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Smith, B.

Publications and source records attributed to Smith, B..

At least 19 recordsLinked to original sources
bioRxiv2026

A patient-derived xenograft model of FUS::TFCP2 intraosseous rhabdomyosarcoma reveals chemoresistance and differential sensitivity to ALK inhibitors

TFCP2-rearranged rhabdomyosarcoma is an exceptionally rare and highly aggressive malignancy driven by TFCP2 gene fusions and associated with a dismal clinical prognosis. Because standardized treatment regimens are lacking, developing representative preclinical models is critical for identifying effective therapies. Here, we present a case of a 29-year-old male with rapidly progressive, metastatic pelvic intraosseous rhabdomyosarcoma (iRMS) harboring a FUS::TFCP2 fusion and anaplastic lymphoma kinase (ALK) overexpression. To evaluate therapeutic vulnerabilities, we established a patient-derived xenograft (PDX) model that faithfully recapitulated the histologic, immunohistochemical, and molecular hallmarks of the primary tumor. High-throughput in vitro pharmacological screening of PDX-derived cells demonstrated notable resistance to standard cytotoxic chemotherapies and revealed a paradoxical and selective sensitivity profile across ALK inhibitors. The PDX-derived cells were susceptible to crizotinib, brigatinib, and ceritinib, yet resistant to the more selective second- and third-generation inhibitors alectinib and lorlatinib. Notably, next-generation ROS1/pan-TRK inhibitors (entrectinib, repotrectinib, and taletrectinib) demonstrated superior efficacy compared to the fourth-generation ALK inhibitor NVL-655. Our findings establish a validated preclinical PDX model for FUS::TFCP2 iRMS and suggest that multi-targeted tyrosine kinase inhibition may offer a more viable therapeutic strategy than narrow-spectrum ALK targeting or conventional chemotherapy.

cancer biology↗
bioRxiv2026

Tension TRAAKer: a chemigenetic fluorescent membrane tension reporter

Mechanical force transduction is essential to survival, underlying biological processes as fundamental as morphogenesis, somatosensation, audition, and interoception; and driving pathologies as diverse as hypertension and cancer metastasis. Exogenous forces are translated to intracellular signals through transient changes in membrane tension which are currently not possible to directly monitor in situ. To remedy this, we have designed and validated Tension TRAAKer, a chemigenetic fluorescent membrane tension reporter for the visualization of tension induction, propagation, and dissipation in living cells. Tension TRAAKer is derived from inserting a tension-sensitive nonconductive variant of the mechanosensitive potassium ion channel TRAAK into a self-labelling HaloTag. Increasing membrane tensions effect conformational changes in the TRAAK channel that are optically monitored by a HaloTag-conjugated fluorogenic (environment-sensitive) dye. EGFP incorporation C-terminal to the HaloTag enables unambiguous tension reporting in mobile membranes via dual-color ratiometric imaging that controls for variations in sensor density. Tension TRAAKer reports membrane tension changes rapidly, reversibly, and with spatiotemporal precision--its fluorescence scaling to both stimulus magnitude and area, with consistent effect sizes observed between diverse cell types. It better distinguishes among elevated membrane tensions than do available indirect chemical reporters, with the additional advantage of being readily genetically targetable. We thus expect Tension TRAAKer to be a powerful tool for the study of membrane tension across biological systems and disease states.

molecular biology↗
bioRxiv2026

Energetic misfires: Hybridization drives transgressive expression in metabolic pathways in thermally divergent Icelandic stickleback

Climate change is causing rapid changes to freshwater environments, driving selection for phenotypes that can cope with altered thermal conditions, while also changing developmental environments. This may promote local adaptation, migration to new habitats, and/or phenotypic plasticity. Climate change may also increase hybridization rates between locally adapted phenotypes, as populations migrate and spatially mix in new ways. Consequently, these conditions may facilitate the production of variation, including both adaptive and maladaptive outcomes. To examine this, we leveraged threespine stickleback (Gasterosteus aculeatus) that have locally adapted to either geothermally warmed or ambient environments in Iceland. We tested the effects of hybridization between thermal ecotypes on gene expression using a common garden experiment, where pure-strain ecotypes and their hybrids were reared under 12{degrees}C and 18{degrees}C. We performed RNA-seq on brain and liver to assess 1) ecotype divergence, 2) plasticity, and 3) the effects of hybridization and inheritance patterns. We identified a low degree of expression divergence between locally adapted ecotypes, despite a high degree of plasticity across rearing environments. Hybrid ecotypes were highly divergent from both geothermal and ambient ecotypes and exhibited transgressive expression under both rearing temperatures. Transgressive expression disrupted gene networks extensively, with broader effects at 18{degrees}C than at 12{degrees}C, primarily associated with metabolism and mitochondrial function. Hybridization between locally adapted thermal ecotypes appears to largely disrupt genes associated with energy balance and metabolic function. While demonstrating mechanisms underlying the rapid evolution of reproductive isolation, these findings also provide insights for how populations may cope or fail within a warming world.

evolutionary biology↗
bioRxiv2026

Effects of Bimodal Olfactory and Mechanosensory Inputs in the Antennal Lobe of the Honeybee Apis mellifera

Animals often aggregate information from multiple different sensory modalities to accurately assess and react to a stimulus. It is often assumed that cross-modality integration mostly occurs at high-level processing centers, such as the mammalian cortex or insect mushroom bodies. However, we hypothesized that integration could occur relatively early in the sensory pathways. The insect antennal lobe is one such location, receiving direct inputs from the antennae via the antennal nerve. These inputs are highly multimodal, including olfactory, mechanosesnory, and gustatory information, all of which are relevant to foraging honeybees (Apis mellifera). Here we assess integration by recording electrophysiological spike data within the honeybee antennal lobe while exposing the bee to various combinations of wind speed and odor concentration. This paper accompanies another publication by Joseph Reed and Mainak Patel approaching the same question from a modelling perspective, where their model corroborates our data and vice versa. Together, we show that integration occurs within this early layer of processing, while also demonstrating the complex relationship of these two closely-linked stimuli. SIGNIFICANCEAccurate perception depends on the brains ability to combine information from multiple senses, commonly thought belonging to high level of information processing. Using the European honeybee, Apis mellifera, we show strong evidence that olfactory and mechanosensory signals interact at an early stage of neural processing, within the antennal lobe, producing stimulus representations closely-linked to the animals navigation and decision-making. By identifying a tractable model for early multisensory processing, this work offers broader insight into how animals construct reliable representations of their environment.

neuroscience↗
bioRxiv2026

Adapting a two-photon scanning microscope for simultaneous single-photon imaging of an infrared dopamine sensor

We describe a novel method for adapting a two-photon scanning microscope to enable simultaneous detection of two-photon generated visible fluorescence and single-photon generated near-infrared (nIR) fluorescence. In this configuration, nIR fluorescence is routed through a single-mode optical fiber before detection by a photomultiplier tube. This fiber coupling offers two advantages: first, the optical fiber functions as a pinhole aperture, allowing for improved optical sectioning of the nIR signal; second, it minimizes nIR background fluorescence. To validate the effectiveness of this design, we conducted two sets of experiments. First, we compare two fluorescence indicators of the neurotransmitter dopamine: the genetically encoded indicator GRABDA and single walled carbon nanotube based optical nanosensors (nIRCats). Although nIRCats exhibit lower affinity for dopamine than GRABDA, this property allows for identification of high concentration release sites in the striatum. Second, we simultaneously imaged depolarization-induced calcium changes and dopamine release in the retina. Together, these results demonstrate the utility of integrating confocal nIR detection into a two-photon platform for simultaneous functional imaging across complementary spectral channels.

bioengineering↗
bioRxiv2025

State-dependent release of extracellular particles with distinct α2,6-sialylation patterns and small RNA cargo related to neuroinflammation

Neuroinflammation is a significant contributor to neurodegenerative diseases, including Alzheimers disease, Parkinsons disease, and related dementias; yet peripheral biomarkers for neuroinflammation remain an unmet medical need. Microglia, the resident immune cells of the central nervous system, play a dual role in maintaining homeostasis under physiological conditions and driving neuronal damage when chronically dysregulated. One mechanism by which microglia influence their environment is through the release of extracellular vesicles (EVs) and non-vesicular extracellular particles (NVEPs), which can serve as biomarkers the reflect cellular states. Here, we systematically isolated and characterized microglia-derived EVs and NVEPs under pro- and anti-inflammatory conditions and profiled their small RNA cargo by small RNA sequencing. We validated these findings in human iPSC-derived microglia and further recapitulated them in EVs and NVEPs from mouse brain and plasma. Using an engineered mouse model, we were able to isolate plasma microglia-specific EVs in vivo and demonstrated that their RNA cargo reflects their inflammatory state. Importantly, microglial EVs and NVEPs display distinct 2,6-sialylation patterns and small RNA signatures implicated in neurological diseases. These findings demonstrate that microglia-derived EVs and NVEPs cargo reflect microglial cellular state and establish them as putative minimally non-invasive biomarkers of early-stage neurodegenerative diseases.

neuroscience↗
bioRxiv2025

Exploring Size Exclusion Chromatography Columns 20 and 35 nm Pore Size Effect for Isolation of Extracellular Vesicles

Extracellular vesicles (EVs) have shown great promise as minimally invasive biomarkers for a variety of diseases. However, challenges persist regarding EV isolation, particularly in their co-isolation with impurities such as soluble proteins and lipoproteins. Among the methods available for EV isolation, size-exclusion chromatography (SEC) is widely used, as it is reproducible and amenable to high-throughput with a rapid turnaround time. However, its size-based separation leads to the co-isolation of EVs with impurities of similar size. This study, for the first time to our knowledge, compares SEC columns with different pore sizes, 20 and 35 nm, to evaluate their efficacy in non-EV contaminant removal and EV recovery from pancreatic EndoC-{beta}H1 cell culture media and human plasma. To assess EV purity and yield, we compare EV particle concentration, the presence of unintended co-isolates, and RNA EV cargo. This study demonstrates that smaller pore size SEC columns enhance EV yield and purity, making them ideal for biomarker studies involving limited biological samples or downstream analysis sensitive to contaminants.

biochemistry↗
bioRxiv2025

Highly efficient anogenital transmission of clade Ia mpox virus associated with increased shedding.

The transmission pattern of mpox has shifted from sporadic zoonotic outbreaks to sustained human-to-human spread. Epidemiological data indicate sexual contact as a crucial driver for efficient transmission and the associated devastating mpox outbreaks in recent years. However, our understanding of exact driving factors and transmission determinants is still limited. Here, we investigated MPXV clade Ia virus pathogenicity, shedding kinetics, and transmission potential in a prairie dog model (Cynomys ludovicianus). All tested mucosal inoculation routes (penile/preputial, vaginal, rectal, intranasal) resulted in a productive, systemic infection. Inoculation via urogenital routes generated the highest virus shedding and most severe clinical disease. A simulated sexual contact transmission resulted in 100% transmission efficiency with high virus shedding in sentinels on day 1, even before the onset of clinical signs. Our findings provide critical insights into mpox transmission, emphasizing the role of anogenital mucosal surfaces in facilitating rapid spread. These results advocate for a stronger focus on mucosal infection when evaluating countermeasures.

microbiology↗
bioRxiv2025

Immune Biomarkers, Profiles, and Responses: A Vaccine Ontology Perspective

BackgroundVaccines have the ability to induce a range of immune responses under different conditions, for example stimulating the production of neutralizing antibodies to block pathogen entry or activating cytotoxic T-cells to eliminate infected cells. Many such immune responses have not been thoroughly examined and classified. The Vaccine Ontology (VO) is a community-based ontology in the domain of vaccinology. We here describe how VO is used to represent the variety of immune responses associated with vaccines, together with associated biomarkers and profiles. ResultsThe VO differentiates vaccination and vaccine immunization. The former is a process of administering a vaccine in vivo; the latter is the outcome of vaccine induction of immune response. This distinction is critical for understanding both the procedure of vaccination and the resulting immune effects. VO also models and represents various vaccine-induced responses at multiple biological levels, including population, organism, organ/tissue, cell, and gene/protein levels. Such an approach captures the complexity of vaccine-induced immunity, from population-wide trend (for example: herd immunity) to molecular mechanisms. VO defines immune biomarkers as material entities such as neutralizing antibodies that signify humoral immune response, and IFN-gamma that is indicative of cell-mediated responses. Such biomarkers provide measurable indicators of the immune systems functional state post vaccination, enabling robust evaluation of vaccine efficacy. VO classifies immune response profile and correlated profile (or correlate) of immune protection as process profiles, a class in the Basic Formal Ontology (BFO 2.0). Immune response profiles, such as Th1 (or Th2)- biased profile, can be induced by various vaccines and vaccine adjuvants. Different types of correlated profile of immune protection are also identified, such as mechanistic and non-mechanistic correlates of immune protection. Such distinctions help us to quickly identify biomarkers and associated prediction and measurement of different kinds of vaccine protection. ConclusionThe important immune-related terms for immune biomarkers, profiles, and responses are modeled ontologically in VO together with their interrelations. The results support enhanced classification and analysis of vaccine-induced immune responses and related biomarkers and immune profiles, leading to further understanding of the vaccine immune mechanisms and enhanced vaccine research and development.

immunology↗
bioRxiv2025

Assessing wetland conservation action effectiveness in the Mekong Delta with Sentinel-1 Synthetic Aperture Radar data

Concerns about the effectiveness of nature conservation efforts have led to the adoption of evidence-based approaches and more rigorous evaluation methods. This is especially relevant to wetlands, which are crucial for ecosystem services and face global threats from human actions. In the present study, 10-m Sentinel-1 synthetic aperture radar (SAR) data, which provide global coverage regardless of cloud cover, are used to assess the effectiveness of wetland restoration activities which aim to promote wetter conditions. These were carried out during 2022-2024 in the Boeung Prek Lapouv area (Mekong delta, Cambodia). A method was developed to separate SAR signals from the dry and wet seasons to infer variations in groundwater level and wetness retention. Analysis of these signals showed that interventions were effective to varying degrees with the construction of new pools, the lowering of grounds and blocking of ditches being the most impactful.

ecology↗
bioRxiv2025

Increased contact transmission of contemporary Human H5N1 compared to Bovine and Mountain Lion H5N1 in a hamster model

The ongoing outbreak of highly pathogenic avian influenza virus (HPAIV) subtype H5N1 in the U.S. poses a significant public health threat. To date, 70 human cases have been confirmed in the United States, including two severe cases and one fatality. While suitable animal models are crucial for predicting the potential pandemic risk of newly emerging pathogens in humans, studies investigating contemporary HPAIV H5N1 transmission dynamics remain limited. Here, we investigated the pathogenicity and transmission efficiency of three recent clade 2.3.4.4b H5N1 viruses isolated from a bovine, mountain lion, and a human case using Syrian hamsters. Intranasal inoculation with 104 TCID50 resulted in productive virus replication in the respiratory tract and shedding for all three isolates. Transmission studies showed limited efficiency via direct contact and airborne routes for all three isolates. Although overall transmission was inefficient, the human H5N1 isolate demonstrated relatively greater contact transmissibility than the bovine and mountain lion isolates. Taken together, our data demonstrate that the Syrian hamster model complements existing animal models for influenza A virus research and expands the resources available for investigating the pathogenicity, transmissibility, and efficacy of countermeasures against HPAIV H5N1. One sentence summaryHuman HPAIV H5N1 exhibits comparatively higher contact transmissibility than bovine and mountain lion isolates, despite limited overall transmission.

microbiology↗
bioRxiv2025

Multiomics Reveals Compartmentalized Immune Responses and Tissue-Vascular Signatures in Lyme Disease

Lyme disease (LD) is growing in incidence, with nearly 500,000 cases diagnosed annually in the United States. Despite treatment, some patients experience persistent symptoms. The immune mechanisms underlying LD remain poorly understood. We conducted a multiomic longitudinal analysis of 49 LD patients and matched controls, integrating plasma proteomics, metabolomics, PBMC immunophenotyping, and a meta-analysis of skin lesions. We identified compartmentalized immune responses in acute LD, with coordinated alterations in circulating plasma proteins and metabolites linked to endothelial barrier stability, metabolic reprogramming, and symptom severity, predominantly traced to tissue and vascular immune processes at the site of infection. In contrast, PBMCs remained largely quiescent, revealing a disconnect between localized tissue responses and systemic immunity. These findings provide novel insights into LD pathophysiology and highlight the potential for diagnostics leveraging tissue and vascular immune markers detectable in blood. They also provide a resource for biomarker discovery and predictive modeling to improve LD management.

immunology↗
bioRxiv2025

Peroxisomes regulate virulence and cell density sensing in Cryptococcus neoformans

Cryptococcus neoformans, a ubiquitous environmental fungus that causes cryptococcosis, survives in diverse environments including human hosts due to metabolic flexibility. Consequently, identifying how C. neoformans connects diverse metabolic pathways and virulence factor expression is important for understanding fungal pathogenesis. Peroxisomes play an essential role in metabolic homeostasis and regulation of carbon and lipid metabolism. In this article, we report a link between nickel exposure, a known hypoxia-mimetic and mitochondrial respiration inhibitor in yeast, and peroxisomal {beta}-oxidation. Loss of the last two genes involved in the peroxisomal {beta}-oxidation pathway, MFE2 (CNAG_05721) and POT1 (CNAG_00490), resulted in cell density-dependent virulence factor defects and growth inhibition attributed to a metabolic state involving large peroxisomes. We found that increasing cell density rescued virulence factor phenotypes and growth. Our results implicate mitochondrial retrograde signaling (RTG), a previously uncharacterized pathway in C. neoformans, in cell density sensing, peroxisomal {beta}-oxidation pathway expression, and virulence, thus highlighting a critical role for metabolism in cryptococcal virulence.

microbiology↗
bioRxiv2025

Cross-membrane cooperation among bacteria can facilitate intracellular pathogenesis

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen able to cause life- and sight-threating infections. Once considered an extracellular pathogen, numerous studies have shown it can survive intracellularly. Previously, we showed that P. aeruginosa inside cells can diversify into distinct subpopulations in vacuoles and the cytoplasm. Here, we report that the transition from vacuoles to cytoplasm requires collaboration with the extracellular subpopulation, through Ca2+ influx enabled by their type III secretion system (T3SS) translocon pore proteins. Moreover, we show that collaboration among P. aeruginosa subpopulations can contribute to disseminating intracellular bacteria in vivo in a mouse infection model. This study provides the basis for future studies to investigate how cooperation of extracellular and intracellular bacteria within the host may contribute to disease progression and persistence.

microbiology↗
bioRxiv2025

Overcoming Fluorescence Loss in mEOS-based AAA+ Unfoldase Reporters Through Covalent Linkage

Recent work has demonstrated that the soluble photoconvertable fluorescent protein mEOS can be a reporter for AAA+ (ATPases Associated with diverse cellular Activities) unfoldase activity. Given that many AAA+ proteins process membrane proteins, we sought to adapt mEOS for use with membrane protein substrates. However, direct genetic fusion of mEOS to a membrane protein completely abolished fluorescence, severely limiting the utility of mEOS for studying AAA+ proteins. To circumvent this challenge, we separately purified mEOS and a AAA+ degron, covalently linked them via Sortase, and photoconverted the linked construct. This innovative approach preserves fluorescence and enables functional analysis, offering a broadly applicable platform for the study of membrane associated AAA+ proteins.

biochemistry↗
bioRxiv2025

APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence

Elucidating the relationships between a class I peptide antigen, a CD8 T cell receptor (TCR) specific to that antigen, and the T cell phenotype that emerges following antigen stimulation, remains a mostly unsolved problem, largely due to the lack of large data sets that can be mined to resolve such relationships. Here, we describe Antigen-TCR Pairing and Multiomic Analysis of T-cells (APMAT), an integrated experimental-computational framework designed for the high-throughput capture and analysis of CD8 T cells, with paired antigen, TCR sequence, and single-cell transcriptome. Starting with 951 putative antigens representing a comprehensive survey of the SARS-CoV-2 viral proteome, we utilize APMAT for the capture and single cell analysis of CD8 T cells from 62 HLA A*02:01 COVID-19 participants. We leverage this unique, comprehensive dataset to integrate with peptide antigen properties, TCR CDR3 sequences, and T cell phenotypes to show that distinct physicochemical features of the antigen-TCR pairs strongly associate with both T cell phenotype and T cell persistence. This analysis suggests that CD8+ T cell phenotype following antigen stimulation is at least partially deterministic, rather than the result of stochastic biological properties.

immunology↗
bioRxiv2024

Sex-specific DNA methylation differences in Amyotrophic lateral sclerosis

Sex is an important covariate in all genetic and epigenetic research due to its role in the incidence, progression and outcome of many phenotypic characteristics and human diseases. Amyotrophic lateral sclerosis (ALS) is a motor neuron disease with a sex bias towards higher incidence in males. Here, we report for the first time a blood-based epigenome-wide association study meta-analysis in 9274 individuals after stringent quality control (5529 males and 3975 females). We identified a total of 226 ALS saDMPs (sex-associated DMPs) annotated to a total of 159 unique genes. These ALS saDMPs were depleted at transposable elements yet significantly enriched at enhancers and slightly enriched at 3UTRs. These ALS saDMPs were enriched for transcription factor motifs such as ESR1 and REST. Moreover, we identified an additional 10 genes associated with ALS saDMPs through chromatin loop interactions, suggesting a potential regulatory role for these saDMPs on distant genes. Furthermore, we investigated the relationship between DNA methylation at specific CpG sites and overall survival in ALS using Cox proportional hazards models. We identified two ALS saDMPs, cg14380013 and cg06729676, that showed significant associations with survival. Overall, our study reports a reliable catalogue of sex-associated ALS saDMPs in ALS and elucidates several characteristics of these sites using a large-scale dataset. This resource will benefit future studies aiming to investigate the role of sex in the incidence, progression and risk for ALS.

genomics↗