Biology subjects

Smith, B. J.

Publications and source records attributed to Smith, B. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Developing and Characterizing a Murine Model of In Utero Transmission of Ebola Virus

Ebola virus (EBOV) disease (EVD) is a hemorrhagic disease caused by EBOV infection. EVD outcomes in pregnant women are similar to non-pregnant women however, EVD is associated with negative fetal outcomes in [~]99% of cases. There is a critical need for a tractable small animal model to study maternal/fetal transmission of EBOV. We utilized interferon /{beta} receptor knock out mice infected and authentic EBOV or the model virus, recombinant vesicular stomatitis virus encoding EBOV glycoprotein (rVSV/EBOV). Infection with either virus during late pregnancy resulted in placental infection and vertical transmission to the fetus within 2-3 days. Robust levels of maternal and fetal proinflammatory cytokines were evident by day 5 after EBOV infection. Within the placenta, trophoblasts and endothelial cells were viral antigen positive. Elimination of the endosomal receptor NPC1 in junctional zone trophoblasts reduced placental infection and virus transmission to the fetus. These studies establish an infectious model that provides EBOV trafficking and pathogenesis insights during pregnancy. TeaserThis model provides key insights into how viral trafficking and maternal immune responses drive adverse fetal outcomes during gestational Ebola virus infection.

microbiology↗

bioRxiv2026

Prey age modifies risk-taking behavior in a multi-predator environment

Many species of animals undergo senescence, impacting predator-prey relationships, yet how senescing prey adjust their risk-taking behavior is poorly understood. We used integrated step selection analysis to quantify risk-taking from empirical data. A graphical framework of age-dependent adaptive risk-taking predicted - and our empirical analysis found - a reduction in female elk (Cervus canadensis) risk-taking with age toward wolves (Canis lupus) but not cougars (Puma concolor), underscoring the role of predator hunting mode in ecological dynamics. We estimated average risk-taking toward wolves would be 42% lower in a population with median age 10 versus 4 years, highlighting how a prey populations age structure likely impacts risk-induced trait responses and the potential emergence of predation-risk effects. Our findings suggest that altered risk-taking may be an adaptive behavioral shift rather than a passive consequence of physical decline. Such adaptive changes to risk-taking may represent an underappreciated link between individual behavior and community-level coexistence.

ecology↗

bioRxiv2026

Jamaican fruit bats are susceptible to henipaviruses but rapidly control infection

Henipaviruses (HNV), Hendra (HeV) and Nipah (NiV) virus, cause severe pulmonary and neurologic disease in humans and other mammals. Bats in the genus Pteropus naturally host HeV and NiV, but their feasibility in experimental studies is limited due to their large size, low fertility rate, and unavailability outside of their native range. Understanding bat-henipavirus interactions that regulate shedding and replication could improve mitigation of spillover events and illuminate the factors that differentiate severe and controlled HNV infection. Here, we assessed the suitability of the Jamaican fruit bat (JFB) (Artibeus jamaicensis) to model HNV infection in vitro and in vivo. JFB primary kidney cells were permissive to HNVs, and HeV and NiV antagonized the induction of the innate antiviral response. JFBs were inoculated via the intranasal and oral routes (IN/PO) with HeV or NiV or intravenously (IV) with HeV and monitored for 7 days. Following IN/PO exposure, infection was quenched rapidly and limited HeV RNA was detected in oral swabs and tissues while NiV RNA was found in only one oral swab. HeV IV inoculation resulted in robust, disseminated infection and viral RNA was detected in oral, rectal, and environmental swabs. Overall, these results support that JFBs are susceptible to both viruses, but replication is quenched rapidly in vivo following IN/PO exposure. Future studies will optimize the in vivo model to leverage the JFB to further our understanding of bat-henipavirus interactions. Author SummaryHenipaviruses (HNV) spillover from pteropid bat species and cause severe diseases in humans. Many gaps limit our understanding of HNV-bat interactions that influence spillover and effective control of infection. Here, we evaluate the Jamaican fruit bat (JFB) as a henipavirus model. We demonstrate that JFB cells are permissive all HNVs evaluated, and that JFBs support Hendra virus replication and shedding without signs of clinical disease.

microbiology↗

bioRxiv2026

A Single-Dose Bundibugyo Virus Vaccine Protects Macaques Within 3 Days

Bundibugyo virus (BDBV), a member of the orthoebolaviruses in the Filoviridae family, causes severe hemorrhagic disease with high case-fatality rates. Currently, there are no medical countermeasures approved for human use hampering the response to the large ongoing outbreak in the Democratic Republic of the Congo and Uganda. While vesicular stomatitis virus (VSV)-based vaccines have demonstrated fast-acting prophylactic single-dose efficacy against multiple filoviruses, it has yet to be defined for VSV-BDBV. Here, we evaluated the rapid protection by a single-dose vaccination of VSV-BDBV in nonhuman primates (NHPs). Vaccination elicited rapid innate and early adaptive immune responses and conferred complete protection from clinical disease against BDBV challenge within 3 days. Vaccinated NHPs exhibited minimal clinical signs, limited systemic inflammation, and no infectious virus was isolated from the blood at any time. Protection correlated with neutralizing antibodies and Fc effector functionality of the humoral immune response. These findings establish VSV-BDBV as a fast-acting vaccine candidate suitable for outbreak response and highlight immune mechanisms underlying rapid protection.

microbiology↗

bioRxiv2026

Cell fusion reprograms tumor cells and promotes RUNX1-mediated invasion and dissemination in colorectal cancer

Metastasis remains the primary cause of cancer-related morbidity and mortality, despite significant advances in targeted therapies. Although metastatic dissemination requires tumor cells to escape the primary lesion and colonize distant organs, the mechanisms by which primary tumor cells gain metastatic competence remain poorly understood. Increasing evidence demonstrates that fusion of tumor (i.e., neoplastic) and immune (e.g., macrophages) cells generate a distinct population of tumor-immune hybrid cells with enhanced functional ability to migrate and disseminate into peripheral blood. Herein, our study investigates tumor-macrophage hybrid cells, an underexplored population of disseminated tumor cells, and their inherent heterogeneity and acquisition of molecular mechanisms underlying their dissemination as metastatic effectors in colorectal cancer (CRC). Through hybrid cell phenotyping utilizing integrative single-cell RNA sequencing (scRNA-seq), cyclic immunofluorescence (cyCIF) and functional assays with an in vitro model of CRC hybrid cells, we identify Runt-related transcription factor 1 (Runx1) as a central regulator of hybrid cell motility and invasion. Runx1 depletion in hybrid cells suppressed functional protease expression, chemotactic activity and extracellular matrix (ECM) invasion. Furthermore, pharmacologic inhibition of RUNX1 in an in vivo model reduced hybrid tumor growth and dissemination into peripheral blood, key attributes of metastatic spread of disease. In patients with CRC, RUNX1+ hybrid cells were identified in both primary tumor and peripheral blood, where circulating hybrid cells (CHCs) exhibited enriched migratory and epithelial-to-mesenchymal transition (EMT) phenotypes. Taken together, these findings reveal a mechanistic role for RUNX1 in driving invasive behavior of tumor-immune hybrids and highlight disseminated CHCs as an under-recognized contributor to metastatic spread and a promising noninvasive biomarker for tumor progression.

cancer biology↗

bioRxiv2026

Quantifying PD1 saturation by PDL1 in tumor tissue using a novel RNA aptamer-based assay

BackgroundTherapeutic agents targeting the PD1-PDL1 interaction are of great clinical value, however accurately predicting which patients are most likely to benefit is challenging. Improved predictive biomarkers for anti-PD1 therapy are clearly needed. Quantifying PD1 saturation by PDL1 in tumor tissue has the potential to serve as such a biomarker. Here we report a novel bioassay called the PD1 Ligand Receptor Complex Aptamer (LIRECAP) assay and demonstrate it can be used to quantify the saturation of PD1 by PDL1 in formalin-fixed paraffin-embedded tumor biospecimens. ResultsThe PD1 LIRECAP assay was developed by identifying a pair of RNA aptamers. One aptamer preferentially binds to unoccupied PD1 (P aptamer) and the other to the PD1-PDL1 complex (C aptamer). P and C aptamers were added together to a formalin-fixed sample, and bound aptamer extracted. A 2-color qRT-PCR assay using a single set of primers was used to determine the ratio of the sample-bound C to P aptamers (C:P ratio) which reflected PD1 saturation by PDL1 in the sample. Quantification of PD1 saturation by PDL1 as determined by the PD1 LIRECAP assay correlated closely with PD1-mediated signaling and PD1-PDL1 proximity. Analysis of sarcoma FFPE biospecimens confirmed the assay is technically reproducible on clinical biospecimens. There were significant differences in PD1 saturation by PDL1 between patients as well as considerable intratumoral heterogeneity. ConclusionsThe PD1 LIRECAP assay is novel assay that can be used to quantify PD1 saturation by PDL1 in clinical biospecimens. The assay is technically feasible, reproducible, and has the potential to serve as a superior predictive biomarker for PD1/PDL1-based therapy. Similar assays based on this platform could be used in other systems and settings to quantify interaction between two molecules.

immunology↗

bioRxiv2026

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models

Causal models of cellular systems hold the promise to empower broad biological discovery, including the systematic identification of novel targets for drug discovery. Predicting how genetic and pathway perturbations reshape gene expression across diverse cellular contexts is a prerequisite for building generalizable cellular foundation models. However, current methods typically fail to extrapolate beyond their training distributions because they rely predominantly on observational expression atlases rather than interventional perturbation data. We present X-Atlas/Pisces, the largest genome-wide CRISPRi Perturb-seq compendium to date, comprising 25.6 million perturbed single-cell transcriptomes across 16 biologically diverse contexts, including widely used cell lines, induced pluripotent stem cells (iPSCs), resting and CD3/CD28 activated Jurkat T lymphoma cells, and multi-lineage differentiating iPSCs. Leveraging this resource, we develop X-Cell, a diffusion language model that predicts perturbation responses by iteratively refining control-to-perturbed state transitions through cross-attention to multi-modal biological priors derived from natural language, protein language models, interaction networks, genetic dependency maps, and morphological profiles. X-Cell outperforms existing state-of-the-art models by up to five-fold on key metrics such as Pearson{Delta} (correlation between predicted and observed perturbation-induced log-fold changes), and demonstrates zero-shot prediction of T cell inactivating perturbations in stimulated Jurkat cells. We scale X-Cell to 4.9 billion parameters (X-Cell-Ultra), the largest causal perturbation model to date. We demonstrate for the first time that perturbation prediction follows power-law scaling with an exponent matching large language models. X-Cell-Ultra demonstrates zero-shot generalization to novel biological contexts, including unseen iPSC-derived melanocyte progenitors and primary human CD4+ T cells from multiple donors, and outperforms all baselines after self-supervised test-time adaptation. These results demonstrate that coordinated scaling of causal perturbation data and model capacity yields foundation models capable of generalizable perturbation prediction across cellular contexts, with potential applications for improving computational target identification, validation, and context-specific therapeutic prioritization.

systems biology↗

bioRxiv2025

Mathematical Modeling of Bone Remodeling after Surgical Menopause

Osteoporosis is a skeletal pathology characterized by decreased bone mass and structural deterioration resulting from an imbalance in bone metabolic processes. Estrogen deficiency in postmenopausal women leads to an increased risk of osteoporosis, while women who have undergone complete oophorectomies display an even higher risk due to the sudden decrease in estrogen. Some evidence indicates that bone loss slows in the period beyond 15 years after surgery; however, there is substantial uncertainty in clinical data. To explore the effects of surgically induced menopausal transition, here we propose a mathematical model for the bone cell dynamical responses to sudden estrogen deficiency, which extends an existing model for osteoporosis due to aging and natural menopause. Using data on the key impacts observed in female mice and humans after bilateral oophorectomy, this new model considers the role of osteocytes embedded within the bone mineralized matrix in regulating osteoclastogenesis, which results in increased bone resorption after surgical menopause. The values of model parameters in natural and surgical menopause were estimated from aggregated human clinical data from existing longitudinal studies. The new model effectively captures the previously unmodeled increase in bone loss during the first 15 years post-surgical menopause and the rebound in bone mineral density in the long-term. With this model, effects of treatments on targeting osteocyte dynamics could be explored in the future.

systems biology↗

bioRxiv2025

Siglec-F Protects Against Elastase-induced Lung Inflammation and Emphysema in Mice

Respiratory surfaces are exposed daily to billions of inhaled particles that could cause injury to alveolar tissues where gas exchange occurs. Accordingly, robust defense is essential but must involve minimal physiologic disruption. Airspace macrophages (AMs) protect lung surfaces while also maintaining tissue integrity through non-inflammatory homeostatic responses in health. However, in chronic obstructive pulmonary disease (COPD), AMs contribute to emphysematous alveolar destruction through mechanisms that are poorly understood. We hypothesized that damaging effects of AMs in emphysema result from loss of mechanisms that normally restrain homeostatic AMs. We found that Siglec-F, a common marker of AMs, exerts suppressive effects on tissue resident AMs (RAMs), thereby supporting alveolar integrity in mouse lungs during health and in a model of elastase-induced alveolar destruction. Siglec-F-deficient mice exhibited decreased alveolar numbers at baseline, and they had worsened alveolar damage after elastase challenge that was unexpectedly RAM-mediated. Transcriptomic profiling revealed dysregulation of key pathways involved in tissue remodeling and repair, including extracellular matrix degradation, TGF-{beta} signaling, and phagocytosis. These findings uncover previously unrecognized roles for RAMs and Siglec-F in preserving alveolar integrity. Our findings implicate RAMs and Siglecs as potential therapeutic targets for preserving alveolar integrity in health and for limiting alveolar damage in COPD.

immunology↗

bioRxiv2025

A cryptic START domain regulates deeply conserved transcription factors

Transcription factors (TFs) integrate a diverse array of inputs to achieve the exquisite control of gene expression necessary for life. In plants, this is exemplified by the deeply conserved CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of TFs. HD-ZIPIII activity is controlled by inputs at transcriptional, post-transcriptional, and post-translational levels. As part of their multidomain architecture, HD-ZIPIII TFs contain a StAR-related lipid transfer (START) domain, a ubiquitously distributed evolutionary module that binds various types of lipophilic ligands. Here, we show that HD-ZIPIII and HD-ZIPIV proteins contain a cryptic, deeply conserved START domain which we term the disorder-containing START domain (dSTART). The dSTART domain is required for HD-ZIPIII developmental function, controlling their subcellular localization and DNA-binding properties. The dSTART domain also helps discriminate responsive from non-responsive binding sites across the HD-ZIPIII shared genetic network. Finally, we identify candidate ligands of the dSTART domain including several species of phosphatidylglycerol and phosphatidic acid. The identification and functional characterization of a cryptic START domain provides new mechanistic insights into a deeply conserved family of TFs with roles in nearly all aspects of plant development.

plant biology↗

bioRxiv2025

Linkage of nucleotide and functional diversity varies across gut bacteria.

Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome (UHGG) collection to characterize patterns of intra-specific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.

microbiology↗

bioRxiv2025

Disabling PSGL-1 abrogates immune suppression and resistance to PD-1 blockade in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer for which there is a critical need to identify novel therapeutic targets. Herein we define PSGL-1 as a checkpoint inhibitor using a syngeneic orthotopic model of PDAC. As with PDAC patients, CD8+ T cells within murine PDAC tumors expressed high levels of PSGL-1. PSGL-1-/- mice displayed striking T cell-dependent control of primary tumors and lung metastases. Extensive spatial remodeling within PDAC tumors occurred in PSGL-1-/- mice with a dramatic loss of proliferating tumor cells and an increase in CD8+ T cell engagement of antigen-presenting cells. The prominent CD8+ T cell infiltrates included subsets of pre-exhausted T cells retaining hallmarks of stemness and multifunctional effector capacity. These changes enabled a near complete response of PDAC to therapeutic PD-1 blockade. Our findings identify PSGL-1 as a key regulator of anti-tumor immunity in PDAC, highlighting its potential as a therapeutic target to limit CD8+ T cell exhaustion and enhance immunotherapy response. SummaryHope et al describe a pivotal function of PSGL-1 in CD8+ T cell responses to pancreatic ductal adenocarcinoma. Genetic deletion of PSGL-1 elicits tumor control by increasing T cell infiltration and maintaining functional subsets, thereby promoting sensitivity to PD-1 blockade.

immunology↗

bioRxiv2025

Lung architecture amplifies tissue deposition in an agent-based model of fibrotic development

Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease where excessive extracellular matrix (ECM) deposition and remodeling stiffens the lung, impeding its function. Many factors are known to contribute to the development of this fibrosis, but a lack of conclusive understanding endures because of their complex nature. The modification of ECM and the unique architecture of the lung are such factors in IPFs propagation and not solely casualties. Their effects on fibrogenesis are not known and tricky to study. We apply a computational methodology known as an agent-based model (ABM) to simulate cellular behavior as automata. Our ABM is a tissue maintenance model where agents modify tissue density to sustain a global mean and variance to represent the cyclic turnover of ECM. Agents traverse and interact with high fidelity architecture obtained through micro computed tomography (microCT) of mouse lung tissue. The properties of the ABM are validated to microCT of fibrotic mouse lung tissue. We find that increasing cell density is sufficient for fibrogenesis, but that the lung architecture led to more tissue deposition. Our model suggests that lung structure is a relevant contributor to the pathogenesis of IPF.

systems biology↗

bioRxiv2025

Single-dose VSV-Sudan virus vaccine protects from lethal Sudan virus infection within one week: a challenge study in macaques

BackgroundThe Sudan virus (SUDV) outbreaks in recent years including the ongoing outbreak in Uganda created a public health emergency beyond the Eastern Africa region. Currently, there are licensed countermeasures for Ebola virus (EBOV); however, there are no licensed vaccines or therapeutics against SUDV. MethodsWe developed a vesicular stomatitis virus (VSV)-based vaccine expressing the SUDV glycoprotein. Cynomolgus macaques were vaccinated intramuscularly with a single dose of VSV-SUDV either one month or one week prior to SUDV challenge. A third group was vaccinated with a single dose of VSV-EBOV one month prior to SUDV challenge to assess its cross-protective potential, and a control group received an unrelated VSV-based vaccine. ResultsAll vaccinated nonhuman primates (NHPs) developed antigen-specific IgG within 2 weeks of vaccination, including cross-reactive responses. After challenge with a lethal dose of SUDV, all VSV-SUDV-vaccinated NHPs were uniformly protected from disease. In contrast, the VSV-EBOV-vaccinated and control NHPs succumbed to disease between day 5 and 7 after challenge presenting with classical signs of Sudan virus disease associated with high titer viremia, high viral organ load, dysregulated cytokine profiles and typical pathological changes. The humoral immune response in the NHPs vaccinated with VSV-SUDV one month before challenge resulted in a profound and sustained antibody response with a diverse functionality profile which was not observed to the same extend in NHPs vaccinated one week before challenge. InterpretationWe demonstrated that a single dose of VSV-SUDV protected NHPs from lethal SUDV infection within one week. The fast-acting nature makes VSV-SUDV an ideal countermeasure for ring vaccination during outbreaks of Sudan virus disease. In contrast, VSV-EBOV provided no relevant protection against SUDV infection in NHPs highlighting the need for species-specific filovirus vaccines.

microbiology↗

bioRxiv2025

An image-based biophysical model of the lung to investigate the effect of pulmonary surfactant on lung function

Lung biomechanics aims to understand the structure-function relationship in the lung under normal and pathological conditions. Pulmonary surfactant has a key structural role in lung function with a significant contribution to the mechanical response of the lungs during respiration. Pulmonary surfactant dynamically regulates surface tension at the air-liquid interface to decrease stiffness during respiration and prevent alveolar collapse during lower volumes. Many lung injuries involve alterations to the contribution of surfactants to lung function. We developed a novel biophysical model using a poroelastic formulation that incorporates pulmonary surfactant dynamics and aims to quantify the contribution of the pulmonary surfactant toward lung compliance. The effect of pulmonary surfactant was modeled as a surface energy function, and the surface behavior was converted to bulk behavior by assuming uniform spherical alveoli. The model was used to simulate respiration and investigate the effect of altered surface tension caused by surfactant dysfunction. The model captured the characteristic sigmoidal inspiratory pressure-volume curve and hysteresis observed during clinical measurements. In addition, the model predicted the expected behavior in surfactant dysfunction in lung injuries. We expect this work to serve as an essential step towards de-convoluting and predicting the contributions of the lung parenchyma and pulmonary surfactant to global and regional lung compliance in health and disease.

biophysics↗

bioRxiv2025

Customizing the Structure of a Minimal TIM Barrel to Craft a De Novo Enzyme

The TIM barrel is the most prevalent fold in natural enzymes, supporting efficient catalysis of diverse chemical reactions. While de novo TIM barrels have been successfully designed, their minimalistic architecture lacks structural elements essential for substrate binding and catalysis. Here, we present CANVAS, a computational workflow that introduces a structural lid into a minimal de novo TIM barrel to anchor catalytic residues and form an active-site pocket for enzymatic function. Starting from two de novo TIM barrels, we designed nine variants with distinct lids to form active sites for the Kemp elimination. Four designs showed measurable activity, with the most active reaching a catalytic efficiency of 21,000 M-{superscript 1} s-{superscript 1} at its optimal pH. A co-crystal structure of this variant bound to a transition-state analogue confirmed the accuracy of the designed lid and active site. Using the X-ray structure of a lower-activity variant (19 M-{superscript 1} s-{superscript 1}), we applied ensemble-based design to optimize its active site, increasing catalytic efficiency by >1,600-fold to 32,000 M-{superscript 1} s-{superscript 1}. These results demonstrate that de novo TIM barrels can be endowed with substrate binding pockets supporting efficient catalytic function, establishing a platform for building enzymes on demand from minimal protein scaffolds.

biochemistry↗

bioRxiv2024

Mathematical Modeling of Estrogen-Mediated Inflammation in the Gut and Immune System

Postmenopausal osteoporosis is a chronic inflammatory disease characterized by decreased bone mass and increased bone fracture risk. Estrogen deficiency during menopause plays a major role in post-menopausal osteoporosis by influencing bone, immune, and gut cell activity. In the gut, estrogen loss decreases tight junction proteins that bind epithelial cells of the intestinal barrier together. This increases gut permeability and alters the balance of T cells, increasing inflammatory T helper (Th17) cells and decreasing anti-inflammatory regulatory T cells (Tregs). Prebiotic dietary fibers are a promising treatment modality for gut-mediated inflammation and bone loss associated with estrogen deficiency. In a previous study, we investigated the effect of butyrate (a prebiotic by-product) on Treg levels in the gut, blood, and bone starting with healthy conditions. However, a gap remains in our mechanistic understanding of how estrogen affects systemic inflammation separately and in combination with prebiotic fibers. We developed a two-compartment dynamic model of estrogen in the gut and immune system to investigate the mechanisms of gut-mediated inflammation induced by estrogen-deficient conditions. Our initial model contains ODEs for estrogen, naive T cells, Tregs, and Th17 cells in gut and blood compartments. Estrogen is modeled using physiological mass balance equations considering its production, migration, and elimination. We integrate our estrogen model with an adapted version of our previous butyrate model, adding a population balance for Th17 cells and terms for bidirectional migration of Tregs and Th17 cells. Estrogen interactions with cells are modeled using Hill-type activation and inhibition functions. Our mathematical model predicts changes in T cell dynamics associated with changes in endogenous estrogen levels. We compare our predictions to in vivo results of estrogen, Tregs, and Th17 levels in the gut and blood after surgical menopause in mice. In the future, we will leverage this model to investigate whether the effect of prebiotic fiber treatment on estrogen-deficient bone loss is significantly affected by gut-mediated inflammation. The emphasis in this preprint is on the methods, particularly those for literature-based model parameterization.

systems biology↗

bioRxiv2024

Ixochymostatin, a trypsin inhibitor-like (TIL) protein from Ixodes scapularis, inhibits chymase and impairs vascular permeability

Ticks, as pool feeders, obtain a blood meal by lacerating small blood vessels and ingesting the blood that flows to the feeding site, which triggers various host-derived responses. However, ticks face the challenge of wound healing, a process involving hemostasis, inflammation, cell proliferation and migration, and remodeling, hindering blood acquisition. To overcome these obstacles, tick salivary glands produce a diverse array of bioactive molecules. Here, we characterize ixochymostatin, an Ixodes scapularis protein belonging to the trypsin inhibitor-like (TIL) family. It is expressed in multiple developmental stages and in tick salivary glands and acts as a slow and tight-binding inhibitor of chymase, cathepsin G, and chymotrypsin. Predictions for the tertiary structure complex between ixochymostatin and chymase suggest a direct interaction between the inhibitors reactive site loop and protease active sites. In vitro, ixochymostatin protects the endothelial cell barrier against chymase degrading action, decreasing cell permeability. In vivo, it reduces vascular permeability induced by chymase and compound 48/80, a mast cell degranulator agonist, in a mouse model. Additionally, ixochymostatin inhibits the chymase-dependent generation of vasoconstrictor peptides. Antibodies against ixochymostatin neutralize its inhibitory properties, with epitope mapping identifying potential neutralization regions. Ixochymostatin emerges as a novel tick protein modulating host responses against tick feeding, facilitating blood acquisition. HighlightsO_LIIxochymostatin is a newly described trypsin inhibitor-like (TIL) protein from Ixodes scapularis. C_LIO_LIIxochymostatin inhibits chymase and reduces vascular permeability. C_LIO_LIIxochymostatin inhibits chymase-dependent generation of vasoconstrictive peptides. C_LIO_LIAntibodies generated against ixochymostatin neutralize its inhibitory functions. C_LIO_LIPotential epitopes responsible for anti-ixochymostatin neutralization were mapped. C_LI

biochemistry↗