Ecotoxicol Environ Saf. 2023 Jul 11;263:115242. doi: 10.1016/j.ecoenv.2023.115242. Online ahead of print.

ABSTRACT

Erythromycin (ERY) is a typical macrolide antibiotic with large production and extensive use on a global scale. Detection of ERY in both freshwaters and coaster seawaters, as well as relatively high ecotoxicity of ERY have been documented. Notably, hormesis has been reported on several freshwater algae under ERY stress, where growth was promoted at relatively lower exposures but inhibited at higher treatment levels. On the contrary, there is limited information of ERY toxicity in marine algae, hampering the risk assessment on ERY in the coaster waters. The presence of hormesis may challenge the current concept of dose-response adopted in chemical risk assessment. Whether and how exposure to ERY can induce dose-dependent toxicity in marine algae remain virtually unknown, especially at environmentally relevant concentrations. The present study used a model marine diatom Thalassiosira weissflogii (T. weissflogii) to reveal its toxicological responses to ERY at different biological levels and decipher the underlying mechanisms. Assessment of multiple apical endpoints shows an evident growth promotion following ERY exposure at an environmentally relevant concentration (1 µg/L), associated with increased contents reactive oxygen species (ROS) and chlorophyll-a (Chl-a), activated signaling pathways related to ribosome biosynthesis and translation, and production of total soluble protein. By contrast, growth inhibition in the 750 and 2500 µg/L treatments was attributed to reduced viability, increased ROS formation, reduced content of total soluble protein, inhibited photosynthesis, and perturbed signaling pathways involved in xenobiotic metabolism, ribosome, metabolism of amino acid, and nitrogen metabolism. Measurements of multiple apical endpoints coupled with de novo transcriptomics analysis applied in the present study, a systems biology approach, can generate detailed mechanistic information of chemical toxicity including dose-response and species sensitivity difference used in environmental risk assessment.

PMID:37441949 | DOI:10.1016/j.ecoenv.2023.115242

Comput Methods Programs Biomed. 2023 Jul 6;240:107697. doi: 10.1016/j.cmpb.2023.107697. Online ahead of print.

ABSTRACT

MOTIVATION: Personalized decision-making for cancer therapy relies on molecular profiling from sequencing data in combination with database evidence and expert knowledge. Molecular tumor boards (MTBs) bring together clinicians and scientists with diverse expertise and are increasingly established in the clinical routine for therapeutic interventions. However, the analysis and documentation of patients data are still time-consuming and difficult to manage for MTBs, especially as few tools are available for the amount of information required.

RESULTS: To overcome these limitations, we developed an interactive web application AMBAR (Alteration annotations for Molecular tumor BoARds), for therapeutic decision-making support in MTBs. AMBAR is an R shiny-based application that allows customization, interactive filtering, visualization, adding expert knowledge, and export to clinical systems of annotated mutations.

AVAILABILITY: AMBAR is dockerized, open source and available at https://sysbio.uni-ulm.de/?Software:Ambar Contact:hans.kestler@uni-ulm.de.

PMID:37441893 | DOI:10.1016/j.cmpb.2023.107697

Curr Opin Genet Dev. 2023 Jul 11;81:102087. doi: 10.1016/j.gde.2023.102087. Online ahead of print.

ABSTRACT

Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations.

PMID:37441873 | DOI:10.1016/j.gde.2023.102087

J Hazard Mater. 2023 Jul 10;458:132023. doi: 10.1016/j.jhazmat.2023.132023. Online ahead of print.

ABSTRACT

Plastic waste is considered a major threat for terrestrial, marine and freshwater ecosystems. Ingestion of primary or secondary microparticles resulting from plastic degradation can lead to their trophic transfer raising serious health concerns. In this study, the effect of amine and carboxy functionalized polystyrene microparticles on the physiology of daphnids was investigated with a combination of phenotypic and metabolic endpoints. Carboxy functionalized microparticles showed higher toxicity in acute exposures compared to their amine counterparts. Accumulation of both microparticles in animal gut was confirmed by stereo-microscopy as well as fluorescent microscopy which showed no presence of particles in the rest of the animal. Fluorescence based quantification of microparticles extracted from animal lysates validated their concentration-dependent uptake. Additionally, exposure of daphnids to amine and carboxy functionalized microparticles resulted in increased activities of key enzymes related to metabolism and detoxification. Finally, significant metabolic perturbations were discovered following exposure to microplastics. These findings suggest that polystyrene microparticles can hinder organism performance of the freshwater species and highlight the importance of seeking for holistic and physiological endpoints for pollution assessment.

PMID:37441864 | DOI:10.1016/j.jhazmat.2023.132023

Microlife. 2023 May 31;4:uqad028. doi: 10.1093/femsml/uqad028. eCollection 2023.

ABSTRACT

Studies of protein-protein interactions in membranes are very important to fully understand the biological function of a cell. The extraction of proteins from the native membrane environment is a critical step in the preparation of membrane proteins that might affect the stability of protein complexes. In this work, we used the amphiphilic diisobutylene/maleic acid copolymer to extract the membrane proteome of the opportunistic pathogen Pseudomonas aeruginosa, thereby creating a soluble membrane-protein library within a native-like lipid-bilayer environment. Size fractionation of nanodisc-embedded proteins and subsequent mass spectrometry enabled the identification of 3358 proteins. The native membrane-protein library showed a very good overall coverage compared to previous proteome data. The pattern of size fractionation indicated that protein complexes were preserved in the library. More than 20 previously described complexes, e.g. the SecYEG and Pili complexes, were identified and analyzed for coelution. Although the mass-spectrometric dataset alone did not reveal new protein complexes, combining pulldown assays with mass spectrometry was successful in identifying new protein interactions in the native membrane-protein library. Thus, we identified several candidate proteins for interactions with the membrane phosphodiesterase NbdA, a member of the c-di-GMP network. We confirmed the candidate proteins CzcR, PA4200, SadC, and PilB as novel interaction partners of NbdA using the bacterial adenylate cyclase two-hybrid assay. Taken together, this work demonstrates the usefulness of the native membrane-protein library of P. aeruginosa for the investigation of protein interactions and membrane-protein complexes. Data are available via ProteomeXchange with identifiers PXD039702 and PXD039700.

PMID:37441524 | PMC:PMC10335732 | DOI:10.1093/femsml/uqad028

Front Endocrinol (Lausanne). 2023 Jun 27;14:1170459. doi: 10.3389/fendo.2023.1170459. eCollection 2023.

ABSTRACT

INTRODUCTION: The gut microbiota (GM) dysbiosis is one of the causal factors for the progression of different chronic metabolic diseases, including type 2 diabetes mellitus (T2D). Understanding the basis that laid this association may lead to developing new therapeutic strategies for preventing and treating T2D, such as probiotics, prebiotics, and fecal microbiota transplants. It may also help identify potential early detection biomarkers and develop personalized interventions based on an individual's gut microbiota profile. Here, we explore how supervised Machine Learning (ML) methods help to distinguish taxa for individuals with prediabetes (prediabetes) or T2D.

METHODS: To this aim, we analyzed the GM profile (16s rRNA gene sequencing) in a cohort of 410 Mexican naïve patients stratified into normoglycemic, prediabetes, and T2D individuals. Then, we compared six different ML algorithms and found that Random Forest had the highest predictive performance in classifying T2D and prediabetes patients versus controls.

RESULTS: We identified a set of taxa for predicting patients with T2D compared to normoglycemic individuals, including Allisonella, Slackia, Ruminococus_2, Megaspgaera, Escherichia/Shigella, and Prevotella, among them. Besides, we concluded that Anaerostipes, Intestinibacter, Prevotella_9, Blautia, Granulicatella, and Veillonella were the relevant genus in patients with prediabetes compared to normoglycemic subjects.

DISCUSSION: These findings allow us to postulate that GM is a distinctive signature in prediabetes and T2D patients during the development and progression of the disease. Our study highlights the role of GM and opens a window toward the rational design of new preventive and personalized strategies against the control of this disease.

PMID:37441494 | PMC:PMC10333697 | DOI:10.3389/fendo.2023.1170459

Front Microbiol. 2023 Jun 12;14:1188526. doi: 10.3389/fmicb.2023.1188526. eCollection 2023.

ABSTRACT

Viruses and tumors are two pathologies that negatively impact human health, but what occurs when a virus encounters a tumor? A global consensus among cancer patients suggests that surgical resection, chemotherapy, radiotherapy, and other methods are the primary means to combat cancer. However, with the innovation and development of biomedical technology, tumor biotherapy (immunotherapy, molecular targeted therapy, gene therapy, oncolytic virus therapy, etc.) has emerged as an alternative treatment for malignant tumors. Oncolytic viruses possess numerous anti-tumor properties, such as directly lysing tumor cells, activating anti-tumor immune responses, and improving the tumor microenvironment. Compared to traditional immunotherapy, oncolytic virus therapy offers advantages including high killing efficiency, precise targeting, and minimal side effects. Although oncolytic virus (OV) therapy was introduced as a novel approach to tumor treatment in the 19th century, its efficacy was suboptimal, limiting its widespread application. However, since the U.S. Food and Drug Administration (FDA) approved the first OV therapy drug, T-VEC, in 2015, interest in OV has grown significantly. In recent years, oncolytic virus therapy has shown increasingly promising application prospects and has become a major research focus in the field of cancer treatment. This article reviews the development, classification, and research progress of oncolytic viruses, as well as their mechanisms of action, therapeutic methods, and routes of administration.

PMID:37440883 | PMC:PMC10335770 | DOI:10.3389/fmicb.2023.1188526

Front Microbiol. 2023 Jun 27;14:1158784. doi: 10.3389/fmicb.2023.1158784. eCollection 2023.

ABSTRACT

INTRODUCTION: Agricultural productivity in the arid hot desert climate of UAE is limited by the unavailability of water, high temperature, and salt stresses. Growing enough food under abiotic stresses and decreasing reliance on imports in an era of global warming are a challenge. Biochar with high water and nutrient retention capacity and acid neutralization activity is an attractive soil conditioner. This study investigates the microbial community in the arid soil of Dubai under shade house conditions irrigated with saline water and the shift in the microbial community, following 1 year of amendment with indigenously prepared biochar from date palm waste.

METHODS: Amplicon sequencing was used to elucidate changes in bacterial, archaeal, and fungal community structures in response to long-term biochar amendment. Samples were collected from quinoa fields receiving standard NPK doses and from fields receiving 20 and 30 tons ha-1 of biochar, in addition to NPK for 1 year. Water holding capacity, pH, electrical conductivity, calcium, magnesium, chloride, potassium, sodium, phosphorus, total carbon, organic matter, and total nitrogen in the soil from biochar-treated and untreated controls were determined.

RESULTS AND DISCUSSION: The results show that soil amendment with biochar helps retain archaeal and bacterial diversity. Analysis of differentially abundant bacterial and fungal genera indicates enrichment of plant growth-promoting microorganisms. Interestingly, many of the abundant genera are known to tolerate salt stress, and some observed genera were of marine origin. Biochar application improved the mineral status and organic matter content of the soil. Various physicochemical properties of soil receiving 30 tons ha-1 of biochar improved significantly over the control soil. This study strongly suggests that biochar helps retain soil fertility through the enrichment of plant growth-promoting microorganisms.

PMID:37440878 | PMC:PMC10335804 | DOI:10.3389/fmicb.2023.1158784

Science. 2023 Jul 14;381(6654):231-239. doi: 10.1126/science.abq3061. Epub 2023 Jul 13.

ABSTRACT

Atrial fibrillation disrupts contraction of the atria, leading to stroke and heart failure. We deciphered how immune and stromal cells contribute to atrial fibrillation. Single-cell transcriptomes from human atria documented inflammatory monocyte and SPP1+ macrophage expansion in atrial fibrillation. Combining hypertension, obesity, and mitral valve regurgitation (HOMER) in mice elicited enlarged, fibrosed, and fibrillation-prone atria. Single-cell transcriptomes from HOMER mouse atria recapitulated cell composition and transcriptome changes observed in patients. Inhibiting monocyte migration reduced arrhythmia in Ccr2-∕- HOMER mice. Cell-cell interaction analysis identified SPP1 as a pleiotropic signal that promotes atrial fibrillation through cross-talk with local immune and stromal cells. Deleting Spp1 reduced atrial fibrillation in HOMER mice. These results identify SPP1+ macrophages as targets for immunotherapy in atrial fibrillation.

PMID:37440641 | DOI:10.1126/science.abq3061

Cell Rep. 2023 Jul 12;42(7):112780. doi: 10.1016/j.celrep.2023.112780. Online ahead of print.

ABSTRACT

Protective immunity following vaccination is sustained by long-lived antibody-secreting cells and resting memory B cells (MBCs). Responses to two-dose SARS-CoV-2 mRNA-1273 vaccination are evaluated longitudinally by multimodal single-cell analysis in three infection-naïve individuals. Integrated surface protein, transcriptomics, and B cell receptor (BCR) repertoire analysis of sorted plasmablasts and spike+ (S-2P+) and S-2P- B cells reveal clonal expansion and accumulating mutations among S-2P+ cells. These cells are enriched in a cluster of immunoglobulin G-expressing MBCs and evolve along a bifurcated trajectory rooted in CXCR3+ MBCs. One branch leads to CD11c+ atypical MBCs while the other develops from CD71+ activated precursors to resting MBCs, the dominant population at month 6. Among 12 evolving S-2P+ clones, several are populated with plasmablasts at early timepoints as well as CD71+ activated and resting MBCs at later timepoints, and display intra- and/or inter-cohort BCR convergence. These relationships suggest a coordinated and predictable evolution of SARS-CoV-2 vaccine-generated MBCs.

PMID:37440409 | DOI:10.1016/j.celrep.2023.112780

Plant Cell. 2023 Jul 13:koad141. doi: 10.1093/plcell/koad141. Online ahead of print.

ABSTRACT

ADAPTOR-ASSOCIATED PROTEIN KINASE1 (AAK1) is a known regulator of clathrin-mediated endocytosis in mammals. Human AAK1 phosphorylates the μ2 subunit of the ADAPTOR PROTEIN-2 (AP-2) complex (AP2M) and plays important roles in cell differentiation and development. Previous interactome studies discovered the association of AAK1 with AP-2 in Arabidopsis (Arabidopsis thaliana), but its function was unclear. Here, genetic analysis revealed that the Arabidopsis aak1 and ap2m mutants both displayed altered root tropic growth, including impaired touch- and gravity-sensing responses. In Arabidopsis, AAK1-phosphorylated AP2M on Thr-163, and expression of the phospho-null version of AP2M in the ap2m mutant led to an aak1-like phenotype, whereas the phospho-mimic forms of AP2M rescued the aak1 mutant. In addition, we found that the AAK1-dependent phosphorylation state of AP2M modulates the frequency distribution of endocytosis. Our data indicate that the phosphorylation of AP2M on Thr-163 by AAK1 fine-tunes endocytosis in the Arabidopsis root to control its tropic growth.

PMID:37440281 | DOI:10.1093/plcell/koad141

J Biomol Struct Dyn. 2023 Jul 13:1-19. doi: 10.1080/07391102.2023.2231544. Online ahead of print.

ABSTRACT

Xiaoyao san (XYS) plays an important role in treatment of non-alcoholic fatty liver disease (NAFLD) with liver stagnation and spleen deficiency, but its specific mechanism is still unclear. This study aimed to investigate the material basis and mechanism by means of network pharmacology, metabolomics, systems biology and molecular docking methods. On this basis, NAFLD rat model with liver stagnation and spleen deficiency was constructed and XYS was used to intervene, and liver histopathology, biochemical detection, enzyme-linked immunosorbent assay, quantitative PCR assay and western blotting were used to further verify the mechanism. Through the above research methods, network pharmacology study showed that there were 94 targets in total for XYS in the treatment of NAFLD. Metabolomics study showed that NAFLD with liver depression and spleen deficiency had a total of 73 differential metabolites. Systems biology found that PTGS2 and PPARG were the core targets; Quercetin, kaempferol, naringenin, beta-sitosterol and stigmasterol were the core active components; AA, cAMP were the core metabolites. And molecular docking showed that the core active components can act well on the key targets. Animal experiments showed that XYS could improve liver histopathology, increase 5HT and NA, decrease INS and FBG, improve blood lipids and liver function, decrease AA, increase cAMP, down-regulate PTGS2, up-regulate PPARG, and decrease PGE2 and 15d-PGJ2. In conclusion, XYS might treat NAFLD with liver depression and spleen deficiency by down-regulating PTGS2, up-regulating PPARG, reducing AA content, increasing cAMP, improving insulin resistance, affecting glucose and lipid metabolism, inhibiting oxidative stress and inflammatory response.Communicated by Ramaswamy H. Sarma.

PMID:37440274 | DOI:10.1080/07391102.2023.2231544

Adv Exp Med Biol. 2023;1415:165-171. doi: 10.1007/978-3-031-27681-1_25.

ABSTRACT

Inherited retinal degenerations (IRDs) are clinically and genetically heterogenous blinding diseases that manifest through dysfunction of target cells, photoreceptors, and retinal pigment epithelium (RPE) in the retina. Despite knowledge of numerous underlying genetic defects, current therapeutic approaches, including gene centric applications, have had limited success, thereby asserting the need of new directions for basic and translational research. Human diseases have commonalities that can be represented in a network form, called diseasome, which captures relationships among disease genes, proteins, metabolites, and patient meta-data. Clinical and genetic information of IRDs suggest shared relationships among pathobiological factors, making these a model case for network medicine. Characterization of the diseasome would considerably improve our understanding of retinal pathologies and permit better design of targeted therapies for disrupted regions within the integrated disease network. Network medicine in synergy with the ongoing artificial intelligence revolution can boost therapeutic developments, especially gene agnostic treatment opportunities.

PMID:37440030 | DOI:10.1007/978-3-031-27681-1_25

mSystems. 2023 Jul 13:e0020623. doi: 10.1128/msystems.00206-23. Online ahead of print.

ABSTRACT

Contamination of hospital sinks with microbial pathogens presents a serious potential threat to patients, but our understanding of sink colonization dynamics is largely based on infection outbreaks. Here, we investigate the colonization patterns of multidrug-resistant organisms (MDROs) in intensive care unit sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. Using culture-based methods, we recovered 822 bacterial isolates representing 104 unique species and genomospecies. Genomic analyses revealed long-term colonization by Pseudomonas spp. and Serratia marcescens strains across multiple rooms. Nanopore sequencing uncovered examples of long-term persistence of resistance-conferring plasmids in unrelated hosts. These data indicate that antibiotic resistance (AR) in Pseudomonas spp. is maintained both by strain colonization and horizontal gene transfer (HGT), while HGT maintains AR within Acinetobacter spp. and Enterobacterales, independent of colonization. These results emphasize the importance of proactive, genomic-focused surveillance of built environments to mitigate MDRO spread. IMPORTANCE Hospital sinks are frequently linked to outbreaks of antibiotic-resistant bacteria. Here, we used whole-genome sequencing to track the long-term colonization patterns in intensive care unit (ICU) sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. We analyzed 822 bacterial genomes, representing over 100 different species. We identified long-term contamination by opportunistic pathogens, as well as transient appearance of other common pathogens. We found that bacteria recovered from the ICU had more antibiotic resistance genes (ARGs) in their genomes compared to matched community spaces. We also found that many of these ARGs are harbored on mobilizable plasmids, which were found shared in the genomes of unrelated bacteria. Overall, this study provides an in-depth view of contamination patterns for common nosocomial pathogens and identifies specific targets for surveillance.

PMID:37439570 | DOI:10.1128/msystems.00206-23

Analyst. 2023 Jul 13. doi: 10.1039/d3an00817g. Online ahead of print.

ABSTRACT

Angiogenesis is one of the most essential developmental processes and plays a key role in organogenesis and tumorigenesis in which epithelial cells proliferate and migrate, thus resulting in sprouting and extension of the existing vasculature. The study of angiogenesis in vivo is limited by difficulties related to imaging of the fine structure of vascular sprouting within non-transparent bulk tissue. Thus, many model systems have been proposed in recent years. However, to meet the urgent need for high-throughput studies and screening, further improvements are still required, particularly in terms of scaling-up. In this study, we combined microchip fabrication with the culture of three-dimensional (3D) spheroids, thus providing a platform for 3D multilayer angiogenesis-on-a-chip. Using this platform, we investigated the precise effects of vascular endothelial growth factor (VEGF) on angiogenesis. In comparison with two-dimensional (2D) angiogenesis assays, our 3D angiogenesis platform demonstrated superior sprouting and provided proof of concept that our 3D biomimetic angiogenesis-on-a-chip could serve as a powerful tool for pro- or anti-angiogenesis candidate drug screening.

PMID:37439439 | DOI:10.1039/d3an00817g

Haematologica. 2023 Jul 13. doi: 10.3324/haematol.2023.283224. Online ahead of print.

ABSTRACT

Not available.

PMID:37439341 | DOI:10.3324/haematol.2023.283224

Nucleic Acids Res. 2023 Jul 13:gkad580. doi: 10.1093/nar/gkad580. Online ahead of print.

ABSTRACT

Genomic and transcriptomic image data, represented by DNA and RNA fluorescence in situ hybridization (FISH), respectively, together with proteomic data, particularly that related to nuclear proteins, can help elucidate gene regulation in relation to the spatial positions of chromatins, messenger RNAs, and key proteins. However, methods for image-based multi-omics data collection and analysis are lacking. To this end, we aimed to develop the first integrative browser called iSMOD (image-based Single-cell Multi-omics Database) to collect and browse comprehensive FISH and nucleus proteomics data based on the title, abstract, and related experimental figures, which integrates multi-omics studies focusing on the key players in the cell nucleus from 20 000+ (still growing) published papers. We have also provided several exemplar demonstrations to show iSMOD's wide applications-profiling multi-omics research to reveal the molecular target for diseases; exploring the working mechanism behind biological phenomena using multi-omics interactions, and integrating the 3D multi-omics data in a virtual cell nucleus. iSMOD is a cornerstone for delineating a global view of relevant research to enable the integration of scattered data and thus provides new insights regarding the missing components of molecular pathway mechanisms and facilitates improved and efficient scientific research.

PMID:37439331 | DOI:10.1093/nar/gkad580

Dev Biol. 2023 Jul 10:S0012-1606(23)00130-6. doi: 10.1016/j.ydbio.2023.07.004. Online ahead of print.

ABSTRACT

As the source of embryonic stem cells (ESCs), inner cell mass (ICM) can form all tissues of the embryo proper, however, its role in early human lineage specification remains controversial. Although a stepwise differentiation model has been proposed suggesting the existence of ICM as a distinct developmental stage, the underlying molecular mechanism remains unclear. In the present study, we perform an integrated analysis on the public human preimplantation embryonic single-cell transcriptomic data and apply a trajectory inference algorithm to measure the cell plasticity. In our results, ICM population can be clearly discriminated on the dimension-reduced graph and confirmed by compelling evidences, thus validating the two-step hypothesis of lineage commitment. According to the branch probabilities and differentiation potential, we determine the precise time points for two lineage segregations. Further analysis on gene expression dynamics and regulatory network indicates that transcription factors including GSC, PRDM1, and SPIC may underlie the decisions of ICM fate. In addition, new human ICM marker genes, such as EPHA4 and CCR8 are discovered and validated by immunofluorescence. Given the potential clinical applications of ESCs, our analysis provides a further understanding of human ICM cells and facilitate the exploration of more unique characteristics in early human development.

PMID:37437860 | DOI:10.1016/j.ydbio.2023.07.004

Dev Cell. 2023 Jul 4:S1534-5807(23)00303-9. doi: 10.1016/j.devcel.2023.06.005. Online ahead of print.

ABSTRACT

The blood-brain barrier (BBB) is a unique set of properties of the brain vasculature which severely restrict its permeability to proteins and small molecules. Classic chick-quail chimera studies have shown that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here, we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non-autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix (ECM), increased endothelial transcytosis, and altered pericyte-endothelial interactions. Furthermore, a single dose of recombinant SPOCK1 partially restores BBB function in spock1 mutants by quenching gelatinase activity and restoring vascular expression of BBB genes including mcamb. These analyses support a model in which neuronally secreted Spock1 initiates BBB properties by altering the ECM, thereby regulating pericyte-endothelial interactions and downstream vascular gene expression.

PMID:37437574 | DOI:10.1016/j.devcel.2023.06.005

Nature. 2023 Jul 12. doi: 10.1038/s41586-023-06322-y. Online ahead of print.

ABSTRACT

Understanding protective immunity to COVID-19 facilitates preparedness for future pandemics and combats new SARS-CoV-2 variants emerging in the human population. Neutralizing antibodies have been widely studied; however, on the basis of large-scale exome sequencing of protected versus severely ill patients with COVID-19, local cell-autonomous defence is also crucial1-4. Here we identify phospholipid scramblase 1 (PLSCR1) as a potent cell-autonomous restriction factor against live SARS-CoV-2 infection in parallel genome-wide CRISPR-Cas9 screens of human lung epithelia and hepatocytes before and after stimulation with interferon-γ (IFNγ). IFNγ-induced PLSCR1 not only restricted SARS-CoV-2 USA-WA1/2020, but was also effective against the Delta B.1.617.2 and Omicron BA.1 lineages. Its robust activity extended to other highly pathogenic coronaviruses, was functionally conserved in bats and mice, and interfered with the uptake of SARS-CoV-2 in both the endocytic and the TMPRSS2-dependent fusion routes. Whole-cell 4Pi single-molecule switching nanoscopy together with bipartite nano-reporter assays found that PLSCR1 directly targeted SARS-CoV-2-containing vesicles to prevent spike-mediated fusion and viral escape. A PLSCR1 C-terminal β-barrel domain-but not lipid scramblase activity-was essential for this fusogenic blockade. Our mechanistic studies, together with reports that COVID-associated PLSCR1 mutations are found in some susceptible people3,4, identify an anti-coronavirus protein that interferes at a late entry step before viral RNA is released into the host-cell cytosol.

PMID:37438530 | DOI:10.1038/s41586-023-06322-y