Biology subjects

Nguyen, A. V.

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

8 recordsLinked to original sources

bioRxiv2026

Mapping bacterial bile amidation across the bile salt hydrolase family

Evaluating enzyme activity and specificity in complex microbiomes is challenging. The recent discovery that bacterial bile salt hydrolases (BSHs) also function as transaminases in the human gut microbiome highlights what remains to be disentangled, even within one of the most extensively studied microbiomes. BSHs as transaminases can conjugate bile acids with bioavailable amines to produce bacterial bile amidates (BBAs). The implications of BBAs for human health are rapidly evolving, but our understanding of which BSHs produce which specific BBAs remains limited. Here, we connect BSH sequence and function by evaluating the transaminase activities of 115 BSHs and reveal distinct amine specificities using molecular networking. Additionally, we identify enzymatically generated BBAs distributed across life-stage, tissue-, and disease-specific human samples by mining public metabolomics repositories, highlighting the previously unrecognized catalytic diversity of BSHs and their potential relevance to human health.

biochemistry↗

bioRxiv2025

Adeno-Associated Virus-Induced Neurotoxicity is Prevented by CpG Depletion

Adeno-associated viruses (AAVs) are the vector of choice for gene delivery to the nervous system. While AAVs have a strong safety profile, recent studies show that AAV causes dendritic loss and synaptic weakening in mouse somatosensory cortex, impacts that are prevented by systemic administration of blockers of Toll-like receptor 9 (TLR9), an innate immunoreceptor that detects unmethylated cytosine-guanine (CpG) motifs. However, TLR9 blockers are immunosuppressive and costly. To realize AAVs full potential, it is critical to identify strategies to protect neurons without compromising immunity. Here we find that partially depleting CpG motifs from the AAV genome prevents AAV-induced dendritic loss and synaptic weakening. CpG depletion of transgene and intronic regions via codon-optimized synonymous mutations was protective and did not impair transgene expression in vivo. To facilitate the production and use of lower-CpG AAVs, we created a web-facing application, CpG-Assist Tool (CpG-AT), which allows researchers to quantify the CpG content of any sequence, explore the CpG content of commonly used AAV components, and generate CpG-depleted coding and non-coding sequences. This study identifies CpG depletion as a practical strategy to prevent AAV-induced neural circuit disruption, and provides tools to facilitate CpG reduction to enhance the safety and efficacy of AAV-mediated gene delivery.

neuroscience↗

bioRxiv2025

GCAD: a Computational Framework for Mammalian Genetic Program Computer-Aided Design

Genetic programs can direct living systems to perform diverse, pre-specified functions. As the library of parts available for building such programs continues to expand, computation-guided design is increasingly helpful and necessary. Predictive models aid the challenging design process, but iterative simulation and experimentation are intractable for complex functions. Computer-aided design accelerates this process, but existing tools do not yet capture the behavior of mammalian-specific parts and population-level effects needed for mammalian synthetic biologists. To address these needs, we developed a framework for mammalian genetic program computer-aided design. Starting with a user-defined design specification to quantify circuit performance, the framework uses a genetic algorithm to search through possible designs. Circuit space is defined by a library of experimentally characterized parts and dynamical systems models for gene expression in a heterogeneous cell population. We developed this genetic algorithm using a directed graph-based formulation with biologically constrained rules to explore regulatory connections and parts. We evaluated the framework for design problems of varying complexity, including programs we describe as an amplifier, signal conditioner, and pulse generator, demonstrating that the algorithm can successfully find optimal circuit designs. Finally, we experimentally evaluated selected circuits, demonstrating the path from a predicted circuit design to experimental testing and highlighting the importance of characterization for enabling predictive design. Overall, this framework establishes general approaches that can be refined and expanded, accelerating the design and implementation of mammalian genetic programs.

synthetic biology↗

bioRxiv2024

Bone marrow microenvironment signatures associate with patient survival after guadecitabine and atezolizumab therapy in HMA-resistant MDS

Almost 50% of patients with myelodysplastic syndrome (MDS) are refractory to first-line hypomethylating agents (HMAs), which presents a significant clinical challenge considering the lack of options for salvage. Past work revealed that immune checkpoint molecules on peripheral myeloblasts and immune cells are up-regulated after HMA treatment. Therefore, we conducted a Phase I/II clinical trial combining guadecitabine (an HMA) and atezolizumab (an immune checkpoint inhibitor) to treat HMA-relapsed or refractory (HMA-R/R) MDS patients. This combination therapy showed median overall survival of 15.1 months relative to historical controls (4-6 months). Here, we profiled the cell composition and gene expression signatures of cells from bone marrow aspirates from trial participants with short-term (<15 months) or long-term (>15 months) survival at single-cell resolution. Long-term survivors showed a significant reduction of immunosuppressive monocytes, and an expansion of effector lymphocytes after combination therapy. Further immune profiling suggests that gamma delta T cell activation through primed dendritic cells was associated with global interferon activation in the bone marrow microenvironment of long-term survivors. Short-term survivors exhibited elevated inflammation and senescence-like gene signatures that were not resolved by combination therapy. We propose that distinct bone marrow microenvironment features, such as senescence-associated inflammation or immunosuppressive monocyte presence, could improve patient stratification for HMA and immunotherapy combinations in HMA-R/R MDS patients.

cancer biology↗

bioRxiv2023

TTBK2 mutations associated with spinocerebellar ataxia type 11 disrupt peroxisome dynamics and ciliary localization of SHH signaling proteins

Frameshift mutations in Tau Tubulin Kinase 2 (TTBK2) cause spinocerebellar ataxia type 11 (SCA11), which is characterized by the progressive loss of Purkinje cells and cerebellar atrophy. Previous work showed that these TTBK2 variants generate truncated proteins that interfere with primary ciliary trafficking and with Sonic Hedgehog (SHH) signaling in mice. Nevertheless, the molecular mechanisms underlying the dominant interference of mutations remain unknown. Herein, we discover that SCA11-associated variants contain a bona fide peroxisomal targeting signal type 1. We find that their expression in RPE1 cells reduces peroxisome numbers within the cell and at the base of the cilia, disrupts peroxisome fission pathways, and impairs trafficking of ciliary SMO upon SHH signaling activation. This work uncovers a neomorphic function of SCA11-causing mutations and identifies requirements for both peroxisomes and cholesterol in trafficking of cilia-localized SHH signaling proteins. In addition, we postulate that molecular mechanisms underlying cellular dysfunction in SCA11 converge on the SHH signaling pathway. SUMMARYMolecular mechanisms underlying spinocerebellar ataxia type 11 are not well understood. In this study, we identified a neomorphic function of the mutated gene (TTBK2) associated with this disease highlighting a functional inter-organelle interaction between peroxisomes and cilia.

cell biology↗

bioRxiv2022

Ladder shaped microfluidic system enabling rapid antibiotic susceptibility testing with standardized concentration panel

Antibiotics are often prescribed before pathogens are identified and susceptibility to the prescribed drug is confirmed; laboratory results may take up to 3 days. Using rapid antibiotic susceptibility testing (AST) this timeline can be compressed. We designed a microfluidic ladder-based system that generates a twofold serial dilution of antibiotics comparable to current national and international standards. This consolidated design, with minimal handling steps, has cut down the time-to-result for AST from 16-20 h to 4-5 h. Our system has a 91.75 % rate of agreement with the commercial AST system for Gram-negative and Gram-positive bacterial isolates from canine urinary tract infections (UTI) tested against seven clinically relevant antibiotics. Overall, the system showed a matching rate of 92.71 % - 94.54 % with Gram-negative pathogens, and 85.00 % - 88.57 % with Gram-positive pathogens with no statistical difference between the pathogens or antibiotics. We also tested bacteria filtered directly from urine samples, potentially reducing the total sample-to-result time from 2-3 days to 4 hours.

microbiology↗

bioRxiv2022

TTBK2 controls cilium stability through actin and the centrosomal compartment

The serine-threonine kinase Tau Tubulin Kinase 2 (TTBK2) is a key regulator of the assembly of primary cilia, which are vital signaling organelles. TTBK2 is also implicated in the stability of the assembled cilium, through mechanisms that remain to be defined. Here, we use mouse embryonic fibroblasts (MEFs) derived from Ttbk2fl/fl; UBC-CreERT+ embryos (hereafter Ttbk2cmut) to dissect the role of TTBK2 in cilium stability. This system depletes TTBK2 levels after cilia formation, allowing us to assess the molecular changes to the assembled cilium over time. As a consequence of Ttbk2 deletion, the ciliary axoneme is destabilized and primary cilia are lost within 48-72 hours following recombination. Axoneme destabilization involves an increased frequency of cilia breaks and is partially driven by altered actin dynamics and a reduction in axonemal microtubule modifications. At the same time, we find that TTBK2 is required to regulate the composition of the centriolar satellites and to maintain the basal body pools of intraflagellar transport (IFT) proteins. Altogether, our results reveal parallel pathways by which TTBK2 maintains cilium stability.

cell biology↗

bioRxiv2020

Plasmidome analysis of carbapenem-resistant Enterobacteriaceae isolated in Vietnam

Carbapenem-resistant Enterobacterales (CRE) represent a serious threat to public health due to the lack of treatment and high mortality. The rate of antimicrobial resistance of Enterobacterales isolates to major antimicrobials, including carbapenems, is much higher in Vietnam than in Western countries, but the reasons remain unknown due to the lack of genomic epidemiology research. A previous study suggested that carbapenem resistance genes, such as the carbapenemase gene blaNDM, spread via plasmids among Enterobacterales in Vietnam. In this study, we characterized blaNDM-carrying plasmids in Enterobacterales isolated in Vietnam, and identified several possible cases of horizontal transfer of plasmids both within and among species of bacteria. Twenty-five carbapenem-nonsusceptible isolates from a medical institution in Hanoi were sequenced on Illumina short-read sequencers, and 13 blaNDM-positive isolates, including isolates of Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii, Morganella morganii, and Proteus mirabilis, were further sequenced on an Oxford Nanopore Technologies long-read sequencer to obtain complete plasmid sequences. Almost identical 73 kb IncFII(pSE11)::IncN hybrid plasmids carrying blaNDM-1 were found in a P. mirabilis isolate and an M. morganii isolate. A 112 kb IncFII(pRSB107)::IncN hybrid plasmid carrying blaNDM-1 in an E. coli isolate had partially identical sequences with a 39 kb IncR plasmid carrying blaNDM-1 and an 88 kb IncFII(pHN7A8)::IncN hybrid plasmid in a C. freundii isolate. 148-149 kb IncFIA(Hl1)::IncA/C2 plasmids and 75-76 kb IncFII(Yp) plasmids, both carrying blaNDM-1 were shared among three sequence type 11 (ST11) isolates and three ST395 isolates of K. pneumoniae, respectively. Most of the plasmids co-carried genes conferring resistance to clinically relevant antimicrobials, including third-generation cephalosporins, aminoglycosides, and fluoroquinolones, in addition to blaNDM-1. These results provide insight into the genetic basis of CRE in Vietnam, and could help control nosocomial infections.

microbiology↗