Biology subjects

Schäfer, A.

Publications and source records attributed to Schäfer, A..

11 recordsLinked to original sources

bioRxiv2025

Duration of immunity following infection with moderately virulent ASFV

African swine fever virus (ASFV) poses a significant threat to pork production and wild pig populations worldwide. The study assessed the long-term fate and immunity of animals recovering from a moderately virulent ASFV infection, following the principles of a duration of immunity study for live vaccines. Pigs inoculated with the moderately virulent ASFV strain Estonia14 largely developed mild clinical signs and only transient viremia. Six months after the initial inoculation and once fully recovered, all the animals were challenged with highly virulent ASFV Armenia08. Only one of the previously exposed pigs exhibited mild clinical signs, while all control animals showed typical signs of acute, lethal ASF. Moreover, only a subset of pigs inoculated with the ASF strain Estonia14 displayed temporary detectability of ASFV genomes following challenge infection. Virus isolation corroborated these findings, with low levels of infectious virus in organs of previously inoculated pigs (28 days post challenge). Furthermore, monitoring of IgM and IgG kinetics enabled the analysis of humoral responses. IgG levels were sustained over the study period and increased slightly upon challenge infection. Lastly, plasma analysis revealed elevated complement factor C3a levels post inoculation and challenge in the recovered pigs, directly correlating with challenge virus presence. In contrast, both C3a and C5a levels were increased in the control group. It could be shown that complement system activation was mediated by the lectin pathway, possibly by interaction of mannose-binding lectins and ASFV particles. This study suggests that protective immunity following recovery can last at least six months. No cases of persistent or chronic disease were observed in convalescent pigs. These findings have implications for both vaccine development and assessment, as well as for disease control strategies including surveillance actions.

immunology↗

bioRxiv2025

HIDE: Hierarchical cell-type Deconvolution

MotivationCell-type deconvolution is a computational approach to infer cellular distributions from bulk transcriptomics data. Several methods have been proposed, each with its own advantages and disadvantages. Reference based approaches make use of archetypic transcriptomic profiles representing individual cell types. Those reference profiles are ideally chosen such that the observed bulks can be reconstructed as a linear combination thereof. This strategy, however, ignores the fact that cellular populations arise through the process of cellular differentiation, which entails the gradual emergence of cell groups with diverse morphological and functional characteristics. ResultsHere, we propose Hierarchical cell-type Deconvolution (HIDE), a cell-type deconvolution approach which incorporates a cell hierarchy for improved performance and interpretability. This is achieved by a hierarchical procedure that preserves estimates of major cell populations while inferring their respective subpopulations. We show in simulation studies that this procedure produces more reliable and more consistent results than other state-of-the-art approaches. Finally, we provide an example application of HIDE to explore breast cancer specimens from TCGA. AvailabilityA python implementation of HIDE is available at zenodo (doi:10.5281/zenodo.14724906). Supplementary informationSupplementary material is available at Bioinformatics online.

bioinformatics↗

bioRxiv2025

JNK regulates GABAAR expression at the cell surface via the receptor clustering protein GIT1 (ArfGAP1)

GABAA-type receptors (GABAARs) mediate fast and tonic inhibition and are essential for maintaining excitatory/inhibitory balance in neural circuits. Disrupted GABAergic signaling leads to maladaptive changes associated with neuropsychiatric disorders, yet the mechanisms that regulate GABAAR surface availability remain incompletely understood. We previously identified that the stress-activated kinase JNK1 drives anxiety-like behaviours in mice suggesting a potential link between stress signalling and GABAergic regulation. Here, we show that genetic deletion or inhibition of JNK1 increases surface expression of {beta}3-containing GABAARs at extrasynaptic sites and at excitatory synapses where they may participate in shunting inhibition. We identify the signalling scaffold GIT1 as a direct JNK1 substrate, phosphorylated at S371, and find that GIT1 accumulates in dendritic spines in Jnk1-/- neurons or following JNK inhibition, whereas the phosphomimetic GIT1-S371D is excluded. Moreover, GIT1 is required for JNK-dependent regulation of {beta}3-GABAAR trafficking. Accordingly, neurons from Jnk1-/- mice exhibit increased spontaneous inhibitory postsynaptic potentials and enhanced tonic inhibition. These results reveal a JNK1-GIT1 signalling axis that suppresses GABAAR stability and inhibitory tone, providing a mechanism by which the stress-activated JNK pathway modulates synaptic and extrasynaptic inhibition.

neuroscience↗

bioRxiv2024

Computationally designed mRNA-launched protein nanoparticle vaccines

Both protein nanoparticle and mRNA vaccines were clinically de-risked during the COVID-19 pandemic1-6. These vaccine modalities have complementary strengths: antigen display on protein nanoparticles can enhance the magnitude, quality, and durability of antibody responses7-10, while mRNA vaccines can be rapidly manufactured11 and elicit antigen-specific CD4 and CD8 T cells12,13. Here we leverage a computationally designed icosahedral protein nanoparticle that was redesigned for optimal secretion from eukaryotic cells14 to develop an mRNA-launched nanoparticle vaccine for SARS-CoV-2. The nanoparticle, which displays 60 copies of a stabilized variant of the Wuhan-Hu-1 Spike receptor binding domain (RBD)15, formed monodisperse, antigenically intact assemblies upon secretion from transfected cells. An mRNA vaccine encoding the secreted RBD nanoparticle elicited 5- to 28-fold higher levels of neutralizing antibodies than an mRNA vaccine encoding membrane-anchored Spike, induced higher levels of CD8 T cells than the same immunogen when delivered as an adjuvanted protein nanoparticle, and protected mice from vaccine-matched and -mismatched SARS-CoV-2 challenge. Our data establish that delivering protein nanoparticle immunogens via mRNA vaccines can combine the benefits of each modality and, more broadly, highlight the utility of computational protein design in genetic immunization strategies.

immunology↗

bioRxiv2022

SpaCeNet: Spatial Cellular Networks from omics data

Advances in omics technologies have allowed spatially resolved molecular profiling of single cells, providing a window not only into the diversity and distribution of cell types within a tissue, but also into the effects of interactions between cells in shaping the transcriptional landscape. Cells send chemical and mechanical signals which are received by other cells, where they can subsequently initiate context-specific gene regulatory responses. These interactions and their responses shape the individual molecular phenotype of a cell in a given microenvironment. RNAs or proteins measured in individual cells together with the cells spatial distribution provide invaluable information about these mechanisms and the regulation of genes beyond processes occurring independently in each individual cell. "SpaCeNet" is a method designed to elucidate both the intracellular molecular networks (how molecular variables affect each other within the cell) and the intercellular molecular networks (how cells affect molecular variables in their neighbors). This is achieved by estimating conditional independence relations between captured variables within individual cells and by disentangling these from conditional independence relations between variables of different cells. A python implementation of SpaCeNet is publicly available at https://github.com/sschrod/SpaCeNet.

bioinformatics↗

bioRxiv2022

A model of persistent post SARS-CoV-2 induced lung disease for target identification and testing of therapeutic strategies

COVID-19 survivors develop post-acute sequelae of SARS-CoV-2 (PASC), but the mechanistic basis of PASC-associated lung abnormalities suffers from a lack of longitudinal samples. Mouse-adapted SARS-CoV-2 MA10 produces an acute respiratory distress syndrome (ARDS) in mice similar to humans. To investigate PASC pathogenesis, studies of MA10-infected mice were extended from acute disease through clinical recovery. At 15-120 days post-virus clearance, histologic evaluation identified subpleural lesions containing collagen, proliferative fibroblasts, and chronic inflammation with tertiary lymphoid structures. Longitudinal spatial transcriptional profiling identified global reparative and fibrotic pathways dysregulated in diseased regions, similar to human COVID-19. Populations of alveolar intermediate cells, coupled with focal upregulation of pro-fibrotic markers, were identified in persistently diseased regions. Early intervention with antiviral EIDD-2801 reduced chronic disease, and early anti-fibrotic agent (nintedanib) intervention modified early disease severity. This murine model provides opportunities to identify pathways associated with persistent SARS-CoV-2 pulmonary disease and test countermeasures to ameliorate PASC.

microbiology↗

bioRxiv2022

Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine

Coronavirus vaccines that are highly effective against SARS-CoV-2 variants are needed to control the current pandemic. We previously reported a receptor-binding domain (RBD) sortase A-conjugated ferritin nanoparticle (RBD-scNP) vaccine that induced neutralizing antibodies against SARS-CoV-2 and pre-emergent sarbecoviruses and protected monkeys from SARS-CoV-2 WA-1 infection. Here, we demonstrate SARS-CoV-2 RBD-scNP immunization induces potent neutralizing antibodies in non-human primates (NHPs) against all eight SARS-CoV-2 variants tested including the Beta, Delta, and Omicron variants. The Omicron variant was neutralized by RBD-scNP-induced serum antibodies with a mean of 10.6-fold reduction of ID50 titers compared to SARS-CoV-2 D614G. Immunization with RBD-scNPs protected NHPs from SARS-CoV-2 WA-1, Beta, and Delta variant challenge, and protected mice from challenges of SARS-CoV-2 Beta variant and two other heterologous sarbecoviruses. These results demonstrate the ability of RBD-scNPs to induce broad neutralization of SARS-CoV-2 variants and to protect NHPs and mice from multiple different SARS-related viruses. Such a vaccine could provide the needed immunity to slow the spread of and reduce disease caused by SARS-CoV-2 variants such as Delta and Omicron.

immunology↗

bioRxiv2021

Predicting brain atrophy from tau pathology: A summary of clinical findings and their translation into personalized models

For more than 25 years, the amyloid hypothesis-the paradigm that amyloid is the primary cause of Alzheimers disease-has dominated the Alzheimers community. Now, increasing evidence suggests that tissue atrophy and cognitive decline in Alzheimers disease are more closely linked to the amount and location of misfolded tau protein than to amyloid plaques. However, the precise correlation between tau pathology and tissue atrophy remains unknown. Here we integrate multiphysics modeling and Bayesian inference to create personalized tau-atrophy models using longitudinal clinical images from the the Alzheimers Disease Neuroimaging Initiative. For each subject, we infer three personalized parameters, the tau misfolding rate, the tau transport coefficient, and the tau-induced atrophy rate from four consecutive annual tau positron emission tomography scans and structural magnetic resonance images. Strikingly, the tau-induced atrophy coefficient of 0.13/year (95% CI: 0.097-0.189) was fairly consistent across all subjects suggesting a strong correlation between tau pathology and tissue atrophy. Our personalized whole brain atrophy rates of 0.68-1.68%/year (95% CI: 0.5-2.0) are elevated compared to healthy subjects and agree well with the atrophy rates of 1-3%/year reported for Alzheimers patients in the literature. Once comprehensively calibrated with a larger set of longitudinal images, our model has the potential to serve as a diagnostic and predictive tool to estimate future atrophy progression from clinical tau images on a personalized basis.

biophysics↗

bioRxiv2020

Cross-reactive coronavirus antibodies with diverse epitope specificities and extra-neutralization functions

The continual emergence of novel coronavirus (CoV) strains, like SARS-CoV-2, highlights the critical need for broadly reactive therapeutics and vaccines against this family of viruses. Coronavirus spike (S) proteins share common structural motifs that could be vulnerable to cross-reactive antibody responses. To study this phenomenon in human coronavirus infection, we applied a high-throughput sequencing method called LIBRA-seq (Linking B cell receptor to antigen specificity through sequencing) to a SARS-CoV-1 convalescent donor sample. We identified and characterized a panel of six monoclonal antibodies that cross-reacted with S proteins from the highly pathogenic SARS-CoV-1 and SARS-CoV-2 and demonstrated a spectrum of reactivity against other coronaviruses. Epitope mapping revealed that these antibodies recognized multiple epitopes on SARS-CoV-2 S, including the receptor binding domain (RBD), N-terminal domain (NTD), and S2 subunit. Functional characterization demonstrated that the antibodies mediated a variety of Fc effector functions in vitro and mitigated pathological burden in vivo. The identification of cross-reactive epitopes recognized by functional antibodies expands the repertoire of targets for pan-coronavirus vaccine design strategies that may be useful for preventing potential future coronavirus outbreaks.

immunology↗

bioRxiv2020

SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo

The D614G substitution in the S protein is most prevalent SARS-CoV-2 strain circulating globally, but its effects in viral pathogenesis and transmission remain unclear. We engineered SARS-CoV-2 variants harboring the D614G substitution with or without nanoluciferase. The D614G variant replicates more efficiency in primary human proximal airway epithelial cells and is more fit than wildtype (WT) virus in competition studies. With similar morphology to the WT virion, the D614G virus is also more sensitive to SARS-CoV-2 neutralizing antibodies. Infection of human ACE2 transgenic mice and Syrian hamsters with the WT or D614G viruses produced similar titers in respiratory tissue and pulmonary disease. However, the D614G variant exhibited significantly faster droplet transmission between hamsters than the WT virus, early after infection. Our study demonstrated the SARS-CoV2 D614G substitution enhances infectivity, replication fitness, and early transmission.

microbiology↗

bioRxiv2020

Remdesivir potently inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 as the causative agent of the novel pandemic viral disease COVID-19. With no approved therapies, this pandemic illustrates the urgent need for safe, broad-spectrum antiviral countermeasures against SARS-CoV-2 and future emerging CoVs. We report that remdesivir (RDV), a monophosphoramidate prodrug of an adenosine analog, potently inhibits SARS-CoV-2 replication in human lung cells and primary human airway epithelial cultures (EC50 = 0.01 M). Weaker activity was observed in Vero E6 cells (EC50 = 1.65 M) due to their low capacity to metabolize RDV. To rapidly evaluate in vivo efficacy, we engineered a chimeric SARS-CoV encoding the viral target of RDV, the RNA-dependent RNA polymerase, of SARS-CoV-2. In mice infected with chimeric virus, therapeutic RDV administration diminished lung viral load and improved pulmonary function as compared to vehicle treated animals. These data provide evidence that RDV is potently active against SARS-CoV-2 in vitro and in vivo, supporting its further clinical testing for treatment of COVID-19.

microbiology↗