Biology subjects

Le, V.

Publications and source records attributed to Le, V..

11 recordsLinked to original sources

bioRxiv2026

Neutralizing vaccination against viral interleukin-6 from a primate rhadinovirus

Herpesviruses are ancient viruses that devote a significant fraction of their protein-coding potential to interference with host immunity. Diverse herpesviruses encode proteins with similarity to host MHC molecules, interferon regulatory factors, complement regulators, G-protein coupled receptors, chemokines, and cytokines. Certain gammaherpesviruses, including Kaposi sarcoma-associated herpesvirus (KSHV) and rhesus rhadinovirus (RRV), encode viral cytokines similar to host IL-6, called viral IL-6 (vIL-6). The potential of vIL-6 to act as a protective vaccine antigen against these rhadinoviruses remains under-explored. We isolated a new RRV strain, which encodes virion surface proteins similar to those of previous isolates and a vIL-6 that is nearly identical. We found that, although unmodified vIL-6 is a poor immunogen eliciting low neutralizing titers, vIL-6-Fc fusion protein elicits high-titer responses after either one or two doses. We detected no adverse effects related to cytokine activity, nor interference with concomitantly administered vaccine against the RRV glycoprotein B. Our results demonstrate an approach for eliciting neutralizing antibodies against a highly conserved viral protein that contributes to rhadinovirus persistence and oncogenesis.

immunology↗

bioRxiv2026

Multisite Evaluation of an Amplification-based Nanopore Sequencing Solution to Analyze Challenging Clinically Relevant Variants in Genes Associated with Hereditary Diseases

PurposeCarrier screening for hereditary conditions is challenged by genes with complex genomic architecture, where short-read sequencing can fail to detect clinically relevant variants. This study evaluated a unified, amplification-based nanopore sequencing workflow across multiple laboratories for comprehensive analysis of such loci. MethodsA modular long-read sequencing assay was evaluated across five laboratories using targeted PCR enrichment, Oxford Nanopore sequencing, and automated variant analysis. The workflow interrogated genes associated with spinal muscular atrophy, thalassemia, cystic fibrosis, fragile X syndrome, congenital adrenal hyperplasia, Gaucher disease, and hemophilia A. Performance was assessed against orthogonal methods for single nucleotide variants (SNVs), indels, copy-number variants, repeat expansions, and structural rearrangements. ResultsAcross 882 unique samples (1,266 tests), overall agreement with comparator methods exceeded 96% for variant-level detection and 97% for genotype status classification. Long-read sequencing enabled phasing of paralogous loci, integrated sizing and interruption analysis for FMR1 repeats, and simultaneous detection of SNVs and structural variants in globin loci and CYP21A2-TNXB region, reducing reliance on multiple workflows. ConclusionThis multisite evaluation suggests that targeted long-read sequencing can consolidate complex variant detection into a single workflow, improving analytical completeness and operational efficiency for carrier screening.

genetics↗

bioRxiv2026

Deep mutational scan of the pore of the cold-sensing TRPM8 channel

Members of the Transient Receptor Potential (TRP) family of ion channels have a nearly ubiquitous role in human physiology, tuning cell signaling to remarkably diverse physical and chemical stimuli. Although there is extensive structural data on TRP channels, a systematic and unbiased interrogation of structure-function relations in these proteins is required to fully elucidate their mechanisms of function. By focusing on a critical pore region of the TRPM8 channel, which is the main detector of cold and cooling agents in sensory neurons, we show how deep mutational scanning can be used in combination with the available structural data to understand how TRP channels respond to stimuli. We define a novel mechanism whereby the extracellular pore loop, which has only been resolved in structures representing desensitized states of the channel, plays an essential role in the response of TRPM8 to menthol or cold by coordinating the movement of the S6 helices that line and gate the pore, and the ion-selectivity filter that binds permeant cations. Moreover, our screen reveals sequence determinants along the S6 helices that explain how their architecture sustains gating and, together, provide strong support for a structural mechanism of TRPM8 pore opening in response to menthol and cold.

biophysics↗

bioRxiv2025

Gene model for the ortholog of Glyp in Drosophila pseudoobscura

Gene model for the ortholog of Glycogen phosphorylase (Glyp) in the Apr. 2013 (BCM-HGSC Dpse_3.0/DpseGB3) Genome Assembly of D. pseudoobscura (GCA_000001765.2). This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

genomics↗

bioRxiv2025

Fluphenazine, an antipsychotic compound, ameliorates Alzheimer's disease by clearing amyloid beta accumulation in

The ageing population worldwide faces an increasing burden of age-related conditions, with Alzheimers disease being a prominent neurodegenerative concern. Drug repurposing, the practice of identifying new therapeutic applications for existing drugs, offers a promising avenue for accelerated intervention. In this study, we utilized the yeast S. cerevisiae to screen a library of 1,760 FDA-approved compounds, both with and without rapamycin, to assess potential synergistic effects on yeast growth. We identified 87 compounds that showed synergistic effect with rapamycin and caused growth defects in yeast. These compounds were further screened for their effects on paralysis in a C. elegans model of Alzheimers disease. We found that three compounds synergistically delayed paralysis in combination with rapamycin. Additionally, four other compounds delayed paralysis when tested at different concentrations. Moreover, we tested fluphenazine, an antipsychotic drug identified in our screen and found that it enhanced the overall health of treated worms. Western blot and X-34 staining confirmed that fluphenazine reduced amyloid-beta accumulation. These results indicate that repurposed drugs have significant potential to accelerate Alzheimers disease drug discovery.

molecular biology↗

bioRxiv2025

Biosynthetic plasticity enables CD8+ T cell functional resilience under nutrient stress

Summary / AbstractTo maintain lineage-specific functions, cells must acquire and allocate nutrients across diverse cellular processes, even in metabolically-dysregulated environments. The mechanisms allowing CD8+ T cells to maintain immune function in perturbed environments are poorly understood. We find that CD8+ T cells adapt to nutrient stresses over time, reconfiguring gene-regulatory and metabolic networks to license functional recovery. Under acute stress, T cells reorient translational programming, limiting nutrient demand while prioritizing stress-sensitive metabolic and transcriptional responses. Within these responses, the transcription factors ATF4 and CEBPG jointly establish an adaptive metabolic program, promoting amino acid synthesis and uptake while maintaining mitochondrial anaplerosis. Despite diminished energetic capacity under environmental stress, this program prevents failure of central carbon metabolism, mitigating stress amplification and cellular dysfunction to potentiate anti-tumor immunity. Altogether, we demonstrate that biosynthetic plasticity via translational and metabolic reprioritization confers functional resilience to immune cells in unfavorable environments, offering novel strategies to enhance immunotherapies.

immunology↗

bioRxiv2024

New insights into the echinocandin resistance in Candida spp. in the clinical setting

Despite a huge consumption of echinocandins, the emergence of resistance in Candida spp has remained overall limited. Here, we depicted the epidemiology of Candida spp in our center face to the echinocandins consumption. We postulate new hypotheses that may explain the shaping of candines resistance in the clinical setting. Epidemiology of Candida infections and echinocandin consumption were evaluated in our center over 12 years (2006-2018). Glucan synthase genes (fks1, fks2) were sequenced. The in vitro fitness was assessed for couple of isogenic strains, of which one was resistant. Finally, the modelling of Candida FKS proteins was realized. Despite a three-fold increase in echinocandin consumption, no significant emergence of resistance was observed. In Candida albicans, fks1 mutations affect the three-dimensional conformation of the glucan synthase, which may result in altered export of the glucan chain, which could explain the observed reduced fitness. In contrast, cross-complementation between FKS1 and FKS2 in Nakaseomyces glabratus might circumvent the negative impact on fitness. ConclusionsOur results support the fact that N. glabratus is more prone to the spread of echinocandin-resistant strains. The link between mutations in the glucan synthase and fitness of Candida strains might explain the difference in the species-specific emergence of echinocandins-resistant strains.

microbiology↗

bioRxiv2023

Development of pre-clinical murine models for fibrolamellar hepatocellular carcinoma

Fibrolamellar hepatocellular carcinoma (FLC) is a rare form of cancer that affects primarily adolescents and young adults. FLC tumors are typically associated with an intrachromosomal deletion resulting in expression of a fusion protein between the chaperone DNAJ1B and the protein kinase PKA. FLC is challenging to study because of its rarity and limited pre-clinical models. Here we developed a novel transgenic mouse model of FLC. In this model, DNAJ1B-PKA expression in the liver of mouse embryos results in perinatal lethality associated with liver developmental defects, while DNAJ1B-PKA expression in the liver of adult mice initiates tumors resembling FLC at low penetrance. We sought to develop ex vivo cell models from these tumors but failed to establish long-term cell lines. New pre-clinical models of FLC will provide novel insights into the biology of this rare cancer and may help identify novel therapeutic strategies.

cancer biology↗

bioRxiv2022

Rhamnan Sulfate Reduces Atherosclerotic Plaque Formation and Vascular Inflammation

ObjectiveWhile lipid-lowering drugs have become a mainstay of clinical therapy these treatments only slow the progression of the disease and can have side effects. Thus, new treatment options are needed to supplement the effects of lipid lowering therapy for treating atherosclerosis. We examined the use of an inexpensive and widely available marine polysaccharide rhamnan sulfate as an oral therapeutic for limiting vascular inflammation and atherosclerosis. Methods and ResultsWe found rhamnan sulfate enhanced the barrier function of endothelial cells, preventing the deposition of LDL and maintaining barrier function even in the presence of glycocalyx-degrading enzymes. Rhamnan sulfate was also found to bind directly to FGF-2, PDGF-BB and NF-{kappa}B subunits with high affinity. In addition, rhamnan sulfate was a potent inhibitor of NF-{kappa}B pathway activation in endothelial cells by TNF-. We treated ApoE-/- mice with a high fat diet for 4 weeks and then an addition 9 weeks of high fat diet with or without rhamnan sulfate. Rhamnan sulfate reduced vascular inflammation and atherosclerosis in both sexes of ApoE-/- mice but had a stronger therapeutic effect in female mice. Oral consumption of rhamnan sulfate induced a significant decrease in cholesterol plasma levels in female mice but not in male mice. ConclusionsRhamnan sulfate has beneficial effects in reducing inflammation, binding growth factors and NF-{kappa}B, enhancing endothelial barrier function and reducing atherosclerotic plaque formation in ApoE-/- mice.

physiology↗

bioRxiv2020

Mechanical Tension in Syndecan-1 is Regulated by Extracellular Mechanical Cues and Fluidic Shear Stress

The endothelium plays a central role in regulating vascular homeostasis and is key in determining the response to materials implanted in the vascular system. Endothelial cells are uniquely sensitive to biophysical cues from applied forces and their local cellular microenvironment. The glycocalyx is a layer of proteoglycans, glycoproteins and glycosaminoglycans that lines the luminal surface of the vascular endothelium, interacting directly with the components of the blood and the forces of blood flow. In this work, we examined the changes in mechanical tension of syndecan-1, a cell surface proteoglycan that is an integral part of the glycocalyx, in response to substrate stiffness and fluidic shear stress. Our studies demonstrate that syndecan-1 is mechanically responsive to extracellular mechanical cues and alters its association with cytoskeletal and adhesion-related proteins in response to substrate stiffness and physiological flow.

bioengineering↗

bioRxiv2019

Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome

Technological advances in next-generation sequencing (NGS) and chromatographic assays [e.g., liquid chromatography mass spectrometry (LC-MS)] have made it possible to identify thousands of microbe and metabolite species, and to measure their relative abundance. In this paper, we propose a sparse neural encoder-decoder network to predict metabolite abundances from microbe abundances. Using paired data from a cohort of inflammatory bowel disease (IBD) patients, we show that our neural encoder-decoder model outperforms linear univariate and multivariate methods in terms of accuracy, sparsity, and stability. Importantly, we show that our neural encoder-decoder model is not simply a black box designed to maximize predictive accuracy. Rather, the networks hidden layer (i.e., the latent space, comprised only of sparsely weighted microbe counts) actually captures key microbe-metabolite relationships that are themselves clinically meaningful. Although this hidden layer is learned without any knowledge of the patients diagnosis, we show that the learned latent features are structured in a way that predicts IBD and treatment status with high accuracy. By imposing a non-negative weights constraint, the network becomes a directed graph where each downstream node is interpretable as the additive combination of the upstream nodes. Here, the middle layer comprises distinct microbe-metabolite axes that relate key microbial biomarkers with metabolite biomarkers. By pre-processing the microbiome and metabolome data using compositional data analysis methods, we ensure that our proposed multi-omics workflow will generalize to any pair of -omics data. To the best of our knowledge, this work is the first application of neural encoder-decoders for the interpretable integration of multi-omics biological data.

bioinformatics↗