Biology subjects

Nash, K.

Publications and source records attributed to Nash, K..

8 recordsLinked to original sources

bioRxiv2026

AEGIS reveals epitope- and clone-resolved convergence of CNS B and T cell autoreactivity in ROHHAD

Autoimmune diseases arise when B and T lymphocytes lose tolerance to self. Yet in most disorders, the underlying molecular determinants, including autoantibodies, epitopes and lymphocyte clones that drive tissue injury remain undefined. Rapid-onset obesity with hypothalamic dysfunction, hypoventilation and autonomic dysregulation (ROHHAD) is a rare and often fatal pediatric neuroendocrine syndrome with strong evidence of antigen-driven paraneoplastic autoimmunity, including association with the intracellular autoantigen ZSCAN1. However, the effector immune circuit and the epitope-level determinants operating within the hypothalamus and brainstem have remained unknown. To address this challenge in ROHHAD and more broadly in autoimmune disease, we developed the Autoimmune Epitope and immunoGlobulin/Immune-receptor identification System (AEGIS), an integrated framework that links immune repertoires to their cognate self-epitopes. AEGIS combines B cell and T cell receptor profiling from sites of tissue injury with high-resolution epitope mapping, direct sequencing of antigen-specific autoantibodies, in silico antibody-antigen folding, selection, and T cell antigen discovery. Applied to a deeply phenotyped child with ROHHAD, AEGIS revealed a compartmentalized, clonally restricted immune response in which brain-deposited IgG and expanded cerebrospinal fluid B cell and CD4 T cell clonotypes converged on shared ZSCAN1 epitopes, resolved to minimal determinants and peptide-MHC ligands. These findings provide a clone- and epitope-linked mechanistic map of ROHHAD autoimmunity and establish a generalizable framework for identifying candidate pathogenic clones and antigens across diverse autoimmune diseases.

immunology↗

bioRxiv2025

Piromyces struthionis, sp. nov., a new anaerobic gut fungus from the feces of ostriches

Anaerobic gut fungi (AGF, Neocallimastigomycota) are a clade of basal, zoospore-producing fungi within the subkingdom Chytridiomyceta and known inhabitants of the alimentary tract of animal hosts. To date, 22 genera and 38 species have been described, most originating from herbivorous mammals. Here, we report on the isolation and characterization of a novel species of Neocallimastigomycota from an avian host. Multiple AGF strains were isolated from ostrich feces obtained from a local farm in Oklahoma (USA). All strains formed small, irregular-shaped white colonies with darker centers, displayed a filamentous rhizoidal structure with monocentric thallus developmental patterns, and produced mostly monoflagellated zoospores. The type strain produced terminal sporangia that were predominantly globose, often exhibiting cup-shaped, and occasionally elongated sporangiophores. Sporangiophores characteristically exhibited constrictions at irregular intervals, giving them a pearls-on-a-chain-like appearance. Phylogenetic analysis using the D1-D2 region of the LSU rRNA gene (D1-D2 LSU), ribosomal internal transcribed spacer-1 (ITS1), and RNA polymerase II large subunit (RPB-II) grouped all isolates as a separate species within the genus Piromyces. Transcriptomic analysis indicated an average amino acid identity (AAI) of 80.34 % ({+/-} 3.27 %) between the type species and members of the genus Piromyces, and 62.93-76.05 % between the type species and all other AGF taxa outside Piromyces. Based on the morphology, phylogenetic analysis, and AAI values, we propose accommodating these strains as a novel species of Piromyces for which the name Piromyces struthionis is proposed. The type strain for this species is Ost1.

microbiology↗

bioRxiv2025

The anaerobic gut fungal community in ostriches (Struthio camelus)

Anaerobic gut fungi (AGF; Neocallimastigomycota) are essential for plant biomass degradation in herbivores. While extensively studied in mammals, information regarding their occurrence, diversity, and community structure in non-mammalian hosts remains sparse. Here, we report on the AGF community in ostriches (Struthio camelus), herbivorous, flightless, hindgut fermenting members of the class Aves (birds). Culture-independent diversity surveys of fecal samples targeting the D2 region of the large ribosomal subunit (28S rRNA) revealed a uniform community with low alpha diversity. The community was mostly comprised of sequences potentially representing two novel species in the genus Piromyces, and a novel genus in the Neocallimastigomycota. Sequences affiliated with these novel taxa were absent or extremely rare in datasets derived from mammalian and tortoise samples, indicating a strong pattern of AGF-host association. One Piromyces strain (strain Ost1) was successfully isolated. Transcriptomics-enabled molecular dating analysis suggested a divergence time of {approx} 30 Mya, a time frame in line with current estimates for ostrich evolution. Comparative gene content analysis between strain Ost1 and other Piromyces species from mammalian sources revealed a high degree of similarity. Our findings expand the range of AGF animal hosts to include members of the birds (class Aves), highlight a unique AGF community adapted to the ostrich alimentary tract, and demonstrate that - like mammals - coevolutionary phylosymbiosis (i.e. concurrent evolution of AGF and their animal hosts) plays a central role in explaining current AGF distribution patterns in Aves.

microbiology↗

bioRxiv2025

Citrullination of TDP-43 is a key post-translation modification associated with structural and functional changes and progressive pathology in TDP-43 mouse models and human proteinopathies

TAR DNA-binding protein 43 (TDP-43) pathology is associated with a spectrum of clinical dementias including limbic-predominant age-related TDP-43 encephalopathy neuropathological changes (LATE-NC). Post-translational modifications (PTM) are linked to TDP-43 toxic gain-of-function and cytoplasmic aggregation1-3. Phosphorylation remains the most investigated PTM and a standard criterion for determining pathology progression and clinical subclassification in TDP-43 proteinopathies4-7. However, full spectrum of PTMs on TDP-43 structure and biology remain unknown. Utilizing mass-spectrometry analysis we identified citrullination as a novel and irreversible "bona-fide" PTM of TDP-43 protein. We recognized peptidyl arginine deiminase 2 and 4 (PAD2 and PAD4) to mediate the conversion of arginine (R) to citrulline (citR) in vitro and demonstrated increased PAD2 and PAD4 expression and TDP-43 citrullination in a human wildtype TDP-43 mouse model (Tg (Thy1-TARDBP4). Transmission electron microscopy imaging analysis revealed citrullination induced vast structural changes while ThT analysis demonstrated altered aggregation kinetics of citrullinated (citR) TDP-43 protein. We further provided mechanistic evidence on reduced electrostatic and pi-pi interactions of citR TDP-43 Low Complexity Domain (LCD) with RNA, favoring liquid-solid phase separation and condensate formation. Generation and validation of several citR TDP-43 specific antibodies against several TDP-43 epitopes revealed epitope and domain-specific effects of citrullination on TDP-43 solubility in vivo. Importantly, we found distinct reactivities of citR TDP-43 antibodies shedding light into the contribution of epitope-specific properties of human citR TDP-43 to novel pathological citR TDP-43 assemblies in human brain tissue from LATE-NC, with or without comorbid Alzheimers disease neuropathologic changes (ADNC). These findings provided a unique look into the temporal citR TDP-43 signatures, and the potential clinical relevance associated with progression of pure LATE-NC and comorbid ADNC + LATE-NC. Collectively, these data reveal the existence of irreversible TDP-43 citrullination at targeted sites via induced PAD2/PAD4 activities, presenting a critical step in TDP-43 proteinopathy.

neuroscience↗

bioRxiv2024

Probing tau citrullination in Alzheimer's disease brains and mouse models of tauopathy

Tauopathies, which include Alzheimers disease (AD) share a common defining factor, namely misfolded tau protein. However, the "upstream" etiology and downstream clinical manifestations of tauopathies are quite diverse. Tau deposition elicits different pathological phenotypes and outcomes depending on the tau strain and regional susceptibility. Posttranslational modifications (PTM) can alter tau structure, function, networks, and its pathological sequalae. We uncovered a novel PTM of tau, named citrullination, caused by peptidyl arginine deiminase (PAD) enzymes. PAD induced citrullination irreversibly converts arginine residues to citrulline, producing net loss of positive charge, elimination of pi-pi interactions, and increased hydrophobicity. We observed increased PAD2 and PAD4 in Alzheimers disease (AD) brain and that they both can citrullinate tau. Tau can become citrullinated by PADs at all 14 arginine residues throughout the N-terminal domain (N-term), proline-rich domain (PR), microtubule binding repeat domain (MBR), and C-terminal domain (C-term) on full length tau (2N4R). Citrullination of tau impacts fibrillization and oligomerization rates in aggregation assays. Utilizing a panel of novel citrullinated tau (citR tau) antibodies, we identified citrullination of tau in vitro, several animal models of tauopathies, and Alzheimers disease (AD). CitR tau increased with Braak stage and was enriched in AD brains with higher phospho-tau burden. This work provides a new area of tau biology that signifies further consideration in the emerging spectrum of tauopathies and its clinical understanding.

neuroscience↗

bioRxiv2024

Nutrient Sensing Receptor GPRC6A Regulates mTORC1 Signaling and Tau Biology

Tauopathies, including Alzheimers disease (AD), comprise microtubule-associated protein tau aggregates that cause neuronal cell death and clinical cognitive decline. Reducing overall tau abundance remains a central strategy for therapeutics; however, no disease-modifying treatment exists to date. One principal pathway for balancing cellular proteostasis includes the mechanistic target of rapamycin complex 1 (mTORC1) signaling. Recently, arginine emerged as one of the primary amino acids to activate mTORC1 through several intracellular arginine sensors and an extracellular arginine receptor, namely the G protein-coupled receptor (GPCR) family C, group 6, member A (GPRC6A). Human AD brains were previously reported with elevated mTORC1 signaling; however, it is unclear whether arginine sensing and signaling to mTORC1 plays a role in tauopathies. Herein, we examined arginine sensing associated with mTORC1 signaling in the human AD and animal models of tauopathy. We found that human AD brains maintained elevated levels of arginine sensors with potential uncoupling of arginine sensing pathways. Furthermore, we observed increased GPRC6A and arginine in the brain, accompanied by increased mTORC1 signaling and decreased autophagy in a mouse model of tauopathy (Tau PS19). We also discovered that both supplementing arginine and overexpressing GPRC6A in cell culture models could independently activate mTORC1 and promote tau accumulation. In addition, we found that suppressing GPRC6A signaling by either genetic reduction or pharmacological antagonism reduced tau accumulation, phosphorylation, and oligomerization. Overall, these findings uncover the crucial role of arginine sensing pathways in deregulating mTORC1 signaling in tauopathies and identify GPRC6A as a promising target for future therapeutics in tauopathies and other proteinopathies. Significance StatementTauopathies, including Alzheimers disease (AD), accumulate pathogenic tau protein inclusions that potentially contribute to the hyperactive mechanistic target of rapamycin complex 1 (mTORC1) signaling and eventually cause neuronal cell death. Here, we presented novel findings that AD and animal models of tauopathy maintained increased expression of arginine sensors and uncoupling of arginine sensing associated with mTORC1 signaling. We investigated the role of a putative extracellular arginine and basic L-amino acid sensing G protein-coupled receptor (GPCR) family C, group 6, member A (GPRC6A) in activating mTORC1 and accelerating pathogenic tau phenotypes in several cell models. Additionally, we showed that genetic repression or antagonism of GPRC6A signaling provides a novel therapeutic target for tauopathies and other proteinopathies.

neuroscience↗

bioRxiv2023

Lung infection by P. aeruginosa induces neuroinflammation and blood-brain barrier dysfunction in mice

BackgroundSevere lung infection can lead to brain dysfunction and neurobehavioral disorders. The mechanisms that regulate the lung-brain axis of inflammatory response to respiratory infection are incompletely understood. This study examined the effects of lung infection causing systemic and neuroinflammation as a potential mechanism contributing to blood-brain barrier (BBB) leakage and behavioral impairment. MethodsPneumonia was induced in adult C57BL/6 mice by intratracheal inoculation of Pseudomonas aeruginosa (PA). Solute extravasation, histology, immunofluorescence, RT-PCR, multiphoton imaging and neurological testing were performed in this study. ResultsLung infection caused alveolar-capillary barrier injury as indicated by leakage of plasma proteins across pulmonary microvessels and histopathological characteristics of pulmonary edema (alveolar wall thickening, microvessel congestion, and neutrophil infiltration). PA also caused significant BBB dysfunction characterized by leakage of different sized molecules across cerebral microvessels and a decreased expression of cell-cell junctions (VE-cadherin, claudin-5) in the brain. BBB leakage peaked at 24 hours and lasted for 7 days post-inoculation. Additionally, mice with lung infection displayed hyperlocomotion and anxiety-like behaviors. To test whether cerebral dysfunction was caused by PA directly or indirectly, we measured bacterial load in multiple organs. While PA loads were detected in the lungs up to 7 days post-inoculation, bacteria were not detected in the brain as evidenced by negative cerebral spinal fluid (CSF) cultures and lack of distribution in different brain regions or isolated cerebral microvessels. However, mice with PA lung infection demonstrated increased mRNA expression in the brain of pro-inflammatory cytokines (IL-1{beta}, IL-6, and TNF-), chemokines (CXCL-1, CXCL-2) and adhesion molecules (VCAM-1 and ICAM-1) along with CD11b+ cell recruitment, corresponding to their increased blood levels of white cells (polymorphonuclear cells) and cytokines. To confirm the direct effect of cytokines on endothelial permeability, we measured cell-cell adhesive barrier resistance and junction morphology in mouse brain microvascular endothelial cell monolayers, where administration of IL-1{beta} induced a significant reduction of barrier function coupled with tight junction (TJ) diffusion and disorganization. Combined treatment with IL-1{beta} and TNF augmented the barrier injury. ConclusionsThese results suggest that lung bacterial infection causes cerebral microvascular leakage and neuroinflammation via a mechanism involving cytokine-induced BBB injury.

pharmacology and toxicology↗

bioRxiv2019

Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis

BackgroundSince 2014, the United States has experienced a biennial spike in pediatric acute flaccid myelitis (AFM). Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF) and only inconsistently identified from the respiratory tract, serum, or stool.\n\nMethodsWe interrogated CSF from children with AFM (n=42) and pediatric controls with other neurologic diseases (OND) (n=58). Samples were incubated with T7 bacteriophage expressing 481,966 sixty-two amino acid peptides with a fourteen amino acid overlap tiled across all known vertebrate virus and arbovirus genomes, an adaption of the VirScan method. Antibody-bound phage were deep sequenced to quantify enriched peptides with normalized counts expressed as reads per hundred thousand (rpK). EV antibody findings were confirmed with ELISA using whole viral protein 1 (VP1) from contemporary enterovirus (EV) A71 and D68 strains. Separately, metagenomic next-generation sequencing (mNGS) of CSF RNA, both unbiased and with targeted enrichment for EVs, was performed.\n\nResultsThe most significantly enriched viral family by VirScan of CSF in AFM versus OND controls was Picornaviridae (mean rpK 11,266 versus mean rpK 950, p-adjusted < 0.001, Wilcoxon signed-rank test with Bonferroni adjustment). Enriched Picornaviridae peptides belonged almost entirely to the genus Enterovirus. The mean EV VP1 ELISA signal in AFM (mean OD 0.51) was significantly higher than OND controls (mean OD 0.08, p-value < 0.001, Mann-Whitney test). mNGS did not detect additional enterovirus RNA in CSF.\n\nConclusionDespite the rare detection of EV RNA in the CNS of patients with AFM, a pan-viral serologic assay identified high levels of CSF EV antibodies in AFM CSF compared to CSF from OND controls. These results provide further evidence for a causal role of non-polio enteroviruses in AFM.

microbiology↗