Biology subjects

Duong, K.

Publications and source records attributed to Duong, K..

4 recordsLinked to original sources

bioRxiv2026

S-SELeCT: A Human-Evolved Serine Integrase System for Efficient Large-Cargo Genome Integration

As a consequence of their sizes, many loss-of-function genetic mutations fall within large genes. A major gene-therapy tool that could be used to solve large swaths of the genetic diseases that result from these inherited mutations is large-fragment knock-in. I.e. instead of attempting to create separate treatments for each and every location that these mutations occur in, large groups of patients could be aided via a single safe-harbor integration of the full-length coding sequence. Towards this goal, we have created a set of early stage gene-editing enzymes that can help mediate large cargo integration at a safe harbor locus in human cells. When expressed in stable lines, our S-SELeCT (Site-Specific Large Cargo Targeting) integrase fusions can facilitate integration of a 10 kb plasmid at frequencies up to 32%, and when delivered transiently via plasmid transfection, we were able to achieve up to 13% knock-in. These are the first serine integrase enzymes that have been evolved fully in human cells, and the first to recognize an endogenous symmetric non-pseudosite - the first true human serine integrase attachment site. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/702954v2_ufig1.gif" ALT="Figure 1"> View larger version (10K): org.highwire.dtl.DTLVardef@1c22676org.highwire.dtl.DTLVardef@16b171corg.highwire.dtl.DTLVardef@1ba4796org.highwire.dtl.DTLVardef@b1d91f_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness

Chemically complex extracellular matrices define cellular microenvironments and shape cell behavior. We hypothesized a composition-properties-function relationship in these natural living materials, where interactions among matrix components govern material properties and cellular physiology. Using Pseudomonas aeruginosa biofilms as a model system, we show that electrostatic interactions between the cationic polysaccharide Pel and extracellular DNA (eDNA) regulate retention of pyocyanin (PYO), a redox-active metabolite that supports anaerobic metabolism via extracellular electron transfer (EET). Biofilm-mimetic hydrogels and natural biofilms revealed that altering Pels charge via pH adjustment or chemical acetylation, or tuning the Pel:eDNA ratio, predictably modulates PYO retention and EET efficiency. Functionally, a lower Pel:eDNA ratio enhances metabolism under oxygen limitation, whereas a higher ratio promotes survival under antibiotic stress. These findings highlight how matrix chemistry encodes tunable material properties that confer biofilm fitness advantages and establish a materials-based framework for understanding extracellular matrices in multicellular communities.

microbiology↗

bioRxiv2020

Inhibition of CAMKK2 impairs autophagy and castration-resistant prostate cancer via suppression of AMPK-ULK1 signaling

Previous work has suggested androgen receptor (AR) signaling mediates cancer progression in part through the modulation of autophagy. Accordingly, we demonstrate that chloroquine, an inhibitor of autophagy, can inhibit tumor growth in preclinical mouse models of castration-resistant prostate cancer (CRPC). However, clinical trials testing chloroquine derivatives in men with CRPC have yet to yield promising results, potentially due to side effects. We hypothesized that identification of the upstream activators of autophagy in prostate cancer could highlight alternative, context-dependent targets for blocking this important cellular process during disease progression. Here, we used molecular (inducible overexpression and shRNA-mediated knockdown), genetic (CRISPR/Cas9), and pharmacological approaches to elucidate an AR-mediated autophagy cascade involving Ca2+/calmodulin-dependent protein kinase kinase 2 (CAMKK2; a kinase with a restricted expression profile), 5-AMP-activated protein kinase (AMPK) and Unc-51 like autophagy activating kinase 1 (ULK1). These findings are consistent with data indicating CAMKK2-AMPK-ULK1 signaling correlates with disease progression in genetic mouse models and patient tumor samples. Importantly, CAMKK2 disruption impaired tumor growth and prolonged survival in multiple CRPC preclinical mouse models. Finally, we demonstrate that, similar to CAMKK2 inhibition, a recently described inhibitor of AMPK-ULK1 signaling blocked autophagy, cell growth and colony formation in prostate cancer cells. Taken together, our findings converge to demonstrate that AR signaling can co-opt the CAMKK2-AMPK-ULK1 signaling cascade to promote prostate cancer by increasing autophagy. Further, we propose that an inhibitor of this signaling cascade could serve as an alternative, more specific therapeutic compared to existing inhibitors of autophagy that, to date, have demonstrated limited efficacy in clinical trials due to their toxicity and poor pharmacokinetics.

cancer biology↗

bioRxiv2019

A human ex vivo dengue virus neutralization assay identifies priority antibodies and epitopes for vaccines and therapeutics.

BackgroundDengue is the most prevalent arboviral disease, for which neither effective vaccines nor antivirals are available. Clinical trials with Dengvaxia, the first licensed dengue vaccine, show the conventional in vitro plaque reduction neutralization test (PRNT) failed to discriminate between neutralizing and non-neutralizing antibodies. A number of human monoclonal antibodies (mAbs) were characterized by PRNT as being neutralizers of virus infectivity for mammalian cells.\n\nMethodolody/Principle findingsWe developed a neutralization assay and tested the capacity of 12 mAbs to neutralize the infectiousness of dengue patient viremic blood in mosquitoes. We identified minimum concentrations of a subset of mAbs required to achieve dengue virus neutralization, and modelled the impact of a therapeutic mAb candidate on viremia.\n\nFive of the 12 mAbs (14c10, 2D22, 1L12, 747(4)B7, 753(3)C10), all of which target quaternary epitopes, potently inhibited dengue virus infection of Ae. aegypti. The potency of several mAbs was compromised in the context of patients with secondary serological profiles, possibly reflecting competition between the exogenously-added mAbs and the patients own antibody responses at or near the target epitopes. The minimum concentrations that mAbs neutralized DENV ranged from 0.1 - 5 {micro}g/mL. An Fc-disabled variant of mAb (14c10-LALA) was as potent as its parent mAb. Within-host mathematical modelling suggests infusion of 14c10-LALA could bring about rapid acceleration of viremia resolution in a typical patient.\n\nConclusions/SignificanceThese data delivered a unique assessment of anti-viral potency of a panel of human mAbs. Results support the advancement of dengue virus neutralization assays, and the development of therapeutics against flaviviruses, to which dengue virus and Zika virus belong.\n\nAuthor summaryDengue is the most prevalent arboviral disease affecting humans. There are no therapeutics for the disease. Antibody-mediated immunity against dengue is also not well-understood, as shown by the failure of the conventional neutralization assay used to predict the efficacy of Dengvaxia, the first licensed vaccine for the disease. It is likely that the neutralization assay targets non-neutralizing antibodies, but there are no validation assays available. To this end, we developed a novel virus neutralization assay, employing Aedes aegypti mosquitoes and viremic blood from dengue patients, to examine the virus-neutralizing potency of 12 human-derived monoclonal antibodies (mAbs). While all of these mAbs neutralized dengue virus using the conventional assay, seven of them failed to block dengue virus infections of mosquitoes using our assay. The remaining five mAbs neutralized at least one serotype of dengue virus and the minimum neutralizing concentrations of range from 0.1 - 5 {micro}g/mL. Using the minimum neutralizing concentration of a therapeutic mAb candidate, we investigated the impact of the mAb on viremia using a mathematical model and found the mAb accelerated the reduction of viremia. The results support the advancement of dengue virus neutralization assays, and the development of therapeutics for dengue.

immunology↗