Biology subjects

Jaworski, J.

Publications and source records attributed to Jaworski, J..

14 recordsLinked to original sources

bioRxiv2026

Loss of Brg1 promotes seizure development via GABAergic system disruption

The Brahma-related gene 1 (BRG1) encodes the catalytic subunit of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex and plays an important role in brain development. Variants in SWI/SNF components are often found in patients with epilepsy, but it is still unclear how loss of BRG1 function contributes to seizure development. In this study, we analyzed the role of Brg1 in seizure susceptibility using zebrafish models with both pharmacological inhibition or genetic reduction of Brg1. Reduced Brg1 function caused seizure-like behavior and increased neuronal activity in larvae, while basic locomotor activity was preserved. Further analyses showed reduced expression of several GABAergic system markers. In contrast, glutamatergic markers did not show major changes. These results point to a selective impairment of inhibitory signaling. When GABA levels were increased pharmacologically, seizure-like behavior was reduced. This suggests that loss of inhibitory transmission plays an important role in the observed hyperexcitability. Unbiased omics analyses also identified changes in proteins associated with vitamin B6 binding. Treatment with active vitamin B6 reduced seizure-like behavior in larvae with reduced Brg1 function. Taken together, these results indicate that Brg1 is required for proper inhibitory neurotransmission and that partial loss of Brg1 function increases seizure susceptibility. These findings may help to better understand why mutations in chromatin remodeling genes are often associated with epilepsy and could support future studies on targeted modulation of inhibitory signaling in these conditions. Significance StatementChromatin remodeling genes are often mutated in patients with epilepsy, but it is still unclear how these mutations lead to seizures. In this study, we show that reduced function of the chromatin remodeler Brg1 affects inhibitory neurotransmission by impairing the GABAergic system. This leads to increased neuronal activity and seizure-like behavior. Our results identify the chromatin remodeler Brg1 as an important regulator of inhibitory neurotransmission and seizure susceptibility, which may be important for understanding epilepsy associated with neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

Zika virus capsid protein C (ZIKV-C) interactors network mapped by proteomic analysis of human neural stem cells expressing FLAG-tagged C protein.

Zika virus is a teratogenic pathogen belonging to the Flaviviridae family. It possesses the ability to penetrate the placenta and affect the brain development of a fetus, resulting in microcephaly and functional impairments. Mechanisms of this neurotoxicity are still unclear, but capsid proteins of Zika and related viruses are known to exert apoptotic effect in different types of cells, including neurons. To explore the pathways affected by the presence of ZIKV-C, we have performed MS-based interactomic experiment in human neural stem cells and managed to identify 149 putative interactors. Our results indicate that the nucleus (especially the nucleolus) and the mitochondria are the main sites of interaction of protein C with host proteins. A number of the proteins we identified have significant links to diseases of the nervous system, including neurodevelopmental diseases. Furthermore, for the first time, we have identified MAM-domain containing glycosylphosphatidylinositol anchor protein 1, T-complex protein 1 subunit beta, lysine-tRNA ligase, calumenin as particularly abundant ZIKV protein C interactors. Data are available via ProteomeXchange with identifier PXD064412.

molecular biology↗

bioRxiv2025

p70S6 kinase-dependent phosphorylation of the μ2 subunit of the AP2 adaptor complex is needed for clathrin-mediated endocytosis.

Clathrin-mediated endocytosis (CME) internalizes cell-surface receptors via clathrin-coated invaginations of the plasma membrane. Both clathrin and endocytic cargo are recruited to these sites by the adaptor protein complex AP2. AP2 cycles between a closed cytoplasmic conformation and an open membrane-bound state, and efficient CME requires both conformations and their dynamic interconversion. The mechanisms regulating these conformational changes, which include post-translational modifications of the AP2, remain incompletely understood. Here, we report that p70S6 kinase phosphorylates the {micro}2 subunit of the AP2 and that the phosphorylation of serine 45 (S45) depends on p70S6K activity. Loss of S45-{micro}2 phosphorylation results in decreased internalization of canonical CME cargo such as transferrin and PDGF receptors. In Caenorhabditis elegans, lack of S45-{micro}2 phosphorylation produces directionally similar but markedly weaker phenotypes than AP2 loss of function. Live imaging and in silico dynamic modelling suggest that S45-2 phosphorylation has impact on the conformational changes of the AP2 complex. These findings identify a p70S6K-dependent mechanism that modulates AP2 function and further strengthen the importance of post-translational regulation in controlling CME. Summary statementClathrin-mediated endocytosis is essential for receptor internalization and cell signaling. This study identifies a novel regulatory mechanism in which p70S6K-mediated phosphorylation of the AP2 subunit 2 at Ser45 modulates AP2 conformational dynamics and facilitates receptor endocytosis.

cell biology↗

bioRxiv2024

Turncoat antibodies unmasked in a model of autoimmune demyelination: from biology to therapy

Autoantibodies contribute to many autoimmune diseases, yet there is no approved therapy to neutralize them selectively. A popular mouse model, experimental autoimmune encephalomyelitis (EAE), could serve to develop such a therapy, provided we can better understand the nature and importance of the autoantibodies involved. Here we report the discovery of autoantibody-secreting extrafollicular plasmablasts in EAE induced with specific myelin oligodendrocyte glycoprotein (MOG) antigens. Single-cell RNA sequencing reveals that these cells produce non-affinity-matured IgG antibodies. These include pathogenic antibodies competing for shared binding space on MOGs extracellular domain. Interestingly, the synthetic anti-MOG antibody 8-18C5 can prevent the binding of pathogenic antibodies from either EAE mice or people with MOG antibody disease (MOGAD). Moreover, an 8-18C5 variant carrying the NNAS mutation, which inactivates its effector functions, can reduce EAE severity and promote functional recovery. In brief, this study provides not only a comprehensive characterization of the humoral response in EAE models, but also a proof of concept for a novel therapy to antagonize pathogenic anti-MOG antibodies.

immunology↗

bioRxiv2024

Platelets are Protective in Early Abdominal Aortic Aneurysm Formation

BackgroundAbdominal aortic aneurysm (AAA) is a disease associated with the pathophysiologic degradation of the tunica media resulting in aortic dilatation, systemic inflammation, and dysregulated hemostasis. Beyond role its role in initiating primary hemostasis, platelets are a source of ROS, inflammatory cytokines and growth factors necessary for angiogenesis and vascular remodeling. Although platelets contribute to the progression of established aneurysms, their role in the initiation of AAA remains undefined. MethodsLow density lipoprotein receptor deficient (Ldlr-/-) mice were examined for platelet accumulation in the angiotensin II (AngII) model of AAA utilizing in vivo labeling techniques. Two platelet antagonists (clopidogrel and aspirin), a thrombin inhibitor (dabigatran) or genetic deficiencies (protease-activated receptor 4, P2Y12, Lnk) were administered to AngII-infused mice to determine the role of platelets in initiation of AAA. The effect of platelet depletion was examined in multiple mouse strains of AngII-induced AAA and two additional aneurysm models. PheWAS and meta-analysis was analyzed in humans for platelet gene SNPs associated with AAA. ResultsWe show that platelets are recruited rapidly to the aorta after the initiation of AngII infusion. Genetic deficiency of platelet receptors had no effect on abdominal aortic diameter, but augmented rupture-induced death in littermate versus placebo controls during AngII-induced AAA. Moreover, Ldlr-/- mice receiving anti-platelet inhibitors or a thrombin inhibitor also had augmented rupture-induced death. Platelet depletion preceding aneurysm formation resulted in pervasive rupture-induced death in several mouse strains and with three different mouse models of AAA. ConclusionsInhibition of platelet function is detrimental in an early expanding aortic lumen resulting in catastrophic rupture and hemodynamic failure in murine AAA models.

pathology↗

bioRxiv2022

Selection of an Ideal Machine Learning Framework for Predicting Perturbation Effects on Network Topology of Bacterial KEGGPathways

Biological networks for bacterial species are used to assign functional information to newly sequenced organisms but network quality can be largely affected by poor gene annotations. Current methods of gene annotation use homologous alignment to determine orthology, and have been shown to degrade network accuracy in non-model bacterial species. To address these issues in the KEGG pathway database, we investigated the ability for machine learning (ML) algorithms to re-annotate bacterial genes based on motif or homology information. The majority of the ensemble, clustering, and deep learning algorithms that we explored showed higher prediction accuracy than CD-hit in predicting EC ID, Map ID, and partial Map ID. Motif-based, machine-learning methods of annotation in new species were more accurate, faster, and had higher precisionrecall than methods of homologous alignment or orthologous gene clustering. Gradient boosted ensemble methods and neural networks also predicted higher connectivity of networks, finding twice as many new pathway interactions than blast alignment. The use of motif-based, machine-learning algorithms in annotation software will allow researchers to develop powerful network tools to interact with bacterial microbiomes in ways previously unachievable through homologous sequence alignment. CCS CONCEPTS* Applied computing [->] Computational biology; Life and medical sciences; Bioinformatics; * Computing methodologies [->] Machine learning algorithms; Machine learning approaches. ACM Reference FormatMichael Robben, Mohammad Sadegh Nasr, Avishek Das, Manfred Huber, Justyn Jaworski, Jon Weidanz, and Jacob Luber. 2022. Selection of an Ideal Machine Learning Framework for Predicting Perturbation Effects on Network Topology of Bacterial KEGG Pathways. In The 13th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 07-10, 2022, Chicago, IL. ACM, New York, NY, USA, 11 pages. https://doi.org/XXXXXXX.XXXXXXX

bioinformatics↗

bioRxiv2022

Dynactin interaction with AP-2 adaptor complex requires CLIP-170 and autophagy

The endocytic adaptor protein 2 (AP-2) complex binds dynactin as part of its noncanonical function, which is necessary for dynein-driven autophagosome transport along microtubules in neuronal axons. The absence of this AP-2-dependent transport causes neuronal morphology simplification and neurodegeneration. The mechanisms that lead to formation of the AP-2-dynactin complex have not been studied to date. However, the inhibition of mammalian/mechanistic target of rapamycin complex 1 (mTORC1) enhances the transport of newly formed autophagosomes by influencing the biogenesis and protein interactions of Rab-interacting lysosomal protein (RILP), another dynein cargo adaptor. We tested effects of mTORC1 inhibition on interactions between the AP-2 and dynactin complexes, with a focus on their two essential subunits, AP-2{beta} and p150Glued. We found that the mTORC1 inhibitor rapamycin enhanced p150Glued-AP-2{beta} complex formation in both neurons and non-neuronal cells. Additional analysis revealed that the p150Glued-AP-2{beta} interaction was indirect and required integrity of the dynactin complex. In non-neuronal cells rapamycin-driven enhancement of the p150Glued-AP-2{beta} interaction also required the presence of cytoplasmic linker protein 170 (CLIP-170), the activation of autophagy, and an undisturbed endolysosomal system. The rapamycin-dependent p150Glued-AP-2{beta} interaction occurred on lysosomal-associated membrane protein 1 (Lamp-1)-positive organelles but without the need for autolysosome formation. Rapamycin treatment also increased the acidification and number of acidic organelles and increased speed of the long-distance retrograde movement of Lamp-1-positive organelles. Altogether, our results indicate that autophagy regulates the p150Glued-AP-2{beta} interaction, possibly to coordinate sufficient motor-adaptor complex availability for effective lysosome transport.

cell biology↗

bioRxiv2022

Rab11 regulates autophagy at dendritic spines in an mTOR- and NMDA-dependent manner

Synaptic plasticity is a process that shapes neuronal connections during neurodevelopment, learning, and memory. Autophagy is a mechanism that allows cells to degrade their unnecessary or dysfunctional components. Autophagosomes appear at dendritic spines in response to plasticity-inducing stimuli. Autophagy defects contribute to altered dendritic spine development, autistic-like behavior in mice, and neurological disease. While several studies explored the involvement of autophagy in synaptic plasticity, the steps preceding autophagosome emergence at the postsynapse remain unknown. Here we show a postsynaptic association of autophagy-related protein 9A (Atg9A), known to be involved in the initial stages of autophagosome formation, with Rab11, a small GTPase that regulates endosomal trafficking. Rab11 activity is necessary for the maintenance of Atg9A-positive structures at dendritic spines. Inhibition of mTOR increased Rab11 and Atg9A interaction and increased the emergence of autophagosomes in dendritic spines when coupled to NMDA receptor stimulation. Dendritic spines with newly formed autophagosomes were more resistant to NMDA-induced morphologic change. These results collectively suggest that autophagy initiation in dendritic spines depends on an activity-dependent Rab11a-Atg9A interaction regulated by mTOR.

neuroscience↗

bioRxiv2021

Phylodynamic modelling of bacterial outbreaks using nanopore sequencing

Nanopore sequencing and phylodynamic modelling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Here, we implement Random Forest models for single nucleotide polymorphism (SNP) polishing to estimate divergence and effective reproduction numbers (Re) of two community-associated, methicillin-resistant Staphylococcus aureus (MRSA) outbreaks in remote Far North Queensland and Papua New Guinea (n = 159). Successive bar-coded panels of S. aureus isolates (2 x 12 per MinION) sequenced at low-coverage (> 5x - 10x) provided sufficient data to accurately infer assembly genotypes with high recall when compared with Illumina references. De novo SNP calling with Clair was followed by SNP polishing using intra- and inter-species models trained on Snippy reference calls. Models achieved sufficient resolution on ST93 outbreak sequence types (> 70 - 90% accuracy and precision) for phylodynamic modelling from lineage-wide hybrid alignments and birth-death skyline models in BEAST2. Our method reproduced phylogenetic topology, geographical source of the outbreaks, and indications of sustained transmission (Re > 1). We provide Nextflow pipelines that implement SNP polisher training, evaluation, and outbreak alignments, enabling reconstruction of within-lineage transmission dynamics for infection control of bacterial disease outbreaks using nanopore sequencing.

bioinformatics↗

bioRxiv2021

Phylodynamic signatures in the emergence of community-associated MRSA

Community-associated, methicillin-resistant Staphylococcus aureus (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 years. Here, we apply consistent phylodynamic methods across multiple community-associated MRSA lineages to describe and contrast their patterns of emergence and dissemination. We generated whole genome sequencing data for the Australian sequence type (ST) 93-MRSA-IV from remote communities in Far North Queensland and Papua New Guinea, and the Bengal Bay ST772-MRSA-V clone from metropolitan communities in Pakistan. Increases in the effective reproduction number (Re) and sustained transmission (Re > 1) coincided with spread of progenitor methicillin-susceptible S. aureus (MSSA) in remote northern Australia, dissemination of the ST93-MRSA-IV geno-type into population centers on the Australian East Coast, and sub-sequent importation into the highlands of Papua New Guinea and Far North Queensland. Analysis of a ST772-MRSA-V cluster in Pakistan suggests that sustained transmission in the community following importation of resistant genotypes may be more common than previously thought. Applying the same phylodynamic methods to existing lineage datasets, we identified common signatures of epidemic growth in the emergence and epidemiological trajectory of community-associated S. aureus lineages from America, Asia, Australasia and Europe. Surges in Re were observed at the divergence of antibiotic resistant strains, coinciding with their establishment in regional population centers. Epidemic growth was also observed amongst drug-resistant MSSA clades in Africa and northern Australia. Our data suggest that the emergence of community-associated MRSA and MSSA lineages in the late 20th century was driven by a combination of antibiotic resistant genotypes and host epidemiology, leading to abrupt changes in lineage-wide transmission dynamics and sustained transmission in regional population centers.

evolutionary biology↗

bioRxiv2021

Notch Intracellular Domain Plasmid Delivery via Poly(lactic-co-glycolic acid)Nanoparticles to Upregulate Notch Signaling

Notch signaling is a highly conserved signaling system that is required for embryonic development and regeneration of organs. When the signal is lost, maldevelopment occurs and leads to a lethal state. Liposomes and retroviruses are most commonly used to deliver genetic material to cells. However, there are many drawbacks to these systems such as increased toxicity, nonspecific delivery, short half-life, and stability after formulation. We utilized the negatively charged and FDA approved polymer poly(lactic-co-glycolic acid) to encapsulate Notch Intracellular Domain-containing plasmid in nanoparticles. In this study, we show that primary human umbilical vein endothelial cells readily uptake the nanoparticles with and without specific antibody targets. We demonstrated that our nanoparticles also are nontoxic, stable over time, and compatible with blood. We also determined that we can successfully transfect primary human umbilical vein endothelial cells (HUVECs) with our nanoparticles in static and dynamic environments. Lastly, we elucidated that our transfection upregulates the downstream genes of Notch signaling, indicating that the payload was viable and successfully altered the genetic downstream effects.

bioengineering↗

bioRxiv2020

Serum response factor is essential for synaptic maturation in the hippocampus

Disturbances of gene expression patterns that occur during brain development can severely affect signal transmission, connectivity, and plasticity--key features that underlie memory formation and storage in neurons. Abnormalities at the molecular level can manifest as changes in the structural and functional plasticity of dendritic spines that harbor excitatory synapses. This can lead to such developmental neuropsychiatric conditions as Autism spectrum disorders, intellectual disabilities, and schizophrenia. The present study investigated the role of the major transcriptional regulator serum response factor (SRF) in synapse maturation and its impact on behavioral phenotypes. Using in vitro and in vivo models of early postnatal SRF deletion, we studied its influence on key morphological and physiological hallmarks of spine development. The elimination of SRF in developing neurons resulted in a phenotype of immature dendritic spines and impairments in excitatory transmission. Moreover, using a combination of molecular and imaging techniques, we showed that SRF-depleted neurons exhibited a lower level of specific glutamate receptor mRNAs and a decrease in their surface expression. Additionally, the early postnatal elimination of SRF in hippocampal CA1 excitatory neurons caused spine immaturity and a specific social deficit that is frequently observed in autism patients. Altogether, our data suggest that the regulation of structural and functional dendritic spine maturation begins at the stage of gene transcription, which underpins the crucial role of such transcription factors as SRF. Moreover, disturbances of the postnatal expression of SRF translate to behavioral changes in adult animals.

neuroscience↗

bioRxiv2020

G3BP1 tethers the TSC complex to lysosomes and suppresses mTORC1 in the absence of stress granules

G3BP1 (Ras GTPase-activating protein-binding protein 1) is widely recognized as a core component of stress granules (SG), non-membranous RNA-protein-assemblies required for cellular survival under stress. We report that in the absence of SG, G3BP1 acts as lysosomal anchor of the Tuberous Sclerosis Complex (TSC) protein complex. By tethering the TSC complex to lysosomes, G3BP1 suppresses signaling through the metabolic master regulator mTORC1 (mechanistic target of rapamycin complex 1). Like the known TSC complex subunits, G3BP1 suppresses phenotypes related to mTORC1 hyperactivity in the context of tumors and neuronal dysfunction. Thus, G3BP1 is not only a core component of SG but also a key element of lysosomal TSC-mTORC1 signaling. HighlightsThe bona fide stress granule component G3BP1 O_LIis a key element of the TSC-mTORC1 signaling axis. C_LIO_LItethers the TSC complex to lysosomes. C_LIO_LIprevents mTORC1 hyperactivation by metabolic stimuli. C_LIO_LIsuppresses mTORC1-driven cancer cell motility and epileptiform activity. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/044081v3_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@77cb4forg.highwire.dtl.DTLVardef@c4d1a0org.highwire.dtl.DTLVardef@19e83acorg.highwire.dtl.DTLVardef@1d6a378_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2018

Amot regulates neuronal dendritic tree through Yap1

The Amot-Yap1 complex plays a major role in the regulation of cell contact inhibition, cellular polarity and growth. However, the function of Angiomotin (Amot) and Hippo pathway transcription co-activator Yap1 in the central nervous system remains unclear. In this study, we demonstrate that Amot is a critical mediator of dendritic morphogenesis in cultured hippocampal cells and Purkinje cells in the brain. Amot function in developing hippocampal neurons depends on interactions with Yap1, which is also indispensable for dendrite growth and arborization in vitro. Conditional deletion of Amot or Yap1 in neurons leads to impaired morphogenesis of Purkinje cell dendritic trees, decreased cerebellar size, and causes defects in locomotor coordination of mutant animals. Thus, our studies identified Amot and Yap1 as novel regulators of dendritic tree morphogenesis.

neuroscience↗