Biology subjects

Duong, V. T.

Publications and source records attributed to Duong, V. T..

6 recordsLinked to original sources

bioRxiv2026

Photo-click Decellularized Matrix Hydrogels for Generating Pancreatic Ductal Organoids

Pancreatic ductal organoids (PDOs) generated from human induced pluripotent stem cells (iPSCs) can be used to model pancreatic diseases and to conduct drug screening/testing. However, current protocols for generating PDOs rely heavily on tumor-derived Matrigel, which has been shown to upregulate oncogenes. Furthermore, Matrigel has undefined composition and weak mechanical properties that hamper mechanistic studies of cell-material interactions. In this study, we explore photo-clickable decellularized small intestine submucosa-norbornene (dSIS-NB) hydrogels as a Matrigel replacement for generating human iPSC-derived PDOs. To achieve this, pancreatic progenitors (PP) were first differentiated in conventional two-dimensional (2D) culture, aggregated into spheroids, then encapsulated and differentiated within dSIS-NB hydrogels with tunable stiffness. The differentiated organoids were analyzed by morphology, expression of key pancreatic ductal markers, and single-cell RNA sequencing (scRNA-seq). Post-differentiation, PDOs generated in stiffer photo-clickable dSIS-NB hydrogels (shear moduli [~]2.5 kPa) maintained ductal epithelial phenotype and exhibited pronounced forskolin-induced swelling. In contrast, differentiation of PP spheroids in softer dSIS-NB gels (shear moduli [~]0.9 kPa) and Matrigel resulted in a persistent mesenchymal phenotype and failed to generate functional PDOs. Finally, scRNA-seq results revealed that stiffer dSIS-NB hydrogels strongly biased ductal cell differentiation, yielding greater than 97% ductal progeny.

bioengineering↗

bioRxiv2025

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae, a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in length in infant and adult guts, and other microbiomes. Of 19 complete plasmid genomes, one was reconstructed from an E. coli isolate; others were linked to species of Citrobacter and Enterobacter via analysis of genome modification patterns. The detection of related plasmids in different Enterobacteriaceae, conjugation machinery, and more diverse modified motifs in certain plasmids compared to hosts suggests that these elements are self-transmissible, with a broad host range. The plasmids encode multi-drug efflux systems and potential secreted effectors. Up to 208 tRNAs are encoded and include sequence variants that may counter tRNA-centric defense mechanisms. Overall, the vast megaplasmid coding capacity may broaden host range, increase competitiveness, control invasion by other elements, and counter programmed cell death.

microbiology↗

bioRxiv2023

Direct extrusion of multifascicle prevascularized human skeletal muscle for volumetric muscle loss surgery

Volumetric skeletal muscle injuries are prevalent, highlighting the imperative need for scaffolds to facilitate the healing process of such wounds. Human skeletal muscle is composed of multiple fascicles, which are parallel bundles of muscle fibres surrounded by a layer of connective tissue that contains blood vessels and nerves. Replicating these structures presents a considerable challenge. Here, we developed a method to fabricate multifascicle human skeletal muscle scaffolds that mimic the natural structure of human skeletal muscle bundles using a seven-barrel nozzle. To form the core material to generate the fascicle structure, human skeletal myoblasts were encapsulated in Matrigel with calcium chloride. Meanwhile, to create the shell that plays a role as the connective tissue structure, human fibroblasts and human umbilical vein endothelial cells within a mixture of porcine muscle decellularized extracellular matrix and sodium alginate at a 95:5 ratio was used. We assessed four types of extruded scaffolds monolithic-monoculture (Mo-M), monolithic-coculture (Mo-C), multifascicle-monoculture (Mu-M), and multifascicle-coculture (Mu-C) to determine the structural effect of muscle mimicking scaffold. The Mu-C scaffold demonstrated cell proliferation, differentiation, vascularization, mechanical properties, and functionality that were superior to those of the other scaffolds. Furthermore, in an in vivo mouse model of volumetric muscle loss, the Mu-C scaffold effectively regenerated the tibialis anterior muscle defect, demonstrating its potential for volumetric muscle transplantation. The multibarrel nozzle device was applied to create functional Mu-C muscle scaffolds that structurally mimicked human skeletal muscle. Our nozzle will be further used to produce other volumetric functional tissues, such as tendons and peripheral nerves.

bioengineering↗

bioRxiv2023

Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 4,,12,i:- ST34 in Southeast Asia

Salmonella enterica serotype 4,[5],12,i:- (Typhimurium monophasic variant) of sequence type (ST) 34 has emerged as the predominant pandemic genotype in recent decades. Despite increasing reports of resistance to antimicrobials in Southeast Asia, Salmonella ST34 population structure and evolution remained understudied in the region. Here we performed detailed genomic investigations on 454 ST34 genomes collected from Vietnam and diverse geographical sources to elucidate the pathogens epidemiology, evolution and antimicrobial resistance. We showed that ST34 has been introduced into Vietnam in at least nine occasions since 2000, forming five co-circulating major clones responsible for paediatric diarrhoea and bloodstream infection. Most expansion events were associated with acquisitions of large multidrug resistance plasmids of IncHI2 or IncA/C2. Particularly, the self-conjugative IncA/C2 pST34VN2 (co-transferring blaCTX-M-55, mcr-3.1, and qnrS1) underlies local expansion and intercontinental spread in two separate ST34 clones. At the global scale, Southeast Asia was identified as a hotspot for the emergence and dissemination of multidrug resistant Salmonella ST34, and mutation analysis suggests of selection in antimicrobial responses and key virulence factors. Our work enriches the understanding on epidemiology and evolution of this variant in Southeast Asia, and determines that multidrug resistance plasmids have driven its local and potentially global success.

genomics↗

bioRxiv2022

Enhanced Effector Activity of Mediator Kinase Module Deficient CAR-T Cells

Adoptive T cell immune therapies mediate impressive clinical benefit in a fraction of patients, but anti-tumor effects are often limited by inadequate T cell potency. To identify genes limiting T cell effector function, we conducted genome-wide CRISPR knock-out screens in human primary CAR-T cells. The top hits were MED12 and CCNC, components of the cyclin-dependent kinase (CDK) module of the Mediator complex, an evolutionarily conserved regulator of gene transcription. MED12 or CCNC deficient CAR-T cells manifest increased expansion, cytokine production, metabolic fitness, effector function, anti-tumor activity and reduced terminal effector differentiation. Chemical inhibition of CDK8/19 kinase activity recapitulated some features of genetic loss of MED12, including increased T cell expansion. MED12 deficient CAR-T cells showed widespread but selective increases in chromatin accessibility, MED1 chromatin occupancy, and H3K27 acetylation at enhancers used by transcription factors playing a critical role in T cell fate, including several STAT and AP1 family members. The most pronounced enhancement was observed for STAT5 which manifested as increased sensitivity to IL-2 in MED12 deficient T cells. These results link Mediator induced transcriptional coactivation with T cell effector programming and identify the CDK module as a target for enhancing the potency of anti-tumor T cell responses. One Sentence SummaryThe Mediator kinase module is a primary regulator of T cell differentiation, and genetic or small molecule-based inhibition of this module enhances effector T cell potency.

immunology↗

bioRxiv2017

Quantifying antimicrobial access and practices for paediatric diarrheal disease in an urban community setting in Southeast Asia

Antimicrobial-resistant infections are increasing across Asia. Aiming to evaluate antimicrobial access and practices in Ho Chi Minh City (HCMC) of Vietnam, we mapped pharmacy locations and used a simulated client method to calculate antimicrobial sales for paediatric diarrheal disease. We additionally evaluated healthcare choices for parents and caregivers when their children experienced diarrhoea. District 8 (population 396,175) of HCMC had 301 pharmacies (one for every 1,316 people), with a density of 15.8 pharmacies/km2. A wide range of different treatments (n=57) were sold for paediatric diarrheal disease, with 8% (3/37) and 22% (8/37) of the sampled pharmacies selling antimicrobials for watery and mucoid diarrhoea, respectively. Despite the apparent abundance of pharmacies, the majority of caregivers chose to take their child to a specialized hospital, with 81% (319/396) and 88% (347/396) of responders selecting this as their first, second, or third choice for watery and mucoid diarrhoea, respectively. Lastly, by combining denominators derived from caregiver interviews and diarrheal incidence figures, we calculated that 16% (2,359/14,427) of watery or mucoid diarrhoea episodes of the District 8 population aged 1 to <5 years would receive an antimicrobial for diarrhoea annually, but antimicrobial prescribing was almost ten times greater in hospitals than in the community. Our novel mixed-methods approach found that, whilst antimicrobials are commonly available for paediatric diarrhoea in the community of HCMC, usage is greater in hospitals. The observed non-standardized approach to diarrheal treatments is indicative of poor recommendations. We advocate better guidelines, training and dissemination of information regarding antimicrobials and their use in this location.

epidemiology↗