Biology subjects

Vu, A.

Publications and source records attributed to Vu, A..

15 recordsLinked to original sources

bioRxiv2026

Optimized AAV capsids robustly transduce airway epithelial cells

Gene therapies have demonstrated transformative potential for a range of genetic disorders, including immunodeficiencies, hematopoietic conditions, and neuromuscular diseases. However, the application of these approaches to cystic fibrosis (CF) and other airway diseases remains constrained by the challenge of efficient gene delivery to target epithelial cells. Adeno-associated virus (AAV) vectors are widely used for in vivo gene delivery due to their favorable safety profile and capacity for long-term transgene expression in non-dividing cells. Nonetheless, current AAV capsids require high doses to achieve therapeutic efficacy in the airways, raising safety concerns. Here we report the development of novel AAV capsid variants with markedly enhanced transduction efficiency of airway epithelial cells. Using unbiased peptide-modified AAV libraries and round-over-round screening in well-differentiated primary cultures of human airway epithelia (HAE), we identified 20 novel capsids that efficiently transduced cells at doses 10- to 100-fold lower than those required by existing vectors (termed AAV-AE). These variants demonstrated high transgene expression in HAE, primary human basal cells, tracheal explants from nonhuman primates, and murine airways in vivo. These optimized AAV capsids represent a significant advancement in pulmonary gene therapy, offering a versatile platform for the delivery of gene addition and editing reagents to treat CF and other respiratory diseases.

molecular biology↗

bioRxiv2026

Functional characterization of a multi-cancer risk locus on chromosome band 2q33.1 near CASP8

Genome-wide association studies (GWAS) of melanoma have identified numerous susceptibility loci. However, causal genes and variants underlying risk have yet to be established for most. It is becoming apparent that many functional variants underlying complex traits act via cis-regulation that may be context-specific, dependent on availability of specific transcription factors/complexes in specific cell types and cell-states. To characterize a risk locus on chromosome band 2q33.1 associated with melanoma, breast cancer, and keratinocyte cancers, we integrated fine-mapping, cell-type specific expression quantitative trait locus (eQTL) analysis, a massively parallel reporter assay, individual luciferase assays, and SNP-based proteomics. Integrated analysis implicates the presence of multiple functional variants lying primarily within a promoter for CASP8. A haplotype containing rs3769823 appeared have the largest effect on expression. Strikingly, both tumor/normal context and this risk-associated haplotype play critical roles in mediating allelic cis-regulatory activity. Quantitative mass spectrometry for rs3769823 identified both E4F1, a transcriptional repressor, and IRF2, a transcriptional activator, as binding preferentially to risk-associated rs3969823-A. The binding of these transcription factors was validated via EMSA, supershift, and chromatin immunoprecipitation (ChIP) assays. The relative levels of E4F1 and IRF2 differ by cell-type and play a role in mediating transcriptional activity in a cell-type specific manner. Our results indicate that the top credible causal set variant rs3769823 likely influences expression of CASP8 and FLACC1 in a cell-type specific manner and may be a relevant functional variant for multiple cancers associated with this locus.

genetics↗

bioRxiv2025

Atom-level backbone engineering preserves peptide function while enhancing stability

Peptide therapeutics offer unmatched potency and selectivity but are limited by rapid proteolysis and poor pharmacokinetics. Backbone engineering provides a rational approach to enhance stability while preserving function, yet direct comparisons across strategies remain scarce. Using bradykinin as a model, we systematically evaluated four backbone modifications--D-amino acid substitution, N-methylation, -methylation, and azapeptide incorporation. Each modification produced distinct outcomes in synthesis, conformation, proteolytic stability, and receptor pharmacology. While D- and N-methyl substitutions yielded high stability, they compromised receptor binding and in vivo function. In contrast, the azapeptide analogue maintained native-like affinity and physiological activity while achieving an enhanced stability profile. These findings highlight the need to balance stability and function in peptide design and position azapeptides as an underexplored class with strong therapeutic potential. More broadly, this study establishes a framework for systematic, data-driven peptide design and optimization.

biochemistry↗

bioRxiv2025

Isotopic Labeling Analysis using Single Cell Mass Spectrometry

Here we show that a recently developed single cell mass spectrometry method can be used to monitor the incorporation of an isotopically labeled precursor into single plant protoplasts. Specifically, we show that we can monitor the incorporation of deuterium-labeled tryptamine into an alkaloid pathway over the course of 24 hours. The resulting data provides a glimpse into the rate of synthesis and transport of chemically complex monoterpene indole alkaloids in single cells across a small population. By measuring the concentration of labeled alkaloids, we gain insight into the flux of an important plant biosynthetic pathway. Stable-isotope labeling is a widely used approach to study metabolic networks by tracking isotopologues over time. This manuscript provides proof of principle that single cell isotopic labeling can be performed in plant pathways.

plant biology↗

bioRxiv2025

High-dose DFMO alters protein translation in neuroblastoma

DFMO has been studied as a cancer therapeutic at doses ranging from 500-9,000 mg/m2/day. Lower doses are favored for cancer prevention studies while higher doses, often with chemotherapy, are studied in refractory cancers. DFMO inhibits the rate-limiting enzyme in polyamine synthesis, ornithine decarboxylase (ODC), an oncogene transcriptionally regulated by MYC. MYC genes are the principal oncogenic drivers of neuroblastoma, and ODC1 is co-amplified in a subset with dismal outcome, so DFMO is a rational therapeutic candidate. Low-dose DFMO has now been FDA-approved for high-risk patients though the mechanisms for its anti-tumor activity, and the exposures required to elicit them, remain obscure. We sought to define biomarkers of activity across exposures achieved in the clinic with low through high-dose DFMO. Polyamines support protein translation by providing spermidine, which is essential to hypusinate (and activate) the elongation factor, eIF5A. Selective binding of polyamines with tRNA and rRNA provide eIF5A-independent mechanisms of translation support. We show that low-dose DFMO does not extend survival in mouse models in vivo nor alter translation biomarkers in vitro. High-dose DFMO consistently extends survival in neuroblastoma models, and, in a subset of neuroblastoma cell lines, inhibits eIF5A hypusination and global translation at achievable concentrations. However, the concentration required to engage these changes across many cell lines exceeded that achievable even with high-dose DFMO. No correlation was seen among MYCN and/or ODC1 copy number and sensitivity to DFMO. Combining high-dose DFMO with additional agents to further deplete tumor polyamines may be necessary to fully engage polyamine-depletion effects on tumors, and more granular measures of translation, including codon-resolution ribosome profiling, may be required to define these effects. STATEMENT OF TRANSLATIONAL RELEVANCELow-dose DFMO is approved by the FDA for the treatment of neuroblastoma. The depletion of tumor polyamines has been shown to have activity against tumors with activated MYC signaling, like neuroblastoma, yet the degree of polyamine depletion required, the mechanisms by which this impedes tumor progression, and the DFMO exposures required to enable these are poorly understood. Here we evaluate alterations in protein translation as putative mechanisms for DFMO activity. Translation biomarkers and colony formation can be inhibited by DFMO in vitro at exposures achievable in vivo with high-dose DFMO. Similarly, high-dose DFMO, but not low-dose DFMO, extends neuroblastoma-prone mouse survival. These findings support studying DFMO at higher doses and in therapeutic combinations that further augment polyamine depletion within tumors.

cancer biology↗

bioRxiv2024

Delayed cerebrovascular dysfunction and social deficits after traumatic brain injury

Traumatic brain injury (TBI) survivors face debilitating long-term psychosocial consequences, including social isolation and depression. Acute TBI modifies neurovascular physiology and behavior but a gap in our understanding are the chronic physiological implications of altered brain perfusion on behavioral activities, particularly social interactions. We investigated longitudinal functional vascular networks across the brain for 2-months post- TBI and its impact on social behavior. Adult C57/BL6 male mice received a moderate cortical TBI. Behavior (foot-fault, open-field, 3-chamber social preference) was assessed at baseline, 3-, 7-, 14-, 30-, and 60-days post injury (dpi) followed by magnetic resonance imaging (MRI, 9.4T). Anatomical MRI (T2-weighted), dynamic susceptibility contrast (DSC) perfusion weighted MRI (PWI) were acquired at each temporal epoch. After the final 60dpi MRI, animals underwent transcardial perfusion fixation to map angioarchitecture. MRI data were analyzed using standardized protocols followed by cross-correlations between social behavior, cerebral perfusion, and vascular metrics. Social behavior deficits at 60dpi emerged as reduced interaction with a familiar cage-mate (partner). We observed multiphasic decrements in cerebral blood flow (CBF) encompassing lesion and perilesional cortex where acute reductions at 3-14dpi partially recovered by 30dpi, followed by significant reductions in perfusion at 60dpi. The CBF perturbations extended antero-posteriorly from the ipsilateral TBI impact site but also adulterated contralateral brain regions. CBF reductions impacted regions known to regulate social behavior including hippocampus, hypothalamus, and rhinal cortex. Alongside perfusion deficits at 60dpi, social isolation in TBI-mice emerged with a significant decline in preference to spend time with a cage mate. Cortical vascular density was also reduced corroborating the decline in brain perfusion and social interaction. Thus, the novel temporal neurovascular loss, and subsequent recovery followed by chronic decrements are broadly reflected by social interaction perturbations. Our correlations strongly implicate a linkage between vascular density, cerebral perfusion, and social interactions, where early evaluation can potentially predict long-term outcomes. Thus, our study provides a clinically relevant timeline of alterations in functional vascular recovery that can guide research for future therapeutics.

neuroscience↗

bioRxiv2024

Reprogramming neuroblastoma by diet-enhanced polyamine depletion

Neuroblastoma is a highly lethal childhood tumor derived from differentiation-arrested neural crest cells1,2. Like all cancers, its growth is fueled by metabolites obtained from either circulation or local biosynthesis3,4. Neuroblastomas depend on local polyamine biosynthesis, with the inhibitor difluoromethylornithine showing clinical activity5. Here we show that such inhibition can be augmented by dietary restriction of upstream amino acid substrates, leading to disruption of oncogenic protein translation, tumor differentiation, and profound survival gains in the TH-MYCN mouse model. Specifically, an arginine/proline-free diet decreases the polyamine precursor ornithine and augments tumor polyamine depletion by difluoromethylornithine. This polyamine depletion causes ribosome stalling, unexpectedly specifically at adenosine-ending codons. Such codons are selectively enriched in cell cycle genes and low in neuronal differentiation genes. Thus, impaired translation of these codons, induced by the diet-drug combination, favors a pro-differentiation proteome. These results suggest that the genes of specific cellular programs have evolved hallmark codon usage preferences that enable coherent translational rewiring in response to metabolic stresses, and that this process can be targeted to activate differentiation of pediatric cancers. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/573662v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1fdbaecorg.highwire.dtl.DTLVardef@fb03f4org.highwire.dtl.DTLVardef@1c0afa7org.highwire.dtl.DTLVardef@14c384f_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Extra-tumoral conversion of arginine feeds tumor ornithine via uptake from circulation in MYCN-neuroblastoma. - A proline and arginine free diet enhances pharmacological polyamine depletion via reduced ornithine substrate availability. - Polyamine depletion disrupts oncogenic translation to induce a pro-differentiation proteome causing neuroblast differentiation and prolonged survival in the TH-MYCN mouse model. - Genes of specific cellular programs have evolved codon usage preferences that enable coherent translational rewiring in response to metabolic stress, such as polyamine depletion.

cancer biology↗

bioRxiv2023

Sequence-based Protein-Protein Interaction Prediction Using Multi-kernel Deep Convolutional Neural Networks with ProteinLanguage Model

Predicting protein-protein interactions (PPIs) using only sequence information represents a fundamental problem in biology. In the past five years, a wide range of state-of-the-art deep learning models have been developed to address the computational prediction of PPIs based on sequences. Convolutional neural networks (CNNs) are widely adopted in these model architectures; however, the design of a deep and wide CNN architecture that comprehensively extracts interaction features from pairs of proteins is not well studied. Despite the development of several protein language models that distill the knowledge of evolutionary, structural, and functional information from gigantic protein sequence databases, no studies have integrated the amino acid embeddings of the protein language model for encoding protein sequences.In this study, we introduces a novel hybrid classifier, xCAPT5, which combines the deep multi-kernel convolutional accumulated pooling siamese neural network (CAPT5) and the XGBoost model (x) to enhance interaction prediction. The CAPT5 utilizes multi-deep convolutional channels with varying kernel sizes in the Siamese architecture, enabling the capture of small- and large-scale local features. By concatenating max and average pooling features in a depth-wise manner, CAPT5 effectively learns crucial features with low computational cost. This study is the first to extract information-rich amino acid embedding from a protein language model by a deep convolutional network, through training to obtain discriminant representations of protein sequence pairs that are fed into XGBoost for predicting PPIs. Experimental results demonstrate that xCAPT5 outperforms several state-of-the-art methods on binary PPI prediction, including generalized PPI on intra-species, cross-species, inter-species, and stringent similarity tasks. The implementation of our framework is available at https://github.com/anhvt00/MCAPS

bioinformatics↗

bioRxiv2023

The universal suppressor mutation in the HSV-1 nuclear egress complex restores membrane budding defects by stabilizing the oligomeric lattice

Nuclear egress is an essential process in herpesviral replication whereby nascent capsids translocate from the nucleus to the cytoplasm. This initial step of nuclear egress - budding at the inner nuclear membrane - is coordinated by the nuclear egress complex (NEC). Composed of the viral proteins UL31 and UL34, NEC deforms the membrane around the capsid as the latter buds into the perinuclear space. NEC oligomerization into a hexagonal membrane-bound lattice is essential for budding because mutations designed to perturb lattice interfaces reduce its budding ability. Previously, we identified an NEC suppressor mutation capable of restoring budding to a mutant with a weakened hexagonal lattice. Here, we show that the suppressor mutation can restore budding to a broad range of budding-deficient NEC mutants thereby acting as a universal suppressor. We demonstrate that the suppressor mutation indirectly promotes the formation of new contacts between the NEC hexamers that, ostensibly, stabilize the hexagonal lattice. This stabilization strategy is powerful enough to override the otherwise deleterious effects of mutations that destabilize the NEC lattice by different mechanisms, resulting in a functional NEC hexagonal lattice and restoration of membrane budding.

biophysics↗

bioRxiv2022

Visual Perception of 3D Space and Shape in Time - Part I: 2D Space Perception by 2D Linear Translation

Visual perception plays a critical role in navigating space and extracting useful semantic information crucial to survival. To identify distant landmarks, we constantly shift gaze vectors through saccades, while still maintaining the visual perception of stable allocentric space. How can we sustain stable allocentric space so effortlessly? To solve this question, we have developed a new concept of NHT (Neural Holography Tomography). This model states that retinotopy is invisible (not available to consciousness) and must be converted to a time code by traveling alpha brainwaves to perceive objects consciously. According to this framework, if identical alpha phases are continually assigned to a landmark, we perceive its exact and consistent allocentric location. To test this hypothesis, we designed reaction time (RT) experiments to observe evidence of the predicted space-to-time conversion. Various visual stimuli were generated at a wide range of eccentricities either on a large TV (up to 40{degrees}) or by LED strips on a hemispherical dome (up to 60{degrees}). Participants were instructed to report the observed patterns promptly under either covert (no eye movement) or overt (with eye movement) conditions. As predicted, stimuli presented at the center of fixation always produced the fastest RTs. The additional RT delay was precisely proportional to the eccentricity of the peripheral stimulus presentation. Furthermore, both covert and overt attention protocols created the same RT delays, and trajectories of saccadic eye motions were in parallel to the overt RT vs. eccentricity. These findings strongly support our NHT model, in which the observed RT-eccentricity dependence is indicative of the spatiotemporal conversion required for maintaining a stable allocentric frame of reference. That is, we perceive space by time.

neuroscience↗

bioRxiv2021

Anti-GD2 antibody therapy alters the neuroblastoma tumor microenvironment and extends survival in TH-MYCN mice

BackgroundNeuroblastoma is a commonly lethal solid tumor of childhood and intensive chemoradiotherapy treatment cures ~50% of children with high-risk disease. The addition of immunotherapy using dinutuximab, a monoclonal antibody directed against the GD2 disialoganglioside expressed on neuroblasts, improves survival when incorporated into front-line therapy and shows robust activity in regressing relapsed disease when combined with chemotherapy. Still, many children succumb to neuroblastoma despite receiving dinutuximab-based immunotherapy, and efforts to counteract the immune suppressive signals responsible are warranted. Animal models of human cancers provide useful platforms to study immunotherapies. TH-MYCN transgenic mice are immunocompetent and develop neuroblastomas at autochthonous sites due to enforced MYCN expression in developing neural crest tissues. However, GD2-directed immunotherapy in this model has been underutilized due to the prevailing notion that TH-MYCN neuroblasts express insufficient GD2 to be targeted. MethodsTH-MYCN mice were treated with 14G2a (anti-GD2 antibody), isotype antibody, or phosphate buffered saline from day 14 of life until day 100 or signs of morbidity. Survival was recorded, and tumors were isolated in terminal surgeries for analysis of GD2 expression and immune cell frequencies. Tumors from untreated mice were explanted for generation into cell lines, and GD2 expression was recorded with serial passage in tissue culture. Immunocytology and immunoblotting were performed to evaluate for adrenergic and mesenchymal markers of neuroblasts. Survival curves compared using Kaplan-Meier method with a log-rank test for significance. Unpaired two-tailed Students t-tests used for comparison of groups in flow cytometry analysis. Results14G2a markedly extends survival in such TH-MYCN mice. Additionally, neuroblasts in 14G2a-treated mice have reduced GD2 expression and fewer macrophage and myeloid-derived suppressor cells in their tumor microenvironments. Neuroblasts in TH-MYCN-driven tumors express GD2 at levels comparable to human neuroblastomas but rapidly lose GD2 expression when explanted ex vivo to establish tumor cell lines. The loss of GD2 expression ex vivo is associated with a transition from an adrenergic to mesenchymal state that is maintained when reimplanted in vivo. ConclusionsOur findings support the utility of the TH-MYCN model to inform GD2-directed immunotherapy approaches for neuroblastoma as well as opportunities to investigate drivers of adrenergic to mesenchymal fate decisions.

cancer biology↗

bioRxiv2021

Bexarotene derivatives modify responses in acute myeloid leukemia

The retinoids all-trans retinoic acid (ATRA) and bexarotene are active in acute myeloid leukemia (AML), but responses beyond acute promyelocytic leukemia (APL) have been more modest than APL responses. To determine whether chemical modification of bexarotene might augment retinoid responses in AML, we screened a series of 38 bexarotene derivatives for activity in a mouse MLL-AF9 leukemia cell line, which exhibits strong synergistic sensitivity to the combination of ATRA and bexarotene. We found that RXRA potency correlated with anti-leukemic activity and that only one compound (103-4) with dual RARA/RXRA activity was capable of ATRA-independent anti-leukemic activity. We evaluated bioisostere and cyclohexane modifications for potential resistance to P450 metabolism and found that bioisosteres reduced potency and that bezopyran, cyclopentane, and cyclohexene modifications only modestly reduced susceptibility to metabolism. Collectively, these studies provide a map of the structure-activity relationships of bexarotene with outcomes related to RXRA and RARA activity, corepressor binding, compound stability, and anti-leukemic potential.

cancer biology↗

bioRxiv2021

REDUCED ER-MITOCHONDRIA CONNECTIVITY PROMOTES NEUROBLASTOMA MULTIDRUG RESISTANCE

Most cancer deaths result from progression of therapy resistant disease, yet our understanding of this phenotype is limited. Cancer therapies generate stress signals that act upon mitochondria to initiate apoptotic programs. We isolated mitochondria from neuroblastoma cell lines obtained from children at diagnosis and after relapse following failed therapy, and profiled responses to tBid and Bim, death effectors activated by therapeutic stress. Mitochondria from post-relapse models had markedly attenuated cytochrome c release (surrogate for apoptotic commitment) in comparison with patient-matched diagnostic models. Mitochondrial DNA content, size, and shape did not differ consistently. However, we used electron microscopy to identify reduced endoplasmic reticulum-mitochondria contacts (ERMCs) as correlated with therapy resistance. ERMCs form microdomains for the transfer of Ca2+ to mitochondria. We confirmed reduced Ca2+ transfer in resistant cells, with restoration by re-opposing ERMCs via genetically-encoded linkers. However, reduced Ca2+ transfer was not present in all ERMC-reduced cancers with therapy resistance, supporting Ca2+-independent mechanisms. Genetically or biochemically reducing ERMCs in therapy sensitive tumors phenocopied resistance, validating these inter-organelle contacts as physiologic regulators of apoptosis. Our work confirms the importance of ERMCs in stress signaling and provides a previously unrecognized mechanism for cancer cell resistance that is not exclusive to other contributors.

cancer biology↗

bioRxiv2019

Massively parallel reporter assays combined with cell-type specific eQTL informed multiple melanoma loci and identified a pleiotropic function of HIV-1 restriction gene, MX2, in melanoma promotion

Genome-wide association studies (GWAS) have identified [~]20 melanoma susceptibility loci. To identify susceptibility genes and variants simultaneously from multiple GWAS loci, we integrated massively-parallel reporter assays (MPRA) with cell type-specific epigenomic data as well as melanocyte-specific expression quantitative trait loci (eQTL) profiling. Starting from 16 melanoma loci, we selected 832 variants overlapping active regions of chromatin in cells of melanocytic lineage and identified 39 candidate functional variants displaying allelic transcriptional activity by MPRA. For four of these loci, we further identified four colocalizing melanocyte cis-eQTL genes (CTSS, CASP8, MX2, and MAFF) matching the allelic activity of MPRA functional variants. Among these, we further characterized the locus encompassing the HIV-1 restriction gene, MX2, on chromosome band Chr21q22.3 and validated a functional variant, rs398206, among multiple high LD variants. rs398206 mediates allelic transcriptional activity via binding of the transcription factor, YY1. This allelic transcriptional regulation is consistent with a significant cis-eQTL of MX2 in primary human melanocytes, where the melanoma risk-associated A allele of rs398206 is correlated with higher MX2 levels. Melanocyte-specific transgenic expression of human MX2 in a zebrafish model demonstrated accelerated melanoma formation in a BRAFV600E background. Thus, using an efficient scalable approach to streamline GWAS follow-up functional studies, we identified multiple candidate melanoma susceptibility genes and variants, and uncovered a pleiotropic function of MX2 in melanoma susceptibility.

genomics↗

bioRxiv2018

The HCP 7T Retinotopy Dataset

About a quarter of human cerebral cortex is dedicated mainly to visual processing. The large-scale organization of visual cortex can be measured with functional magnetic resonance imaging (fMRI) while subjects view spatially modulated visual stimuli, also known as retinotopic mapping. One of the datasets collected by the Human Connectome Project (HCP) involved ultra-high-field (7 Tesla) fMRI retinotopic mapping in 181 healthy young adults (1.6-mm resolution), yielding the largest freely available collection of retinotopy data. Here, we describe the experimental paradigm and the results of model-based analysis of the fMRI data. These results provide estimates of population receptive field position and size. Our analyses include both results from individual subjects as well as results obtained by averaging fMRI time-series across subjects at each cortical and subcortical location and then fitting models. Both the group-average and individual-subject results reveal robust signals across much of the brain, including occipital, temporal, parietal, and frontal cortex as well as subcortical areas. The group-average results agree well with previously published parcellations of visual areas. In addition, split-half analyses show strong within-subject reliability, further demonstrating the high quality of the data. We make publicly available the analysis results for individual subjects and the group average, as well as associated stimuli and analysis code. These resources provide an opportunity for studying fine-scale individual variability in cortical and subcortical organization and the properties of high-resolution fMRI. In addition, they provide a set of observations that can be compared with other HCP measures acquired in these same participants.

neuroscience↗