Biology subjects

Nguyen, H. H.

Publications and source records attributed to Nguyen, H. H..

At least 19 recordsLinked to original sources

bioRxiv2026

Senescent cell networks link matrix remodeling and vascular dysfunction in human fibroids

Uterine fibroids (leiomyomas) are highly prevalent benign tumors defined by excessive extracellular matrix (ECM) deposition, altered vascular structure, and progressive tissue stiffening, yet the cellular programs that coordinate these features remain poorly understood. Cellular senescence has been implicated in fibroid biology, but whether senescence represents a uniform state or distinct, functionally specialized cell identities within fibroids is unknown. Here, we identify the distinct heterogeneous populations of senescent cells ("senotypes") present in human fibroids and characterize their role in shaping the fibroid microenvironment. Using single-cell RNA sequencing (scRNA-seq) integrated with a senescence gene signature and protein-level validation, we identify senescent cells (SnC) distributed across fibroblast, mural, and endothelial compartments, each exhibiting distinct transcriptional programs. SnC endothelial cells (ECs) are enriched in fibroids relative to matched myometrium and activate TEAD4-associated mechanosensing, angiogenic, and immune signaling pathways, despite being associated with impaired vessel maturation in situ. In parallel, SnC fibroblast and mural populations in fibroids upregulated SRF-associated cytoskeletal and ECM programs, accompanied by increased COL6A3 expression and collagen VI deposition, consistent with tissue stiffening. Ligand-receptor and spatial analyses reveal that these SnC populations function as interconnected signaling hubs, coordinating immune cell recruitment and stromal remodeling. Importantly, analysis of human fibroids treated with collagenase demonstrated a reduction in both ECM density and SnC burden, supporting a reinforcing relationship between matrix mechanics and senescence. Together, these findings establish senescence in fibroids as a heterogeneous, mechanically reinforced, and network-driven process that links vascular dysfunction, immune signaling, and fibrosis, highlighting distinct SnC states as potential translational targets for non-surgical therapies.

cell biology↗

bioRxiv2026

Membrane-Free Alveolus-on-a-Chip via Biodegradable Scaffold Recapitulates Interstitial Mechanics, Immune Trafficking, and Aerosolized mRNA Delivery

The pulmonary alveolus is a highly specialized microenvironment where epithelial, interstitial, and immune components interact to maintain gas exchange and tissue homeostasis. In vivo, the air-blood barrier consists of an epithelial layer and a capillary endothelium separated by an ultrathin interstitium composed of extracellular matrix (ECM) and lung fibroblasts. However, most existing lung-on-a-chip platforms rely on permanent synthetic membranes, which fail to recapitulate the dynamic biological and mechanical properties of the native interstitium. Here, we present a membrane-free human alveoli-on-a-chip enabled by a biodegradable poly(lactic-co-glycolic acid) (PLGA) scaffold that is progressively replaced by fibroblast-derived ECM. This process reconstructs a biologically formed interstitial layer while preserving an alveolus-like dome architecture. The resulting system supports multicellular organization under air-liquid interface conditions, enabling epithelial barrier formation and surfactant-related phenotypes. Additionally, direct epithelial-fibroblast interactions enhanced surfactant-related phenotypes, as evidenced by increased SPC and LAMP3 expression. Importantly, we demonstrate that conventional rigid substrates promote fibroblast-to-myofibroblast differentiation, leading to elevated reactive oxygen species (ROS) production, increased epithelial cell death, and compromised barrier integrity. In contrast, the membrane-free PLGA system mitigates stiffness-driven myofibroblast activation, preserving epithelial viability and maintaining barrier function. These findings highlight the critical role of interstitial mechanics in regulating alveolar homeostasis and reveal limitations of conventional membrane-based platforms. The platform further enables chemokine-driven monocyte migration across the alveolar barrier, recapitulating key immune trafficking processes observed in vivo. In addition, aerosolized metal-organic framework (MOF) nanoparticles efficiently mediated mRNA delivery to epithelial and interstitial cells with minimal cytotoxicity and modest inflammatory responses. Together, this membrane-free alveoli-on-a-chip reconstructs essential structural, mechanical, and functional features of the human alveolar microenvironment and provides a physiologically relevant platform for studying pulmonary biology, fibrosis-related mechanisms, immune cell trafficking, and inhaled nanomedicine delivery.

bioengineering↗

bioRxiv2026

Loss of interruption in the HTT CAG repeat is associated with increased somatic expansion and loss of medium spiny neurons in HD

Synonymous loss of interruption variants in the expanded CAG repeat sequence of Huntingtin (HTT) accelerate the clinical onset and progression of Huntington disease (HD). Medium spiny neurons (MSNs) are gradually lost in HD and undergo selective somatic CAG expansion, but it is unclear how CAG expansion in MSNs relates to HD pathology. Here, we show that MSNs with large (111-150 CAG) and very large (>150 CAG) somatic expansions are rare in early manifest HD, but accumulate in proportion with duration of disease and inherited CAG repeat length. In patients with the deleterious CAG-CCG loss-of-interruption (CAG-CCG LOI) modifier, the proportion of MSNs with large and very large expansions is increased [~]5-fold despite reduced small somatic expansions in blood, and direct caudate MSN counts are reduced. Our findings suggest that increased somatic CAG expansion contributes to accelerated striatal MSN pathology and hastened onset of HD, but that MSNs with very large genomic CAG expansions can persist among surviving neurons of the HD brain.

neuroscience↗

bioRxiv2025

γδ17 T cell-stromal networks modulate matrix composition and vascularity in foreign body response

Immune-stromal crosstalk governs tissue fibrosis, which is marked by dysregulated extracellular matrix (ECM) production and aberrant vasculature. Here, we investigate how {gamma}{delta} T cell interactions with stromal cells shape fibrosis in the foreign body response. During the acute reaction, type-1 ({gamma}{delta}IFN{gamma}) and type-17 ({gamma}{delta}17) effector subsets accumulated at the implant. While {gamma}{delta}IFN{gamma} decreased as fibrosis progressed, activated {gamma}{delta}17 persisted as dominant interleukin-17 producers. The {gamma}{delta}17 increased with aging and high-fat diet, both factors associated with chronic inflammation and fibrosis. Co-culture with {gamma}{delta}17 stimulated fibroblast expression of collagen genes and intercellular communication inference linked {gamma}{delta} T cell ligands to activation of ECM remodeling and vascular development programs in fibroblasts and endothelial cells. Finally, genetic deletion of {gamma}{delta} T cells altered expression of ECM components and increased vessel size within the fibrotic matrix. Altogether, our findings implicate {gamma}{delta} T cells in regulating stromal behavior to modulate composition and vascularity of fibrotic tissues.

immunology↗

bioRxiv2025

The axonal ER couples translation and secretion machineries for local delivery of axonal transmembrane proteins to promote axonal development

Neuronal development and function rely on the polarized sorting of transmembrane proteins (TMPs). Most TMPs follow a conventional secretory pathway confined to the cell soma, where ER-translated TMPs exit the ER through ERES to reach the Golgi, prior to PM delivery. We recently found that the axonal ER regulates local translation; however, how this is linked to secretion remains unknown. Here, we find that axonally translated TMPs exit the ER and reach the axonal PM via an ERES-dependent/Golgi-independent route. Intriguingly, we uncover a feedback loop linking translation and secretion at axonal ERES. HDLBP-dependent TMP synthesis regulates ERES formation, and axonal ERES in turn modulate TMP translation. Subsequently, the NRZ-SEC22B tethering complex links local TMP ER exit to PM delivery, dependent on ER-PM contacts. Axonal ERES and these associated molecular players support axon growth and bouton assembly. We propose a novel mechanism in which coupling of axonal TMP synthesis and secretion is essential for neuronal development.

cell biology↗

bioRxiv2025

Selective manipulation of excitatory and inhibitory neurons in top-down and bottom-up visual pathways using ultrasound stimulation

IntroductionTechniques for precise manipulation of neurons in specific neural pathways are crucial for excitatory/inhibitory (E/I) balance and investigation of complex brain circuits. Low-intensity focused ultrasound stimulation (LIFUS) has emerged as a promising tool for noninvasive deep-brain targeting at high spatial resolution. However, there is a lack of studies that extensively investigate the modulation of top-down and bottom-up corticothalamic circuits via selective manipulation of excitatory and inhibitory neurons. Here, a comprehensive methodology using electrophysiological recording and c-Fos staining is employed to demonstrate pulse repetition frequency (PRF)-dependent E/I selectivity of ultrasound stimulation in the top-down and bottom-up corticothalamic pathways of the visual circuit in rodents. Materials and methodsUltrasound stimulation at various PRFs is applied to either the lateral posterior nucleus of the thalamus (LP) or the primary visual cortex (V1), and multi-channel single-unit activity is recorded from the V1 using a silicon probe. Results and conclusionOur results demonstrate that high frequency PRFs, particularly at 3 kHz and 1 kHz, are effective at activating the bidirectional corticothalamic visual pathway. In addition, brain region-specific PRFs modulate E/I cortical signals, corticothalamic projections, and synaptic neurotransmission, which is imperative for circuit-specific applications and behavioral studies.

neuroscience↗

bioRxiv2024

Transferability of stream benthic macroinvertebrate distribution models to drought-related conditions

Freshwater ecosystems increasingly face pressures from climate change induced extreme events, like droughts, posing significant threats to biodiversity. While Species Distribution Models (SDMs) serve as vital tools for predicting species responses to environmental shifts, their transferability to novel environmental conditions, especially during and after drought remains poorly understood. In this study, we delve into the transferability of SDMs for freshwater macroinvertebrates from drought-free to drought-influenced conditions. We examine how sensitive the transferability is to traits such as tolerance scores according to their distribution along longitudinal gradients, as well as the used modelling method. We constructed and validated SDMs for freshwater macroinvertebrates in a central German catchment under drought-free conditions using four different algorithms (Generalised linear models; GLM, Spatial Stream Networks; SSN, Random Forests; RF, and Maximum Entropy; MaxEnt). We then projected these models to environmental conditions influenced by drought, and obtained their transferability by computing the difference in accuracy when predicting under drought-free and drought-influenced conditions (AUCgap). Our findings reveal a marked reduction in SDM accuracy under drought conditions, illustrating the challenges of accurately predicting species distributions into novel environmental conditions. Our results show a slightly better transferability when using SSN and RF. In addition, we observed that SDM transferability can be influenced by species tolerance, with sensitive and tolerant species presenting higher AUCgap (i.e. lower transferability). Furthermore, we found that when sensitive species were modelled using SSNs, the AUCgap was reduced. Our study underscores the limitations of SDMs in capturing species responses to drought and advocates for integrating ecologically relevant predictors and modelling methods that account for the stream connectivity to allow for robust predictions. These considerations could enhance the ability of SDMs to effectively estimate the impacts of extreme events on freshwater biodiversity.

ecology↗

bioRxiv2024

Modular mechanisms of immune priming and growth inhibition mediated by plant effector-triggered immunity

Excessive activation of effector-triggered immunity (ETI) in plants inhibits plant growth and activates cell death. ETI mediated by intracellular Toll/Interleukin-1 receptor/Resistance protein (TIR) nucleotide-binding leucine-rich-repeat receptors (NLRs) involves two partially redundant signalling nodes in Arabidopsis, EDS1-PAD4-ADR1 and EDS1-SAG101-NRG1. Genetic and transcriptomic analyses show that EDS1-PAD4-ADR1 primarily enhances the immune component abundance and is critical for limiting pathogen growth, whereas EDS1-SAG101-NRG1 mainly activates the hypersensitive cell death response (HR) but is dispensable for immune priming. This study enhances our understanding of the distinct contributions of these two signalling modules to ETI and suggests potential strategies for improving disease resistance in crops without compromising yield.

plant biology↗

bioRxiv2023

Scalable bio-platform to recover critical metals fromcomplex waste sources

Chemical methods for extraction and refinement of technologically critical rare earth elements (REEs) are energy intensive, hazardous, and environmentally destructive. Current bio-based extraction systems rely on extremophilic organisms and generate many of the same detrimental effects as chemical methodologies. The mesophilic methylotrophic bacterium Methylobacterium extorquens AM1 was previously shown to grow using electronic waste by naturally acquiring REEs to power methanol metabolism. Here we show that growth using electronic waste as a sole REE source is scalable up to 10 L with consistent metal yields, without the use of harsh acids or high temperatures. Addition of organic acids increases REE leaching in a nonspecific manner. REE-specific bioleaching can be engineered through the overproduction of REE-binding ligands (called lanthanophores) and pyrroloquinoline quinone. REE bioaccumulation increases with leachate concentration and is highly specific. REEs are stored intracellularly in polyphosphate granules, and genetic engineering to eliminate exopolyphosphatase activity increases metal accumulation, confirming the link between phosphate metabolism and biological REE use. Finally, we report the innate ability of M. extorquens to grow using other complex REE sources including pulverized smart phones, demonstrating the flexibility and potential for use as a recovery platform for these critical metals.

bioengineering↗

bioRxiv2023

Identification of a Novel PARP14 Site Motif and Glycohydrolase Specificity Using TLC-MALDI-TOF

Transfer of ADP-ribose (ADPr) from nicotinamide adenine dinucleotide (NAD+) to target proteins is mediated by a class of human poly-ADP-ribose polymerases, PARPs, and removal of ADPr is catalyzed by a family of glycohydrolases. Although thousands of potential ADPr modification sites have been identified using high-throughput mass-spectrometry, relatively little is known about sequence specificity encoded near the modification site. Herein, we present a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method that facilitates the discovery and validation of ADPr site motifs. We identify a minimal 5-mer peptide sequence that is sufficient to drive PARP14 specific activity while highlighting the importance of the adjacent residues in PARP14 targeting. We measure the stability of the resultant ester bond and show that non-enzymatic removal is sequence independent and occurs within hours. Finally, we use the ADPr--peptide to highlight differential activities within the glycohydrolase family and their sequence specificities. Our results highlight: 1) the utility of MALDI-TOF in motif discovery and 2) the importance of peptide sequence in governing ADPr transfer and removal.

biochemistry↗

bioRxiv2022

Axonal ER tubules regulate local translation via P180/RRBP1-mediated ribosome interactions

Local mRNA translation in axons is critical for the spatial and temporal regulation of the axonal proteome. A wide variety of mRNAs are localized and translated in axons, however how protein synthesis is regulated at specific subcellular sites in axons remains unclear. Here, we establish that the axonal endoplasmic reticulum (ER) supports axonal translation. Axonal ER tubule disruption impairs local translation and ribosome distribution. Using nanoscale resolution imaging, we find that ribosomes make frequent contacts with ER tubules in the axon in a translation-dependent manner and are influenced by specific extrinsic cues. We identify P180/RRBP1 as an axonally distributed ribosome receptor that regulates local translation in an mRNA-dependent manner. Our results establish an important role for the axonal ER in localizing mRNA translation and in dynamically regulating the axonal proteome in response to neuronal stimuli.

neuroscience↗

bioRxiv2022

Elucidating the molecular programming of a nonlinear nonribosomal peptide synthetase responsible for fungal siderophore biosynthesis.

Siderophores belonging to the ferrichrome family are essential for the viability of fungal species and play a key role for virulence of numerous pathogenic fungi. Despite their biological significance, our understanding of how these iron-chelating cyclic hexapeptides are assembled by non-ribosomal peptide synthetase (NRPS) assembly lines remains poorly understood, primarily due to the nonlinearity exhibited by the domain architecture. Herein, we report the biochemical characterization of the SidC NRPS, responsible for construction of the intracellular siderophore ferricrocin. In vitro reconstitution of purified SidC revealed its ability to produce ferricrocin and its structural variant, ferrichrome. Application of intact protein mass spectrometry uncovered several non-canonical events during peptidyl siderophore biosynthesis, including inter-modular loading of amino acid substrates and an adenylation domain capable of poly-amide bond formation. This work expands the scope of NRPS programming, allows biosynthetic assignment of ferrichrome NRPSs, and sets the stage for reprogramming towards novel hydroxamate scaffolds.

biochemistry↗

bioRxiv2022

Transfer learning of an in vivo-derived senescence signature identifies conserved and tissue-specific senescence across species and diverse pathologies

Senescent cells (SnCs) contribute to normal tissue development and repair but accumulate with aging where they are implicated in a number of pathologies and diseases. Despite their pathological role and therapeutic interest, SnC phenotype and function in vivo remains unclear due to the challenges in identifying and isolating these rare cells. Here, we developed an in vivo-derived senescence gene expression signature using a model of the foreign body response (FBR) fibrosis in a p16Ink4a-reporter mouse, a cell cycle inhibitor commonly used to identify SnCs. We identified stromal cells (CD45-CD31- CD29+) as the primary p16Ink4a expressing cell type in the FBR and collected the cells to produce a SnC transcriptomic signature with bulk RNA sequencing. To computationally identify SnCs in bulk and single-cell data sets across species and tissues, we used this signature with transfer learning to generate a SnC signature score (SenSig). We found senescent pericyte and cartilage-like fibroblasts in newly collected single cell RNAseq (scRNASeq) data sets of murine and human FBR suggesting populations associated with angiogenesis and secretion of fibrotic extracellular matrix, respectively. Application of the senescence signature to human scRNAseq data sets from idiopathic pulmonary fibrosis (IPF) and the basal cell carcinoma microenvironment identified both conserved and tissue-specific SnC phenotypes, including epithelial-derived basaloid and endothelial cells. In a wound healing model, ligand-receptor signaling prediction identified putative interactions between SnC SASP and myeloid cells that were validated by immunofluorescent staining and in vitro coculture of SnCs and macrophages. Collectively, we have found that our SenSig transfer learning strategy from an in vivo signature outperforms in vitro-derived signatures and identifies conserved and tissue-specific SnCs and their SASP, independent of p16Ink4a expression, and may be broadly applied to elucidate SnC identity and function in vivo.

bioengineering↗

bioRxiv2021

Age-related Immune-Stromal Networks Inhibit Response to Regenerative Immunotherapies

Aging is associated with immunological changes that compromise response to infections and vaccines, exacerbate inflammatory diseases and could potentially mitigate tissue repair. Even so, age-related changes to the immune response to tissue damage and regenerative medicine therapies remain unknown. Here, we characterized how aging induces senescence and immunological changes that inhibit tissue repair and therapeutic response to a clinical regenerative biological scaffold derived from extracellular matrix. Tissue signatures of inflammation and interleukin (IL)-17 signaling increased with injury and treatment in aged animals, and computational analysis uncovered age-associated senescent-T cell communication that promotes type 3 immunity in T cells. Local inhibition of type 3 immune activation using IL17-neutralizing antibodies improved healing and restored therapeutic response to the regenerative biomaterial, promoting muscle repair in older animals. These results provide insights into tissue immune dysregulation that occurs with aging that can be targeted to rejuvenate repair.

bioengineering↗

bioRxiv2020

Leveraging immonium ions for identifying and targeting acyl-lysine modifications in proteomic datasets

Acyl modifications vary greatly in terms of elemental composition and site of protein modification. Developing methods to identify these modifications more confidently can help assess the scope of these modifications in large proteomic datasets. Herein we analyze the utility of acyl-lysine immonium ions for identifying the modifications in proteomic datasets. We demonstrate that the cyclized immonium ion is a strong indicator of acyl-lysine presence when its rank or relative abundance compared to other ions within a spectrum is considered. Utilizing a stepped collision energy method in a shotgun experiment highlights the immonium ion strongly. Implementing an analysis that accounted for features within each MS2 spectra, this method allows peptides with short chain acyl-lysine modifications to be clearly identified in complex lysates. Immonium ions can also be used to validate novel acyl-modifications; in this study we report the first examples of 3-hydroxylpimelyl-lysine modification and validate them using immonium ions. Overall these results solidify the use of the immonium ion as a marker for acyl-lysine modifications in complex proteomic datasets. Statement of SignificanceAcyl-lysine modifications come in a variety of elemental compositions. There is increasing evidence that these modifications can have a functional effect on protein and are present in proteomes across all domains of life. Here we describe a new method that can allow for more confident identification of acyl modifications in proteomes by utilizing the immonium ion of these modifications. Our utilization of these ions allows for more comprehensive insight into the role of acyl modifications at the systems level.

biochemistry↗

bioRxiv2020

Cold priming memory reduces plant pathogen susceptibility based on a functional plastid peroxidase system

Chloroplasts, as recently shown, serve as cold priming hubs in modulating the transcriptional response of Arabidopsis thaliana to a second cold stimulus after a stress-free interphase of several days. Here, we studied if such a single 24 h cold stress at 4 {degrees}C also alters the susceptibility of Arabidopsis to virulent Pseudomonas syringae pv. tomato DC3000. Our data show that cold priming did not only increase resistance of Arabidopsis to a subsequent infection immediately, but also after a memory phase of 5 days, during which thylakoid ascorbate peroxidases accumulate. Contrasting to susceptibility, the prior cold exposure did not alter resistance against avirulent and effector-triggered immunity-inducing Pseudomonas syringae strains. The effect of cold priming on the plant pathogen susceptibility was independent of the central nucleo-cytoplasmic immune regulator EDS1 (Enhanced Disease Susceptibility 1) and uncoupled from classical immune gene activation. The priming benefits against pathogens required thylakoid and stromal ascorbate peroxidase activity. Combinatorial priming of Arabidopsis pathogen susceptibility by metastable regulation of stromal ascorbate peroxidase activity and post-cold expression of thylakoid ascorbate peroxidase guarantees immediate protection without latency time and prolonged protection by the memory element that regulates future cold responses. One-sentence summary24 hour cold exposure reduces plant susceptibility against virulent pathogens dependent on chloroplast ascorbate peroxidases.

plant biology↗

bioRxiv2019

N-terminal autoprocessing and acetylation of MARTX Makes-Caterpillars Floppy-like effector is stimulated by ADP-Ribosylation Factor 1 in advance of Golgi fragmentation

Studies have successfully elucidated the mechanism of action of several effector domains that comprise the MARTX toxins of Vibrio vulnificus. However, the biochemical linkage between the cysteine proteolytic activity of Makes Caterpillars Floppy-like (MCF) effector and its cellular effects remains unknown. In this study, we identify the host cell factors that activate in vivo and in vitro MCF autoprocessing as ADP-Ribosylation Factor 1 (ARF1) and ADP-ribosylation Factor 3 (ARF3). Autoprocessing activity is enhanced when ARF1 is in its active (GTP-bound) form compared to the inactive (GDP-bound) form. Subsequent to auto-cleavage, MCF is acetylated on its exposed N-terminal glycine residue. Acetylation apparently does not dictate subcellular localization, as MCF is found localized throughout the cell. However, the cleaved form of MCF gains the ability to bind to the specialized lipid phosphatidylinositol 5-phosphate enriched in Golgi and other membranes necessary for endocytic trafficking, suggesting a fraction of MCF may be subcellular localized. Traditional thin-section electron microscopy, high-resolution cryoAPEX localization, and fluorescent microscopy show that MCF causes Golgi dispersal resulting in extensive vesiculation. In addition, host mitochondria are disrupted and fragmented. Surprisingly, ARF1 is not itself processed or post-translationally modified by MCF. Further, only catalytically inactive MCF stably associates with ARF1, thus serving as a substrate trap. Our data indicate that ARF1 is a cross-kingdom activator of MCF, but reveal that MCF mediates cytotoxicity likely by directly targeting another yet to be identified protein. This study begins to elucidate the biochemical activity of this important domain and gives insight into how it may promote disease progression.

microbiology↗

bioRxiv2019

Serum Amyloid A Proteins Induce Pathogenic TH17 Cells and Promote Inflammatory Disease

Lymphoid cells that produce IL-17 cytokines protect barrier tissues from pathogenic microbes, but are also prominent effectors of inflammation and autoimmune disease. T-helper (TH17) cells, defined by ROR{gamma}t-dependent production of IL-17A and IL-17F, exert homeostatic functions in the gut upon microbiota-directed differentiation from naive CD4+ T cells. In the non-pathogenic setting, their cytokine production is regulated by serum amyloid A proteins (SAA1 and SAA2) secreted by adjacent intestinal epithelial cells. However, TH17 cell behaviors vary markedly according to their environment. Here we show that SAAs additionally direct a pathogenic pro-inflammatory TH17 cell differentiation program, acting directly on T cells in collaboration with STAT3-activating cytokines. Using loss- and gain-of-function mouse models, we show that SAA1, SAA2, and SAA3 have distinct systemic and local functions in promoting TH17-mediated inflammatory diseases. These studies suggest that T cell signaling pathways modulated by the SAAs may be attractive targets for anti-inflammatory therapies.

immunology↗