Biology subjects

Nguyen, M. A.

Publications and source records attributed to Nguyen, M. A..

6 recordsLinked to original sources

bioRxiv2026

Consequences of sustained modulation of VIP-expressing neurons in mouse corticolimbic regions on anxiety-related avoidance behaviors, social functioning, and associative fear learning

GABAergic inhibitory neurons play a central role in shaping network dynamics, and accordingly, their dysfunction is implicated in the pathophysiology of various psychiatric, neurodevelopmental, and neurological disorders. In the past decade, studies on vasoactive intestinal polypeptide-expressing inhibitory neurons (VIP+ neurons) have positioned them as critical components of this circuitry. In particular, VIP+ neurons have been proposed to function within a canonical disinhibitory circuit motif, preferentially inhibiting other interneuron subtypes, to ultimately modulate the gain and activity of local pyramidal neurons. However, their contribution to psychiatrically relevant behavioral endophenotypes is still not fully understood, limiting our ability to target these neurons for therapeutic purposes. In the present study, we systematically assessed the functional contribution of VIP+ neurons to affective and social behaviors. To this end, we used a chemogenetic approach to manipulate the activity of VIP+ neurons in core corticolimbic regions, including the medial prefrontal cortex (mPFC), basolateral amygdala (BLA), and ventral hippocampus (vHPC). The consequences of either activating or inhibiting VIP+ neurons in these regions were observed while mice underwent a battery of behavioral tasks assessing anxiety-related avoidance behaviors, social interest and recognition, and associative fear learning. While sustained modulation of VIP+ neurons had no significant effect on anxiety-related or social behaviors in any of the brain regions assessed, it produced a robust reduction in associative fear learning specifically in the mPFC. These findings demonstrate that the consequences of sustained VIP+ neuron modulation depend on both anatomical location and behavioural context. Moreover, they identify VIP+ neurons in the mPFC as potentially clinically relevant targets for interventions aimed at modulating fear-related circuits.

neuroscience↗

bioRxiv2026

ImmunoPheno: A Computational Framework for Data-Driven Design and Analysis of Immunophenotyping Experiments

Immunophenotyping is fundamental to characterizing tissue cellular composition, pathogenic processes, and immune infiltration, yet its accuracy and reproducibility remain constrained by heuristic antibody panel design and manual gating. Here, we present ImmunoPheno, an open-source computational platform that repurposes large-scale single-cell proteo-transcriptomic data to guide immunophenotyping experimental design and analysis. ImmunoPheno integrates existing datasets to automate the design of optimal antibody panels, gating strategies, and cell identity annotation. We used ImmunoPheno to construct a harmonized reference (HICAR) comprising 390 monoclonal antibodies and 93 human immune cell populations. Leveraging this resource, we algorithmically designed minimal panels to isolate rare populations, such as MAIT cells and pDCs, which we validated experimentally. We further demonstrate accurate cell identity annotation across publicly available and newly generated cytometry datasets spanning diverse technologies, including spatial platforms like CODEX. ImmunoPheno complements expert curation and supports continual expansion, providing a scalable framework to enhance the accuracy, reproducibility, and resolution of immunophenotyping.

bioinformatics↗

bioRxiv2024

Scalable assessment of genome editing off-targets associated with genetic variants

Genome editing with RNA-guided DNA binding factors carries risk of off-target editing at homologous sequences. Genetic variants may introduce sequence changes that increase homology to a genome editing target, thereby increasing risk of off-target editing. Conventional methods to verify candidate off-targets rely on access to cells with genomic DNA carrying these sequences. However, for candidate off-targets associated with genetic variants, appropriate cells for experimental verification may not be available. Here we develop a method, Assessment By Stand-in Off-target LentiViral Ensemble with sequencing (ABSOLVE-seq), to integrate a set of candidate off-target sequences along with unique molecular identifiers (UMIs) in genomes of primary cells followed by clinically relevant gene editor delivery. Gene editing of dozens of candidate off-target sequences may be evaluated in a single experiment with high sensitivity, precision, and power. We provide an open-source pipeline to analyze sequencing data. This approach enables experimental assessment of the influence of human genetic diversity on specificity evaluation during gene editing therapy development.

genomics↗

bioRxiv2024

Direct delivery of stabilized Cas-embedded base editors achieves efficient and accurate editing of clinically relevant targets

Over the last 5 years, cytosine base editors (CBEs) have emerged as a promising therapeutic tool for specific editing of single nucleotide variants and disrupting specific genes associated with disease. Despite this promise, the currently available CBEs have the significant liabilities of off-target and bystander editing activities, in part due to the mechanism by which they are delivered, causing limitations in their potential applications. In this study we engineeredhighly stabilized Cas-embedded CBEs (sCE_CBEs) that integrate several recent advances, andthat are highly expressible and soluble for direct delivery into cells as ribonucleoprotein (RNP) complexes. Our resulting sCE_CBE RNP complexes efficiently and specifically target TC dinucleotides with minimal off-target or bystander mutations. Additional uracil glycosylase inhibitor (UGI) protein in trans further increased C-to-T editing efficiency and target purity in a dose-dependent manner, minimizing indel formation to untreated levels. A single electroporation was sufficient to effectively edit the therapeutically relevant locus for sickle cell disease in hematopoietic stem and progenitor cells (HSPC) in a dose dependent manner without cellular toxicity. Significantly, these sCE_CBE RNPs permitted for the transplantation of edited HSPCs confirming highly efficient editing in engrafting hematopoietic stem cells in mice. The success of the designed sCBE editors, with improved solubility and enhanced on-target editing, demonstrates promising agents for cytosine base editing at other disease-related sites in HSPCs and other cell types.

biochemistry↗

bioRxiv2023

Gene editing without ex vivo culture evades genotoxicity in human hematopoietic stem cells

Gene editing the BCL11A erythroid enhancer is a validated approach to fetal hemoglobin (HbF) induction for {beta}-hemoglobinopathy therapy, though heterogeneity in edit allele distribution and HbF response may impact its safety and efficacy. Here we compared combined CRISPR-Cas9 endonuclease editing of the BCL11A +58 and +55 enhancers with leading gene modification approaches under clinical investigation. We found that combined targeting of the BCL11A +58 and +55 enhancers with 3xNLS-SpCas9 and two sgRNAs resulted in superior HbF induction, including in engrafting erythroid cells from sickle cell disease (SCD) patient xenografts, attributable to simultaneous disruption of core half E-box/GATA motifs at both enhancers. We corroborated prior observations that double strand breaks (DSBs) could produce unintended on- target outcomes in hematopoietic stem and progenitor cells (HSPCs) such as long deletions and centromere-distal chromosome fragment loss. We show these unintended outcomes are a byproduct of cellular proliferation stimulated by ex vivo culture. Editing HSPCs without cytokine culture bypassed long deletion and micronuclei formation while preserving efficient on-target editing and engraftment function. These results indicate that nuclease editing of quiescent hematopoietic stem cells (HSCs) limits DSB genotoxicity while maintaining therapeutic potency and encourages efforts for in vivo delivery of nucleases to HSCs.

genetics↗

bioRxiv2022

A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes

Type I interferons (IFN) induce powerful anti-viral and innate immune responses via the transcription factor, IFN-stimulated gene factor (ISGF3). However, in some pathological contexts type I IFNs are responsible for exacerbating inflammation. Here, we show that a high dose of IFN-{beta} also activates an inflammatory gene expression program in contrast to IFN-{lambda}3, a type III IFN, which elicits only the common anti-viral gene program. We show that the inflammatory gene program depends on a second, potentiated phase in ISGF3 activation. Iterating between mathematical modeling and experimental analysis we show that the ISGF3 activation network may engage a positive feedback loop with its subunits IRF9 and STAT2. This network motif mediates stimulus-specific ISGF3 dynamics that are dependent on ligand, dose, and duration of exposure, and when engaged activates the inflammatory gene expression program. Our results reveal a previously underappreciated dynamical control of the JAK-STAT/IRF signaling network that may produce distinct biological responses, and suggest that studies of type I IFN dysregulation, and in turn therapeutic remedies, may focus on feedback regulators within it. HIGHLIGHTSO_LIHigh dose IFN-{beta} activates a pro-inflammatory gene program in epithelial cells. C_LIO_LIIFN-{beta}, but not IFN-{lambda}3, induces a second, potentiated phase in ISGF3 activity. C_LIO_LIISGF3 induces its subunits to form a stimulus-contingent positive feedback loop. C_LIO_LIThe positive feedback motif is required for the pro-inflammatory gene program. C_LI

immunology↗