepsin L in the productive entry and fusion process of SARS-CoV-2. Investigating authentic virus in various cell types, we demonstrated that SARS-CoV-2 developed the ability to use different entry pathways, depending on the proteases expressed by the target cell. Our results have strong implications for future research on the apparent broad tropism of the virusin vivo. This study also provides a handle to develop novel antiviral strategies aiming to block virus entry, as illustrated with the several drugs that we identified to prevent SARS-CoV-2 infection, some with low IC50.
No evidence for human monocyte-derived macrophage infection and antibody-mediated enhancement of SARS-CoV-2 infection
Authors: García-Nicolás O , V’kovski P , Zettl F , Zimmer G , Thiel V , Summerfield A
Published: December 2020

Vaccines are essential to control the spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and to protect the vulnerable population. However, one safety concern of vaccination is the possible development of antibody-dependent enhancement (ADE) of SARS-CoV-2 infection. The potential infection of Fc receptor bearing cells such as macrophages, would support continued virus replication and inflammatory responses, and thereby potentially worsen the clinical outcome of COVID-19. Here we demonstrate that SARS-CoV-2 and SARS-CoV-1 neither infect human monocyte-derived macrophages nor induce inflammatory cytokines in these cells, in sharp contrast to Middle East respiratory syndrome (MERS) coronavirus and the common cold human coronavirus 229E. Furthermore, serum from convalescent COVID-19 patients neither induced enhancement of SARS-CoV-2 infection nor innate immune response in human macrophages. These results support the view that ADE may not be involved in the immunopathological processes associated with COVID-19, however, more studies are necessary to understand the potential contribution of antibodies-virus complexes with other cells expressing FcR receptors.
Sting orchestrates the crosstalk between polyunsaturated fatty acids metabolism and inflammatory responses
Authors: Vila Isabelle K. , Chamma Hanane , Steer Alizée , Taffoni Clara , Reinert Line S. , Turtoi Evgenia , Saccas Mathilde , Marines Johanna , Jin Lei , Bonnefont Xavier , Paludan Soren R. , Vlachakis Dimitrios , Turtoi Andrei , Laguette Nadine
Published: December 2020

Inflammatory disorders are major health issues in which immune function and metabolic homeostasis are concertedly altered. Yet, the molecular mechanisms coordinating innate and metabolic pathways in homeostatic conditions are poorly understood. Here, we unveil a negative regulatory feedback loop involving the Stimulator of interferon genes (Sting) and the Fatty acid desaturase 2 (Fads2). At steady state, Sting regulates FA metabolism by repressing the activity of the Fads2 enzyme responsible for the desaturation of polyunsaturated FAs (PUFAs). Importantly, Sting activation increased Fads2 activity, while antagonizing Fads2 enhanced Sting activation, promoting the establishment of an anti-viral state. Remarkably, the cross-regulation between Sting and Fads2 is mediated by the cyclic GMP-AMP (cGAMP) Sting agonist and PUFAs. Indeed, we found that PUFAs inhibit Sting activation, while Sting agonists bind Fads2. Thus, our study identifies Sting as a master regulator of FA metabolism, and PUFAs as modulators of Sting-dependent inflammation. The interplay between Fads2 and Sting determines the fine-tuning of inflammatory responses, but comes at the expense of metabolic alterations, which are critical to consider in human pathologies associated with aberrant Sting activation.
WormPaths:Caenorhabditis elegansmetabolic pathway annotation and visualization
Authors: Walker Melissa D. , Giese Gabrielle E. , Holdorf Amy D. , Bhattacharya Sushila , Diot Cédric , García-González Aurian P. , Horowitz Brent , Lee Yong-Uk , Leland Thomas , Li Xuhang , Mirza Zeynep , Na Huimin , Nanda Shivani , Ponomarova Olga , Zhang Hefei , Zhang Jingyan , Yilmaz L. Safak , Walhout Albertha J.M.
Published: December 2020

In our group, we aim to understand metabolism in the nematodeCaenorhabditis elegansand its relationships with gene expression, physiology and the response to therapeutic drugs. On March 15, 2020, a stay-at-home order was put into effect in the state of Massachusetts, USA, to flatten the curve of the spread of the novel SARS-CoV2 virus that causes COVID-19. For biomedical researchers in our state, this meant putting a hold on experiments for nine weeks until May 18, 2020. To keep the lab engaged and productive, and to enhance communication and collaboration, we embarked on an in-lab project that we all found important but that we never had the time for: the detailed annotation and drawing ofC. elegansmetabolic pathways. As a result, we present WormPaths, which is composed of two parts: 1) the careful manual annotation of metabolic genes into pathways, categories and levels, and 2) 66 pathway maps that include metabolites, metabolite structures, genes, reactions, and pathway connections between maps. These maps are available on our WormFlux website. We show that WormPaths provides easy-to-navigate maps and that the different levels in WormPaths can be used for metabolic pathway enrichment analysis of transcriptomic data. In the unfortunate event of additional lockdowns, we envision further developing these maps to be more interactive, with an analogy of road maps that are available on mobile devices.
The schizophrenia-associated variant inSLC39A8alters N-glycosylation in the mouse brain
Authors: Mealer Robert G. , Williams Sarah E. , Noel Maxence , Yang Bo , D’Souza Alexandria , Nakata Toru , Graham Daniel B. , Creasey Elizabeth A. , Cetinbas Murat , Sadreyev Ruslan , Scolnick Edward M. , Woo Christina M. , Smoller Jordan W. , Xavier Ramnik J. , Cummings Richard D.
Published: December 2020

A missense mutation (A391T) in the manganese transporterSLC39A8is strongly associated with schizophrenia in genomic studies, though the molecular connection to the brain remains hypothetical. Human carriers of A391T have reduced serum manganese, altered plasma glycosylation, and brain MRI changes consistent with altered metal transport. Here, using a knock-in mouse model homozygous for A391T, we show that the schizophrenia-associated variant changes protein glycosylation in the brain. N-linked glycosylation was most significantly impaired, with effects differing between regions. RNAseq analysis showed negligible regional variation, consistent with changes in the activity of glycosylation enzymes rather than gene expression. Finally, nearly one third of detected glycoproteins were differentially N-glycosylated in the cortex, including members of several pathways previously implicated in schizophrenia such as cell adhesion molecules and neurotransmitter receptors. These findings provide a mechanistic link between a risk allele and biochemical changes in the brain, furthering our molecular understanding of the pathophysiology of schizophrenia.
Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8
Authors: Shin GiWon , Greer Stephanie U. , Hopmans Erik , Grimes Susan M. , Lee HoJoon , Zhao Lan , Miotke Laura , Suarez Carlos , Almeda Alison F. , Haraldsdottir Sigurdis , Ji Hanlee P.
Published: December 2020

Colorectal carcinomas(CRCs)which have lost DNA mismatch repair display hypermutability evident in a molecular phenotype called microsatellite instability(MSI). These mismatch repair deficient tumors are thought to lack widespread genomic instability features, such as copy number changes and rearrangements. To identify MSI for clinical diagnosis, current molecular testing looks for changes in mononucleotide or dinucleotide repeats. However, microsatellites have other types of sequence tandem repeats such as tri- and tetranucleotide motifs. These additional classes of microsatellites are generally not examined for MSI but are known to be unstable in a phenotype known as elevated microsatellite alterations at selected tetranucleotide repeats, orEMAST. We developed a sequencing approach that provides ultra-high coverage (>2500X) of microsatellite targets and cancer genes for profiling genomic instability. We assessed the diverse repeat motifs across 200 microsatellites. Our approach provides highly sensitive detection of MSI with high specificity, evaluates copy number alterations with high accuracy, delineates chromosomal instability(CIN)classification and deconvolutes subclonal architecture. By examining both MSI and CIN, we discovered mutations and copy number alterations that defined mixed genomic instability states of CIN and MSI, which are normally considered exclusive. An increase in copy number of chromosome arm 8q was prevalent among MSI tumors. Moreover, we identified an inter-chromosomal translocation event from a CRC with co-occurrence of MSI. Subclonal analysis demonstrated that mutations which are typically considered to be exclusive in MSI, shows mutual occurrence in MSI tumors with more sensitive characterization. Our approach revealed thatMSH3mutations are a potential source of mixed genomic instability features. Overall, our study demonstrates that some colorectal cancers have features of both microsatellite and chromosomal instability. This result may have implications for immunotherapy treatment.
Biological Correlations and Confounding Variables for Quantification of Retinal Ganglion Cells Based on Optical Coherence Tomography using Diversity Outbred Mice
Authors: Hedberg-Buenz Adam , Meyer Kacie J. , van der Heide Carly J. , Deng Wenxiang , Lee Kyungmoo , Soukup Dana A. , Kettelson Monica , Pellack Danielle , Mercer Hannah , Wang Kai , Garvin Mona K. , Abramoff Michael D. , Anderson Michael G.
Published: December 2020

Purpose

Despite popularity of optical coherence tomography (OCT) in glaucoma studies, it’s unclear how well OCT-derived metrics compare to traditional measures of retinal ganglion cell (RGC) abundance. Here, Diversity Outbred (J:DO) mice are used to directly compare ganglion cell complex (GCC)-thickness measured by OCT to metrics of retinal anatomy measured ex vivo with retinal wholemounts or optic nerve cross sections.

Methods

J:DO mice (n= 48) underwent OCT and fundoscopic exams, with GCC-thickness measured using automated segmentation. Following euthanasia, RGC axons were quantified from para-phenylenediamine-stained optic nerve cross sections and RGC somas from BRN3A-immunolabeled retinal wholemounts with total cellularity assessed by TO-PRO or hematoxylin nuclear staining.

Results

J:DO tissues lacked overt disease. GCC-thickness (62.4 ± 3.7 µm), RGC abundance (3,097 ± 515 BRN3A+nuclei/mm2; 45,533 ± 9,077 axons), and total inner retinal cell abundance (6,952 ± 810 nuclei/mm2) varied broadly. GCC-thickness correlated significantly to RGC somal density (r = 0.46) and axon number (r = 0.49), whereas total inner retinal cellularity did not. Retinal area (20.3 ± 2.4 mm2) and optic nerve (0.09 ± 0.02 mm2) cross-sectional area varied widely. Sex did not significantly influence any of these metrics. In bilateral comparisons, GCC-thickness (r = 0.89), inner retinal cellularity (r = 0.47), and RGC axon abundance (r = 0.72) all correlated significantly.

Conclusions

Amongst outbred mice with widely variable phenotypes, OCT-derived measurements of GCC thickness correlate significantly to RGC abundance and axon number. The extensive phenotypic variability exhibited by J:DO mice make them a powerful resource for studies of retinal anatomy using quantitative genetics.
GeneNetwork: a continuously updated tool for systems genetics analyses
Authors: Watson Pamela M. , Ashbrook David G.
Published: December 2020

GeneNetwork and its earlier iteration, WebQTL, have now been an important database and toolkit for quantitative trait genetics research for two decades. Recent improvements to GeneNetwork have reinvigorated it, including the addition of data from 10 species, multi-omics analysis, updated code, and new tools. The new GeneNetwork is now an exciting resource for predictive medicine and systems genetics, which is constantly being maintained and improved. Here, we give a brief overview of the process for carrying out some of the most common functions on GeneNetwork, as a gateway to deeper analyses, demonstrating how a small number of plausible candidate genes can be found for a typical immune phenotype.
PolyJet 3D Printing of Tissue Mimicking Materials: An Investigation of Characteristic Properties of 3D Printed Synthetic Tissue
Authors: Lee Vania , Severseike Leah , Bakken Chris , Bermel Emily , Bhatia Varun
Published: December 2020

Current anatomical 3D printing has been primarily used for education, training, and surgical planning purposes. This is largely due to the models being printed in materials which excel at replicating macro-level organic geometries; however, these materials have the drawback of unrealistic mechanical behavior and system properties compared to biological tissue. The new Digital Anatomy (DA) family of materials from Stratasys utilizes composite printed materials to more closely mimic mechanical behavior of biological tissue, potentially allowing more realistic models for design evaluation. Various experimental DA Solid Organ (SO) configurations were quantitatively evaluated under axial loading for comparison with porcine liver in terms of stiffness. Additionally, Structural Heart - Myocardium (Myo) configurations were quantitatively evaluated under different lubricant conditions for comparison with porcine epicardium and aorta in terms of lubricity. Finally, experimental DA Subcutaneous Tissue configurations were qualitatively evaluated by experts with significant pre-clinical implant experience for cutting, tunneling, and puncture procedures.

In general, the experimental SO configurations showed promising compliance results when compared to porcine liver. The stiffness of DA configurations was either within the same range or on the lower bound of porcine tissue stiffness values. The lubricity of DA configurations with surface treatments was comparable with porcine epicardium and aorta. In terms of qualitative cutting, DA did not perform well for any of the configurations; however, tunneling and puncture were rated favorably for some of the experimental configurations. Despite some limitations, DA feels closer to real tissue than other commercially available 3D printed materials. Furthermore, the lower sample-to-sample variability of DA allows for repeatability not provided by biological tissue. The promising results and repeatability indicate that DA materials can be used to configure structures with similar characteristic mechanical properties to porcine liver, epicardium, and subcutaneous tissue, adding new value as not only an educational, training, and surgical tool, but also as a research tool.
Genome-wide identification, characterization and expression analysis of the Bcl-2 associated athanogene (BAG) gene family inPhyscomitrium patens
Authors: Castro Alexanda , Saavedra Laura , Ruibal Cecilia , Lascano Ramiro , Vidal Sabina
Published: December 2020

The Bcl-2-associated athanogene (BAG) family is an evolutionarily conserved, multifunctional group of co-chaperones regulators that modulate a number of diverse processes. PlantBAGgenes were identified to play an extensive role in processes of programmed cell death (PCD) ranging from growth and development to stress responses. In this study, we identifiedBAGgenes from different photosynthetic organisms in order to gather evolutionary insights on these proteins followed by anin silicocharacterization of theBAGfamily in the bryophytePhyscomitrium patens. Ten putativePpBAGsharbouring a characteristic BAG domain were grouped into two subfamilies based on the presence of additional conserved domains and phylogenetic distances. Group I consisted of PpBAG4 and PpBAG5, containing an additional ubiquitin-like domain, and PpBAG10 with only the BAG domain. Group II consisted of PpBAG1–3 and PpBAG6-9, containing a calmodulin-binding IQ motif, a novel feature associated with plant BAG proteins. Interestingly, PpBAG9 exhibits an EF-Hand domain, not reported to date in this class of proteins. Caspase cleavage sites in PpBAG1, PpBAG3, PpBAG4-5 and PpBAG9 were predicted.In silicoanalysis ofBAGgenes revealed the presence of stress responsive elements, and a stress-regulated expression pattern which appears to be dependent on specifically organized promoter regulatory elements. According to our analyses, the present data suggest that some members ofP. patens BAGgene family may play a role in heat responses, autophagy and pathogen immunity. Further studies are required to unveil the role of specific members of this gene family in PCD and stress responses inP. patens.

Key message

Genome-wide identification and phylogenetic relationships combined within silicogene-expression profiling and protein-interaction analysis of PpBAGs inPhyscomitrium patens, highlight the importance of a particular set in stress tolerance.
cDC1 and interferons promote spontaneous CD4+and CD8+T cell protective responses to breast cancer
Authors: Mattiuz Raphaël , Brousse Carine , Ambrosini Marc , Cancel Jean-Charles , Bessou Gilles , Mussard Julie , Sanlaville Amélien , Caux Christophe , Bendriss-Vermare Nathalie , Valladeau-Guilemond Jenny , Dalod Marc , Crozat Karine
Published: December 2020

Here we show that efficient breast cancer immunosurveillance relies on cDC1, conventional CD4+T cells, CD8+cytotoxic T lymphocytes (CTL) and later NK/NK T cells. For this process, cDC1 were required constitutively, but especially during the T cell priming phase. In the tumor microenvironment, cDC1 interacted physically and jointly with both CD4+T cells and tumorspecific CD8+T cells. We found that interferon (IFN) responses were necessary for the rejection of breast cancer, including cDC1-intrinsic signaling by IFN-γ and STAT1. Surprisingly, cell-intrinsic IFN-I signaling in cDC1 was not required. cDC1 and IFNs shaped the tumor immune landscape, notably by promoting CD4+and CD8+T cell infiltration, terminal differentiation and effector functions. XCR1, CXCL9, IL-12 and IL-15 were individually dispensable for breast cancer immunosurveillance. Consistent with our experimental results in mice, high expression in the tumor microenvironment of genes specific to cDC1, CTL, helper T cells or interferon responses are associated with a better prognosis in human breast cancer patients. Our results show that immune control of breast cancer depends on cDC1 and IFNs as previously reported for immunogenic melanoma or fibrosarcoma tumor models, but that the underlying mechanism differ. Revisiting cDC1 functions in the context of spontaneous immunity to cancer should help defining new ways to mobilize cDC1 functions to improve already existing immunotherapies for the benefits of patients.

Synopsis

Type 1 conventional dendritic cells cross-present tumor antigens to CD8+T cells. Understanding the regulation of their antitumor functions is important. Cell-intrinsic STAT1/IFN-γ signaling licenses them for efficient CD4+and CD8+T cell activation during breast cancer immunosurveillance.
The Prevalence of the Val66Met Polymorphism in Musicians: Possible Evidence for Compensatory Neuroplasticity from a pilot study
Authors: Henechowicz T.L. , Chen J.L. , Cohen L.G. , Thaut M.H.
Published: December 2020

It has been reported that MET carriers may express deficits in motor learning and neuroplasticity, possibly deterring musicianship. Here, we compared the prevalence of the Val66Met Brain-derived Neurotrophic Factor single nucleotide polymorphism (rs6265) in a sample of musicians (N=50) and an ethnically matched subset from the 1000 Human Genome Project (N-424). We report no differences in genotype or allele frequencies. Results are consistent with the view that hypothesized Met-dependent deficits in neuroplasticity are either mild or can be overcome by long-term practice.
Amblyomma mixtumfree-living stages: Summer and winter use, preference, and niche width in an agroecosystem (Yopal, Casanare, Colombia)
Authors: Forero-Becerra Elkin , Acosta Alberto , Benavides Efraín , Hidalgo Marylin
Published: December 2020

Studying a species’ tolerance to an ecosystem’s environmental conditions and its selection of available resources is relevant in ecological and evolutionary terms. Moreover, formulation of effective control strategies implicitly includes the study of habitat use and preference and niche width in anthropogenically transformed natural landscapes. Here, we evaluated whether the use, habitat preference, and niche range of theAmblyomma mixtumtick changed between stages, habitats, and seasons (summer-winter 2019) on a farm in Yopal (Casanare, Colombia). To this end, the presence and relative abundance of larvae, nymphs, and free-living adults was quantified in four different habitats according to the type of vegetation cover (Riparian Forest, Cocoa Crop, King Grass Crop, and Star Grass Paddock). Habitat availability was calculated, environmental variables were analyzed, and various indices of habitat use and preference and niche width were calculated.A. mixtum’s habitat use and preference and niche width changed between stages, habitat types, and time of the year. The total abundance ofA. mixtumwas an order of magnitude greater in summer than winter. Nymphs and larvae dominated it in the summer and adults in the winter. In summer, all the stages used the four habitats. In winter, the larvae did not use two habitats (Riparian Forest and Cocoa Crop); nymphs did not use the cocoa crop.A. mixtumadults used all the habitats in both seasons. In summer, the nymphs and larvae preferred three of the four habitats (King Grass Crop, Star Grass Paddock, and Cocoa Crops), while adults preferred the King Grass Crop. In winter, the nymphs and larvae preferred the King Grass Crop and Star Grass Paddock, while the adults preferred the King Grass Crop. The value of the niche width index was high for larvae, nymphs, and adults in summer, while it was high only for adults in winter.A. mixtumis exposed to significant daily, seasonal, and multiannual variations in relative humidity (minimum 30%), ambient temperature (minimum 18°C), solar radiation (maximum 800 W/m2), and precipitation (maximum 481 mm/month). Thus, the localA. mixtumpopulation could rapidly acclimatize to changing habitats (unstable or temporary) under fluctuating environmental conditions (e.g., King Grass Crop). However, the winter flood season in Yopal could exceedA. mixtum’s adaptive capacity during its most vulnerable stages. Mathematically, a low number of femaleA. mixtum, surviving the most demanding environmental conditions, could sufficiently ensure the population’s persistence, which, coupled with the vast host range, could facilitate the ticks stages’ dispersal among habitats to complete their life cycle.A. mixtum’s population control should be carried out during its season of greater vulnerability (winter), when the population is low, particularly the females.
Cisplatin-inducible death receptor 5 antisense long non-coding RNA modulates cell cycle and proliferation in HeLa cells
Authors: Gürer Dilek Cansu , Erdoğan İpek , Ahmadov Ulvi , Sweef Osama , Akgül Bünyamin
Published: December 2020

Cisplatin is a chemotherapeutic drug with pleiotropic effects known to modulate the expression of long non-coding RNAs (lncRNAs). With the annotation of many novel lncRNAs, it is imperative to employ a more comprehensive approach to identify cisplatin-mediated changes in the expression of lncRNAs. Next generation sequencing (NGS)-based profiling of total RNAs from cisplatin-treated HeLa cells identified 3489 expressed lncRNAs, of which 1930 and 1051 were up- and downregulated upon cisplatin treatment, respectively. For functional analyses, we selected one of the cisplatin inducible lncRNAs situated antisense to the death receptor 5 and thus named death receptor 5 antisense lncRNA (DR5-AS). Knock-down of DR5-AS lncRNA caused a morphological change in cell shape without inducing any cell death. A second round of NGS-based profiling of total RNAs from DR5-AS-silenced cells revealed differential expression of genes associated with the immune system and cell cycle. Further analyses showed that DR5-AS reduces cell proliferation and causes a cell cycle arrest at S and G2/M phases. These results suggest that cisplatin-mediated reduction in cell proliferation and cell cycle may be mediated by long non-coding RNAs.

Significance

Cisplatin is known to induce DNA-damage-induced cell death, which is used in combination chemotherapies in various cancer types. However, many patients develop resistance to cisplatin, which involves both protein-coding and noncoding genes. Although a number of long noncoding RNAs are linked to cisplatin resistance, a more comprehensive study is required. In this study, we took advantage of next-generation-sequencing based lncRNA profiling to unveil the extent of cisplatin inducible lncRNAs in HeLa cells. Additionally, we functionally characterized one of the cisplatin-inducible lncRNA, death receptor 5 antisense. Interestingly, this spesific lncRNA modulates cell morphology, proliferation and cell cycle without affecting cell death.
Vangl2 regulates the dynamics of Wnt cytonemes in vertebrates
Authors: Brunt Lucy , Greicius Gediminas , Evans Benjamin D , Virshup David M , Wedgwood Kyle CA , Scholpp Steffen
Published: December 2020

The Wnt signalling network regulates cell proliferation and cell differentiation as well as migration and polarity in development of multicellular organisms. However, it is still unclear how distribution of Wnt ligands is precisely controlled to fulfil all of these different functions. Here, we show that the four-pass transmembrane protein Vangl2 occupies a central role in determining the distribution of Wnt by cytonemes in vertebrate tissue. In zebrafish epiblast cells, mouse intestinal telocytes and human gastric cancer cells, activation of Vangl2 leads to the generation of fewer but extremely long cytonemes, which start to branch and deliver Wnt protein to multiple cells. The Vangl2-activated cytonemes increase Wnt/β-catenin signalling in the surrounding cells. Concordantly, inhibition of Vangl2 function leads to the formation of shorter cytonemes and reduced paracrine Wnt/β-catenin signal activation. A mathematical model simulating the observed Vangl2 functions on cytonemes in zebrafish gastrulation predicts an anterior shift of the morphogenetic signalling gradient, altered tissue patterning, and a loss of the sharpness of tissue domains. We confirmed these predictions during anteroposterior patterning in the zebrafish neural plate. In summary, we show that Vangl2 - a core member of the PCP signalling component - is fundamental to paracrine Wnt/β-catenin signalling by controlling cytoneme behaviour in vertebrate development and tissue homeostasis.
Ecm29-dependent proteasome localization regulates cytoskeleton remodeling at the immune synapse
Authors: Ibañez-Vega Jorge , Valle Felipe Del , Saez Juan José , Diaz Jheimmy , Soza Andrea , Yuseff María Isabel
Published: December 2020

The formation of an immune synapse (IS) enables B cells to capture membrane-tethered antigens, where cortical actin cytoskeleton remodeling regulates cell spreading and depletion of F-actin at the centrosome promotes the recruitment of lysosomes to facilitate antigen extraction. How B cells regulate both pools of actin, remains poorly understood. We report here that decreased F-actin at the centrosome and IS relies on the distribution of the proteasome, regulated by Ecm29. Silencing Ecm29 decreases the proteasome pool associated to the centrosome of B cells and shifts its accumulation to the cell cortex and IS. Accordingly, Ecm29-silenced B cells display increased F-actin at the centrosome, impaired centrosome and lysosome repositioning to the IS and defective antigen extraction and presentation. Ecm29-silenced B cells, which accumulate higher levels of proteasome at the cell cortex, display decreased actin retrograde flow in lamellipodia and enhanced spreading responses. Our findings support a model where B the asymmetric distribution of the proteasome, mediated by Ecm29, coordinates actin dynamics at the centrosome and the IS, promoting lysosome recruitment and cell spreading.
Receptor-linked environment-sensitive probe monitors the local membrane environment surrounding the insulin receptor
Authors: Umebayashi Miwa , Takemoto Satoko , Reymond Luc , Sundukova Mayya , Hovius Ruud , Bucci Annalisa , Heppenstall Paul A. , Yokota Hideo , Johnsson Kai , Riezman Howard
Published: December 2020

Functional membrane proteins in the plasma membrane are suggested to have specific membrane environments that play important roles to maintain and regulate the function of proteins. However, the local membrane environments of membrane proteins remain largely unexplored due to the lack of techniques allowing to monitor them in living cells. We have developed a method to probe the local membrane environment surrounding a membrane protein in the plasma membrane by covalently tethering a solvatochromic, environment-sensitive dye, Nile red, to a membrane protein via a flexible linker. Our direct imaging reported on the spatio-temporal properties of membrane fluidity of the local environment surrounding the insulin receptor. The local environment was distinct from the average plasma membrane fluidity and was quite dynamic and heterogeneous. Upon addition of insulin, the local membrane environment surrounding the receptor increased in fluidity in an insulin receptor-kinase dependent manner. This new technology should allow researchers to examine changes in membrane properties caused by receptor activation and devise ways to address the role of these changes in physiological processes.
Single cell analysis of blood mononuclear cells stimulated through CD3 and CD28 shows collateral activation of B and NK cells and demise of monocytes
Authors: Lawlor Nathan , Nehar-Belaid Djamel , Grassmann Jessica D.S. , Stoeckius Marlon , Smibert Peter , Stitzel Michael L. , Pascual Virginia , Banchereau Jacques , Williams Adam , Ucar Duygu
Published: December 2020

Immune cell activation assays have been widely used for immune monitoring and for understanding disease mechanisms. However, these assays are typically limited in scope. A holistic study of circulating immune cell responses to different activators is lacking. Here we developed a cost-effective high-throughput multiplexed single-cell RNA-seq combined with epitope tagging (CITE-seq) to determine how classic activators of T cells (anti-CD3 coupled with anti-CD28) or monocytes (LPS) alter the cell composition and transcriptional profiles of peripheral blood mononuclear cells (PBMCs) from healthy human donors. Anti-CD3/CD28 treatment activated all classes of lymphocytes either directly (T cells) or indirectly (B and NK cells) but reduced monocyte numbers. Activated T and NK cells expressed senescence and effector molecules, whereas activated B cells transcriptionally resembled autoimmune disease- or age-associated B cells (e.g., CD11c, T-bet). In contrast, LPS specifically targeted monocytes and induced two main states: early activation characterized by the expression of chemoattractants and a later pro-inflammatory state characterized by expression of effector molecules. These data provide a foundation for future immune activation studies with single cell technologies (https://czi-pbmc-cite-seq.jax.org/).

Graphical abstract
A hypothesis for theta rhythm frequency control in CA1 microcircuits
Authors: Skinner Frances K , Rich Scott , Lunyov Anton R , Lefebvre Jeremie , Chatzikalymniou Alexandra P
Published: December 2020

Computational models of neural circuits with varying levels of biophysical detail have been generated in pursuit of an underlying mechanism explaining the ubiquitous hippocampal theta rhythm. However, within the theta rhythm are at least two types with distinct frequencies associated with different behavioural states, an aspect that must be considered in pursuit of these mechanistic explanations. Here, using our previously developed excitatory-inhibitory network models that generate theta rhythms, we investigate the robustness of theta generation to intrinsic neuronal variability by building a database of heterogeneous excitatory cells and implementing them in our microcircuit model. We specifically investigate the impact of three key ‘building block’ features of the excitatory cell model that underlie our model design: these cells’ rheobase, their capacity for post-inhibitory rebound, and their spike-frequency adaptation. We show that theta rhythms at various frequencies can arise dependent upon the combination of these building block features, and we find that the speed of these oscillations are dependent upon the excitatory cells’ response to inhibitory drive, as encapsulated by their phase response curves. Taken together, these findings support a hypothesis for theta frequency control that includes two aspects: (i) an internal mechanism that stems from the building block features of excitatory cell dynamics; (ii) an external mechanism that we describe as ‘inhibition-based tuning’ of excitatory cell firing. We propose that these mechanisms control theta rhythm frequencies and underlie their robustness.
Bacteriophage infection produces membrane vesicles inEscherichia colivia both explosive cell lysis and membrane blebbing
Authors: Mandal Pappu K. , Ballerin Giulia , Nolan Laura M. , Petty Nicola K. , Whitchurch Cynthia B.
Published: December 2020

Membrane Vesicles (MVs) are membrane-bound spherical nanostructures that prevail in all three domains of life. In Gram-negative bacteria, MVs are thought to be produced through blebbing of the outer membrane and are often referred to as outer membrane vesicles (OMVs). We have recently described another mechanism of MV biogenesis inPseudomonas aeruginosathat involves explosive cell lysis events which shatters cellular membranes into fragments that rapidly anneal into MVs. Interestingly, MVs are often observed within preparations of lytic bacteriophage, however the source of these MVs and their association with bacteriophage infection has not been explored. In this study we aimed to determine if MV biogenesis is associated with lytic bacteriophage infection. Live super-resolution microscopy demonstrated that explosive cell lysis ofE. colicells infected with either bacteriophage T4 or T7, produced MVs derived from shattered membrane fragments. Infection by either bacteriophage was also associated with the formation of membrane blebs on intact bacteria. TEM revealed multiple classes of MVs within phage lysates, consistent with multiple mechanisms of MV biogenesis. These findings suggest that bacteriophage infection may be a major contributor to the abundance of bacterial MVs in nature.
Temporal resolution relates to sensory hyperreactivity independently of stimulus detection sensitivity in individuals with autism spectrum disorder
Authors: Yaguchi Ayako , Atsumi Takeshi , Fukatsu Reiko , Ide Masakazu
Published: December 2020

Background

Researchers have been focused on perceptual characteristics of autism spectrum disorder (ASD) in terms of sensory hyperreactivity. Previously, we demonstrated that temporal resolution, which is the accuracy in differentiating the order of two successive vibrotactile stimuli, is associated with the severity of sensory hyperreactivity (Ide et al. 2019). Herein, we examined whether an increase in the perceptual intensity of a tactile stimulus, despite its short duration, is derived from high temporal resolution and a high frequency of sensory temporal summation.

Method

Sixteen participants with ASD and fifteen typically developing (TD) participants performed two psychophysical experimental tasks, and we evaluated the detectable duration of vibrotactile stimuli with the same amplitude and temporal resolution. Sensory hyperreactivity was estimated using a self-reported questionnaire.

Results

There was no relationship between temporal resolution and the duration of detectable stimuli in either group. However, the ASD group showed more severe sensory hyperreactivity in daily life than the TD group did, and ASD participants with severe sensory hyperreactivity tended to have high temporal resolution but not high sensitivity for detectable duration.

Conclusion

Contrary to our hypothesis, there might be different processing between temporal resolution and sensitivity for stimulus detection. Sensory reactivity in daily life would not be based on sensitivity for stimulus detection measured in an experimental task, and we suggest that atypical temporal processing would affect sensory reactivity in ASD. Keywords (within 6 keywords): Temporal resolution, Temporal summation, Autism spectrum disorder, Hyperreactivity, Gap detection