Biology subjects

Schmidt, C.

Publications and source records attributed to Schmidt, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Subacute effects of ketamine on neural correlates of reward processing

ObjectivesKetamines prohedonic properties have been linked to enhanced reward-related brain activation during the early post-infusion phase. Its effects during the subacute period ([~]2-24 h post-infusion), when psychotomimetic symptoms fade and neuroplastic adaptations emerge, are less well characterised. This study assessed ketamines subacute effects on reward processing using the Monetary Incentive Delay (MID) task. MethodsIn a randomised, placebo-controlled, crossover study, 28 healthy participants received 0.5 mg/kg racemic ketamine or placebo via 40-minute intravenous infusion. Functional magnetic resonance imaging (fMRI) was acquired [~]5 h post-infusion. Plasma concentrations of ketamine and norketamine were obtained for individual area under the curve (AUC) estimation. Analyses focused on the contrast between expected and actual trial outcomes. ResultsAt five hours post-infusion, ketamine did not significantly modulate MID task-related brain activation, despite pronounced subjective drug effects. Pharmacokinetic modelling confirmed expected ketamine and norketamine profiles, but neither drug exposure (AUC) nor subjective measures correlated with neural activation. ConclusionsProhedonic effects of ketamine may not sufficiently manifest in MID task-related activation in healthy individuals [~]5 hours after infusion. The lack of significant effects provides valuable extension of the existing literature, as ketamines effects might be confined to a more acute time window or differ in clinical populations.

neuroscience↗

bioRxiv2025

OmniPath: integrated knowledgebase for multi-omics analysis

Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods. We developed OmniPath (https://omnipathdb.org/), a database combining diverse molecular knowledge from 168 resources. It covers causal protein-protein, gene regulatory, miRNA, and enzyme-PTM (post-translational modification) interactions, cell-cell communication, protein complexes, and information about the function, localization, structure, and many other aspects of biomolecules. It prioritizes literature curated data, and complements it with predictions and large scale databases. To enable interactive browsing of this large corpus of knowledge, we developed OmniPath Explorer, which also includes a large language model (LLM) agent that has direct access to the database. Python and R/Bioconductor client packages and a Cytoscape plugin create easy access to customized prior knowledge for omics analysis environments, such as scverse. OmniPath can be broadly used for the analysis of bulk, single-cell and spatial multi-omics data, especially for mechanistic and causal modeling. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/675512v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@17c2b6borg.highwire.dtl.DTLVardef@1069835org.highwire.dtl.DTLVardef@1f2ce76org.highwire.dtl.DTLVardef@1d0b34f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Membrane binding of a cyanobacterial ESCRT-III protein crucially involves the helix α1-3 hairpin conserved in all superfamily members

IM30, the inner membrane-associated protein of 30 kDa (also known as Vipp1) is essential for thylakoid membrane biogenesis and/or maintenance in chloroplasts and cyanobacteria. IM30 and its bacterial homolog PspA belong to the ESCRT-III superfamily, proteins previously thought to be restricted to eukaryotes and archaea. Despite low sequence similarity, IM30 shares key structural and functional features with eukaryotic ESCRT-IIIs, including a conserved 1-2 helical hairpin core and the ability to form oligomeric barrel- or rod assemblies that mediate membrane remodeling. Using IM30 variants, we now show that initial membrane recruitment of IM30 is driven by electrostatic interactions between the positively charged 1-3 helical hairpin and negatively charged lipid surfaces, paralleling the role of charged helical regions in some eukaryotic ESCRT-IIIs. This likely initiates lateral assembly of IM30 into higher-order barrel or rod structures on the membrane. Once assembled, 0 helices within these oligomers engage and stabilize internalized membrane tubules, mirroring membrane interaction strategies of eukaryotic ESCRT-IIIs, which use both N-terminal sequences and charged residues on 1/2. Thus, our findings demonstrate a conserved membrane binding and remodeling mechanism across the ESCRT-III superfamily, underscoring an evolutionary link in membrane dynamics between pro- and eukaryotes. SignificanceIM30, a membrane-associated protein found in cyanobacteria and chloroplasts, along with its bacterial homolog PspA, belongs to the ESCRT-III superfamily. Despite low sequence conservation, these proteins share structural and functional features with eukaryotic ESCRT-III proteins. We show that IM30 binds membranes via a conserved structural motif, followed by lateral assembly into higher-order complexes. This supports a mechanism of membrane remodeling that is conserved in prokaryotic and eukaryotic members of the ESCRT-III superfamily.

biochemistry↗

bioRxiv2025

Evaluation of Data-based Motion Correction Techniques for High Temporal Resolution Functional PET

Functional Positron Emission Tomography (fPET) data offers novel insights into brain energy demands and molecular connectivity. Recent advances in improving temporal resolutions for this imaging technique have opened up new research possibilities. However, lower signal-to-noise ratios (SNR) inherent to short PET frames bring into question whether current realignment approaches still provide appropriate motion correction. Thus, we aimed to evaluate the effectiveness of standard motion correction methods and explore potential improvements for high temporal resolution fPET with 3s frames. We investigated two techniques aimed at improving the SNR to facilitate more accurate realignment of fPET images, in comparison to conventional motion correction: a deep-learning technique based on the application of a conditional generative adversarial network and an exponentially weighted sliding window average. Performance was evaluated by correlating rigid motion parameters between approaches and with simultaneously acquired fMRI data, and by assessing magnitudes of task-induced activation. Our results indicate that neither of the two methods substantially improve mitigation of motion artefacts. Given the increased computational effort of both techniques, we propose that the standard motion correction procedure is adequate for processing high temporal resolution fPET data. Nevertheless, future development of targeted strategies to enhance motion correction may further advance this imaging technique.

neuroscience↗

bioRxiv2025

Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz

With the growing number of metabolomics and lipidomics studies, robust strategies for bioinformatic analyses are increasingly important. However, the absence of standardized and reproducible workflows, coupled with ambiguous metabolite annotations, hampers effective analysis, particularly when integrating prior knowledge with metabolomics data. Moreover, the limited availability of comprehensive, curated prior knowledge further limits functional analyses and reduces the extraction of meaningful biological insights. Here we present MetaProViz (Metabolomics Processing, functional analysis and Visualization), a free open-source R package for metabolomics data analysis that integrates prior knowledge to generate mechanistic hypotheses (https://saezlab.github.io/MetaProViz/). MetaProViz offers a flexible framework consisting of five modules: processing, differential analysis, prior knowledge integration, functional analysis and visualisation, applicable to both intracellular and exometabolomics experiments. To improve functional analysis, we created the Metabolism Signature Database (MetSigDB), a collection of annotated metabolite sets. MetSigDB includes classical pathway-metabolite sets, metabolite-receptor and metabolite-transporter sets, and chemical class-metabolite sets. In addition, MetaProViz enables the conversion of gene sets to metabolite sets by using enzyme-metabolic reaction associations. In addition, MetaProViz translates between metabolite identifiers of commonly used databases, analyzes mapping ambiguities and completes missing annotations. The MetaProViz functional analysis toolkit includes sample metadata analysis, classical enrichment analysis and biologically informed clustering. We showcase MetaProViz functionalities using kidney cancer metabolomics data from cell lines, cell-culture media, and tumour tissue. We found increased methionine usage in clear-cell renal cell carcinoma (ccRCC) cell lines in line with decreased methionine levels in tumour samples. Further, we link this observation to enzymes and transporters crucial for overall survival in ccRCC and suggest that the increased methionine usage reflects the elevated DNA-hypermethylation landscape, a known characteristic in ccRCC. In summary, MetaProViz facilitates and improves the analysis and interpretation of metabolomics data. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/670781v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@10a7a39org.highwire.dtl.DTLVardef@de4c4forg.highwire.dtl.DTLVardef@64041dorg.highwire.dtl.DTLVardef@4a427c_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Multi-omics guided pathway and network analysis of clinical metabolomics and proteomics data

Metabolomics, the study of small molecules in biological systems, is a powerful tool for understanding biochemical pathways, discovering biomarkers, and elucidating disease mechanisms. This chapter provides a guide to performing metabolomics data analysis in R, focusing on enrichment analysis and network-based approaches. It covers essential steps in data processing, quality control (QC), differential expression analysis, integration with proteomics using multi-omics factor analysis (MOFA) and statistical network analysis, as well as enrichment analysis using prior knowledge. The methods outlined provide a framework for biomarker discovery and advancing systems-level understanding of disease processes using metabolomics data in combination with prior knowledge and proteomics data.

bioinformatics↗

bioRxiv2025

Napping alters Functional Brain Responses in the Aged

Circadian rhythms shape the temporal organization of sleep and wakefulness and evolve throughout the adult lifespan, leading to higher sleep-wake cycle fragmentation with ageing. The increasing prevalence of daytime napping represents a visible manifestation of such fragmentation and has been suggested to forecast age-related cognitive decline. Here, we assessed the impact of napping on functional brain correlates of performance on a Sternberg working memory (WM) task using functional magnetic resonance imaging in 60 healthy older individuals, prospectively recruited with respect to their napping habits (39 females, age: 59-82y). As compared to non-nappers, nappers showed reduced hemispheric asymmetry in the dorsolateral prefrontal cortex (DLPFC, p< 0.001) and decreased performance at high WM load levels. Only in non-nappers was increased ipsilateral activation in the DLPFC associated with better performance at high WM load levels (p < 0.05), while contralateral activation across all WM load levels was not associated with better performance. These findings indicate that functional brain compensation and dedifferentiation processes vary according to an individuals napping phenotype, potentially serving as a marker of inter-individual differences in cognitive and brain aging.

neuroscience↗

bioRxiv2025

Ambient temperature structural studies of Penicillin-binding Protein 2a of Methicillin-Resistant Staphylococcus aureus with XFELs and synchrotrons

Penicillin-binding protein 2a (PBP2a) is a transpeptidase responsible for the {beta}-lactam resistance in methicillin-resistant Staphylococcus aureus (MRSA), posing significant challenges to antibiotic therapy. PBP2as unique structural features, including its highly flexible active site and allosteric regulation, enable it to maintain catalytic activity even in the presence of {beta}-lactam antibiotics. Despite extensive characterization using cryogenic crystallography, key questions remain about its dynamic properties and conformational changes under near-physiological conditions. Room-temperature crystallography methods, particularly serial femtosecond X-ray crystallography (SFX) at XFELs, provide a powerful approach to capture these dynamics. Unlike cryogenic conditions that can constrain protein flexibility, SFX enables the study of conformational variability and interaction networks closer to physiological states. Here, we present the first room-temperature structures of PBP2a obtained using SFX to uncover insights into the enzymes flexibility, allosteric communication, and catalytic mechanisms. These findings are built upon optimized large-scale production and crystallization protocols for PBP2a, ensuring high-quality microcrystals suitable for SFX data collection. The room-temperature structures reveal novel interaction patterns, including unique salt bridge networks and dynamic structural elements absent in cryogenic studies. Furthermore, comparative analyses highlight how environmental conditions influence the conformational states of PBP2a, providing new perspectives on its resistance mechanisms. By integrating structural data from EuXFEL and LCLS, this study not only enhances our understanding of PBP2as functional dynamics but also underscores the value of room-temperature crystallography in studying antibiotic resistance. These insights could guide the design of next-generation {beta}-lactam antibiotics capable of overcoming PBP2a-mediated resistance.

biochemistry↗

bioRxiv2025

Intracellular Trafficking SNARE Protein, Syntaxin-6, is a Modifier of Prion and Tau Pathogenesis in vivo and in Cellular Models

Syntaxin-6, a SNARE protein involved in intracellular protein trafficking, is a proposed risk factor for sporadic prion disease, progressive supranuclear palsy and Alzheimers disease. However, no study has validated its functional role in these diseases, explored the disease stage at which it is acting nor its mechanism of action. Here, we show that syntaxin-6 acts at early stages of prion disease in experimental mice by increasing disease transmission risk following inoculation with low prion doses. Conversely, syntaxin-6 does not affect prion propagation kinetics or toxicity during established disease. Syntaxin-6 manipulation in cellular models profoundly alters the subcellular distribution and morphologies of disease-related PrP and modifies prion export. Furthermore, syntaxin-6 knockout in a transgenic tauopathy mouse model exerts protective effects on numerous physiological, behavioural and neuropathological outcome measures. Therefore, our studies firmly establish syntaxin-6 as a modifier of prion and tau pathogenesis, providing key insights into a fundamental mechanism of neurodegeneration.

neuroscience↗

bioRxiv2024

A novel menthol-DCMU bleaching method for foraminifera: Generating aposymbiotic hosts for symbiosis research

Predicting the response and resilience of coral reefs to climate change can be achieved through better understanding the cellular symbiosis between coral reef holobionts and their associated endosymbiotic algae. Larger benthic foraminifera (LBF) are key calcium carbonate producers, of which two species were investigated for their suitability for menthol bleaching. The LBF Amphistegina lobifera, hosting diatoms, and Sorites orbiculus, hosting dinoflagellates of the family Symbiodiniaceae. This study aimed to rapidly generate symbiont-free (aposymbiotic) hosts via treatment with menthol and DCMU. The first experiment, Menthol Concentration Comparison (MCC), aimed to find a non-lethal and effective dose for both species. The second experiment, Menthol-bleaching Ecophysiology Assessment (MEA), used a larger sample size of both species to test the response to one concentration 0.19 mmol L-1 and measured growth, motility (an indicator for overall fitness) and mortality over a 4-week time frame. Menthol led to an aposymbiotic state in 100% of A. lobifera and only minimally impacted its motility and mortality. The method was effective for S. orbiculus, where an aposymbiotic state, defined as no visible remains of symbiont cells inside the host at the end of the experimental period, occurred in 66% of specimens of the MCC experiment. Growth was strongly impacted by the bleaching protocol in both species, allowing no new calcite to be formed during the acute exposure. This method can be applied for testing aspects of symbiosis establishment in LBF as well as their potential to take up different symbionts in a short-to medium time frame.

cell biology↗

bioRxiv2024

The deubiquitinating enzyme CYLD impairs NF-κB- and STAT1-dependent macrophage intrinsic immunity to Staphylococcus aureus

In atopic dermatitis (AD), lesional skin is frequently colonized by Staphylococcus (S.) aureus, contributing to the severity and clinical symptoms of the disease. The inflammatory milieu in the skin is characterized by a type 2 inflammatory signature, including M2 macrophages, which cannot eradicate S. aureus. Since S. aureus is effectively controlled in macrophages activated by pattern recognition receptor (PRR)-induced NF-{kappa}B and interferon (IFN)-{gamma}-induced STAT1 stimulation, we hypothesized that pre-treatment with LPS as a PRR/TLR4-activating agent and IFN-{gamma} would induce effective control of S. aureus in monocyte-derived macrophages (MDMs) of AD patients. Our data show that the deubiquitinating enzyme CYLD is strongly expressed in skin macrophages and MDMs from AD patients compared to healthy controls and impairs the anti-staphylococcal activity of PRR-activated and IFN-treated MDMs. Functionally, CYLD impaired M1 macrophage polarization, as evidenced by reduced expression of CD80, TNF, and IL-6 upon LPS- and IFN-{gamma} treatment in CYLD-deficient as compared to wild-type (WT) MDM/THP1 macrophages. Mechanistically, CYLD inhibited IFN-{gamma}-induced STAT1 phosphorylation and activation by binding to STAT1 and inducing its K63 deubiquitination. CYLD also interacted with TRAF6 and NEMO/IKK{gamma} in the MYD88 signaling pathway and with RIPK2 in the NOD2 pathway, leading to impaired activation of NF-{kappa}B. Inhibition of both STAT1 by siRNA and NF-{kappa}B by IKK inhibitor treatment, respectively, independently abolished the control of S. aureus in both CYLD-deficient and WT THP1 macrophages, which harbored identical high numbers of the pathogen. The in vivo inhibitory function of CYLD on the control of S. aureus was also observed upon infection of Cyld-deficient and WT mice. Collectively, these data illustrate that the increased expression of CYLD in macrophages of AD patients is a factor contributing to the ineffective control of S. aureus, diminishes M1 macrophage polarization, and that CYLD deletion unleashes the break on effective STAT1 and NF-{kappa}B-dependent control of S. aureus.

immunology↗

bioRxiv2024

Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users

Modern bioimaging core facilities at research institutions are essential for managing and maintaining high-end instruments, providing training and support for researchers in experimental design, image acquisition and data analysis. An important task for these facilities is the professional management of complex multi-dimensional bioimaging data, which are often produced in large quantity and very different file formats. This article details the process that led to successfully implementing the OME Remote Objects system (OMERO) for bioimage-specific research data management (RDM) at the Core Facility Cellular Imaging (CFCI) at the Technische Universitat Dresden (TU Dresden). Ensuring compliance with the FAIR (findable, accessible, interoperable, reusable) principles, we outline here the challenges that we faced in adapting data handling and storage to a new RDM system. These challenges included the introduction of a standardized group-specific naming convention, metadata curation with tagging and Key-Value pairs, and integration of existing image processing workflows. By sharing our experiences, this article aims to provide insights and recommendations for both individual researchers and educational institutions intending to implement OMERO as a management system for bioimaging data. We showcase how tailored decisions and structured approaches lead to successful outcomes in RDM practices.

bioinformatics↗

bioRxiv2024

Merkel cell polyomavirus small tumor antigen contributes to immune evasion by interfering with type I interferon signaling

Merkel cell polyomavirus (MCPyV) is the causative agent of the majority of Merkel cell carcinomas (MCC). The virus has limited coding capacity, with its early viral proteins, large T (LT) and small T (sT), being multifunctional and contributing to infection and transformation. A fundamental difference in early viral gene expression between infection and MCPyV-driven tumorigenesis is the expression of a truncated LT (LTtr) in the tumor. In contrast, sT is expressed in both conditions and contributes significantly to oncogenesis. Here, we identified novel functions of early viral proteins by performing genome-wide transcriptome and chromatin studies in primary human fibroblasts. Due to current limitations in infection and tumorigenesis models, we mimic these conditions by ectopically expressing sT, LT or LTtr, individually or in combination, at different time points. In addition to its known function in cell cycle and inflammation modulation, we reveal a fundamentally new function of sT. We show that sT regulates the type I interferon (IFN) response downstream of the type I interferon receptor (IFNAR) by interfering with the interferon-stimulated gene factor 3 (ISGF3)-induced interferon-stimulated gene (ISG) response. Expression of sT leads to a reduction in the expression of interferon regulatory factor 9 (IRF9) which is a central component of the ISGF3 complex. We further show that this function of sT is conserved in BKPyV. We provide a first mechanistic understanding of which early viral proteins trigger and control the type I IFN response, which may influence MCPyV infection, persistence and, during MCC progression, regulation of the tumor microenvironment. Author SummaryMerkel cell polyomavirus (MCPyV) is the only human polyomavirus that causes cancer in humans. As with all human polyomaviruses, the available infection models are limited. Thus, many processes such as the host response to infection and its regulation by the virus to establish infection and persistence are poorly understood. To better understand this interplay of viral MCPyV proteins, we performed genome-wide transcriptome and chromatin studies in primary human fibroblasts and simulated infection and tumorigenesis conditions by ectopically expressing the early viral proteins individually or in combination at different time points. This allowed us to uncover a novel, previously undescribed function of polyomavirus sT, namely the reduction of the ISG response by affecting the ISGF3 complex, specifically by reducing IRF9 protein levels. This work sheds light on how early viral proteins influence the type I IFN response and how their interplay may affect MCPyV infection, persistence, and MCC progression.

molecular biology↗

bioRxiv2024

Minimized Sample Consumption for Time-Resolved Serial Crystallography Applied to the Redox Cycle of Human NQO1

Sample consumption for serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) remains a major limitation preventing broader use of this powerful technology in macromolecular crystallography. This drawback is exacerbated in the case of time-resolved (TR)-SFX experiments, where the amount of sample required per reaction time point is multiplied by the number of time points investigated. Thus, in order to reduce the limitation of sample consumption, here we demonstrate the implementation of segmented droplet generation in conjunction with a mix-and-inject approach for TR studies on NAD(P)H:quinone oxidoreductase 1 (NQO1). We present the design and application of mix-and-inject segmented droplet injectors for the Single Particles, Clusters, and Biomolecules & Serial Femtosecond Crystallography (SPB/SFX) instrument at the European XFEL (EuXFEL) with a synchronized droplet injection approach that allows liquid phase protein crystal injection. We carried out TR-crystallography experiments with this approach for a 305 ms and a 1190 ms time point in the reaction of NQO1 with its coenzyme NADH. With this successful TR-SFX approach, up to 97% of the sample has been conserved compared to continuous crystal suspension injection with a gas dynamic virtual nozzle. Furthermore, the obtained structural information for the reaction of NQO1 with NADH is an important part of the future elucidation of the reaction mechanism of this crucial therapeutic enzyme.

biochemistry↗

bioRxiv2024

Variations of autonomic arousal mediate the reportability of mind-blanking occurrences

Mind-blanking (MB) is the inability to report mental events during unconstraint thinking. Previous work shows that MB is linked to decreased levels of cortical arousal, indicating dominance of cerebral mechanisms when reporting mental states. What remains inconclusive is whether MB can also ensue from autonomic arousal manipulations, pointing to the implication of peripheral physiology to mental events. Using experience-sampling, neural, and physiological measurements in 26 participants, we first show that MB was reported more frequently in low arousal conditions, elicited by sleep deprivation. Also, there was partial evidence for a higher number of MB reports in high arousal conditions, elicited by intense physical exercise. Transition probabilities revealed that, after sleep deprivation, mind-wandering was more likely to be followed by MB and less likely to be followed by more mind-wandering reports. Using classification schemes, we show higher performance of a balanced random forest classifier trained on both neural and physiological markers in comparison to performance when solely neural or physiological were used. Collectively, we show that both cortical and autonomic arousal affect MB report occurrences. Our results establish that MB is supported by combined brain-body configurations, and, by linking mental and physiological states they pave the way for novel, embodied accounts of spontaneous thinking.

neuroscience↗

bioRxiv2024

Urbanization is associated with reduced genetic diversity in marine fish populations

The economic and ecological benefits of living by the ocean have led many coastal settlements to grow into large densely populated cities. Large coastal cities have had considerable environmental effects on marine ecosystems through resource extraction, waste disposal, and use for transportation. Thus, it is important to understand the consequences of urbanization and human activities on evolutionary processes and biodiversity in marine fishes. Using published population genetic datasets for marine fishes amounting to 75,496 individuals sampled from 73 species at 1143 sample sites throughout the worlds oceans, we evaluated how human population density and a composite measure of cumulative human impacts affected genetic diversity and differentiation. We found that genetic diversity was significantly lower in marine fish populations associated with denser human populations regardless of species and locality. The effects of cumulative human impacts on genetic diversity were less prominent, perhaps due to this measure capturing more spatially varying processes. Urbanization in coastal regions has degraded marine biodiversity in a way that erodes adaptive potential for marine fish populations. This highlights the need to mitigate threats from human activities and focus efforts on sustainable urban planning and resource use to conserve marine biodiversity sustaining coastal fisheries and ecosystems.

evolutionary biology↗

bioRxiv2024

A Genome-Wide Arrayed CRISPR Screen Reveals PLSCR1 as an Intrinsic Barrier to SARS-CoV-2 Entry

Interferons (IFNs) play a crucial role in the regulation and evolution of host-virus interactions. Here, we conducted a genome-wide arrayed CRISPR knockout screen in the presence and absence of IFN to identify human genes that influence SARS-CoV-2 infection. We then performed an integrated analysis of genes interacting with SARS-CoV-2, drawing from a selection of 67 large-scale studies, including our own. We identified 28 genes of high relevance in both human genetic studies of COVID-19 patients and functional genetic screens in cell culture, with many related to the IFN pathway. Among these was the IFN-stimulated gene PLSCR1. PLSCR1 did not require IFN induction to restrict SARS-CoV-2 and did not contribute to IFN signaling. Instead, PLSCR1 specifically restricted spike-mediated SARS-CoV-2 entry. The PLSCR1-mediated restriction was alleviated by TMPRSS2 over-expression, suggesting that PLSCR1 primarily restricts the endocytic entry route. In addition, recent SARS-CoV-2 variants have adapted to circumvent the PLSCR1 barrier via currently undetermined mechanisms. Finally, we investigate the functional effects of PLSCR1 variants present in humans and discuss an association between PLSCR1 and severe COVID-19 reported recently.

immunology↗

bioRxiv2024

Somatic gene delivery for flexible in vivo modeling of high-risk sarcoma

A particular challenge hampering therapeutic advancements for high-risk sarcoma patients is the broad spectrum of molecularly distinct sarcoma entities and the corresponding lack of suitable model systems to recapitulate and study these diseases. To overcome this predicament, we developed a novel genetically-controlled, yet versatile mouse modeling platform allowing delivery of different genetic lesions by electroporation (EPO) of the thigh muscle wildtype mice. This optimized sarcoma EPO-GEMM (EPO-based genetically engineered mouse model) platform allowed the generation of ten biologically distinct sarcoma entities, including Synovial Sarcoma (SS), fusion-positive and fusion-negative Rhabdomyosarcoma (RMS), Alveolar Soft Part Sarcoma (ASPS), Undifferentiated Pleomorphic Sarcoma (UPS) and Infantile Fibrosarcoma (IFS). Comprehensive molecular profiling and cross-species analyses confirmed faithful recapitulation of the human disease, including the expression of relevant immunotherapy targets. Syngeneic allografting enabled reliable preservation and scalability of Sarcoma-EPO-GEMMs for treatment trials, such as B7-H3-directed CAR-T cell therapy in an immunocompetent background.

cancer biology↗