Biology subjects

Chen, W.-R.

Publications and source records attributed to Chen, W.-R..

3 recordsLinked to original sources

bioRxiv2026

A High-Throughput Platform for Rapidly Adapting DNA Aptamers to SARS-CoV-2 Evolution

Rapid pathogen evolution threatens public health by eroding the effectiveness of vaccines, therapeutics, and diagnostic tools. Although spike protein targeting monoclonal antibodies (mAbs) were developed within 10-12 months of the initial outbreak to serve as key theranostic agents, their redesign has struggled to keep pace with viral evolution, rendering many neutralizing antibodies ineffective. Here we demonstrate a novel platform that combines a random-rational hybrid library diversification with high-throughput MiSeq screening to rapidly reprogram aptamers against emerging SARS-CoV-2 spike variants. Interactions between 3 different spike proteins and 11,806 unique aptamer variant designs were profiled within a few days. Starting from a 40-nt aptamer originally selected against wild-type (WT) spike protein, our screen identified a Delta-binding mutant with a 4-fold affinity improvement and an Omicron-binding mutant that converted undetectable binding into nanomolar affinity. We also identified a WT-selective mutant with substantially reduced affinity for Delta, as well as previously unrecognized bases that critically contribute to spike recognition. Integrating high-throughput binding data with molecular dynamics simulations further revealed sequence-dependent structural features underlying variant-specific aptamer-spike interactions. Finally, we developed a sensor based on the identified WT-selective aptamer mutant, enabling highly specific detection of the WT spike protein with robust performance. Together, this work establishes a rapid and adaptable aptamer engineering platform for rapid adaptation of aptamers to evolving pathogens in future pandemics.

bioengineering↗

bioRxiv2026

Mechanistic insights into the color transformation of a non-FRET substrate for RNase activity detection

DNA-templated silver nanoclusters (DNA/AgNCs) have created a new class of non-FRET DNase substrates, termed Subak, that exhibits a color change upon DNase digestion. Although Subak substrates offer advantages such as ratiometric readouts and low manufacturing costs over traditional FRET substrates, the mechanism governing AgNC color switching remains unclear. Here, using a site-specific cleavage strategy, we identify color-switching hotspots and demonstrate that AgNC transformation can be controlled by the cleavage positions within the nucleic acid host. Our data support a cleavage-driven reorganization of the AgNC coordination environment, converting a non-emissive precursor into a red-emitting cluster, rather than direct enzyme-cluster interactions. Leveraging this insight, we engineer rSubak, an RNA-incorporated Subak that displays 95 nm red shift (530 to 625 nm) upon RNase cleavage. In amplification-free CRISPR/Cas13 assays for SARS-CoV-2, influenza A (A/H5N1), and measles viruses (MV) detection, rSubak achieved a limit of detection of 0.3 pM, superior to that of the commercial RNaseAlert ([~]250 pM). Collectively, our results establish Subak as a generalizable, non-FRET platform for sensitive ratiometric reporting the activities of diverse nucleases.

bioengineering↗

bioRxiv2022

Aldo-Keto Reductase Family 1 Member A1 (AKR1A1) Deficiency Exacerbates Alcohol-Induced Hepatic Oxidative Stress, Inflammation, Steatosis, and Fibrosis

BackgroundAlcohol-associated liver disease (ALD) covers a wide range of hepatic lesions that depend on the amount and duration of alcohol consumption, from early and reversible conditions to hepatic steatosis and severe lesions, including steatohepatitis and alcoholic fibrosis, to irreversible cirrhosis. AKR1A1, an aldo-keto reductase family member, participates in the detoxification of alcohol-derived acetaldehyde, but its role in ALD remains unclear. In this study, we studied the role of AKR1A1 in the development of ALD using Akr1a1-/- knockout mice and palmitic acid/oleic acid (P/O) plus ethanol-treated AML12 hepatocyte cells. MethodsLevels of AKR1A1 were measured in mice fed with the Lieber-DeCarli diet containing 5% alcohol (alcohol-fed, AF) or control liquid diet (pair-fed, PF). The effects of AKR1A1 on the liver function, inflammation, oxidative stress, lipid accumulation, and fibrosis were assessed in AF-induced Akr1a1-/- and ICR control mice. ResultsData showed that AF-Akr1a1-/- mice exhibited an exacerbation of liver injury and increased gene and protein levels of inflammatory mediators, oxidative stress, lipid accumulation, and fibrosis, whilst decreased expression of antioxidant enzymes in their livers than the AF-ICR mice. Therefore, loss of AKR1A1 can activate 4-HNE/p53 signaling to modulate ROS and antioxidant balance, increase lipid peroxidation, fatty acid synthesis and lipid droplet formation, reduced fatty acid {beta}-oxidation, and elevated proinflammatory and fibrotic mediator, eventually exacerbate the ALD. In in vitro study, we further demonstrated that knockdown of Akrlal aggravated the effects of alcohol plus P/O-induced oxidative stress and steatosis, LPS-stimulated inflammation, and TGF-{beta}1-induced fibrosis in AML12 hepatocyte cells. Conclusionour results revealed that AKR1A1 exerts protective effects on alcohol-induced liver injury, steatosis, and fibrosis, possibly by regulating the 4-HNE-p53 signaling pathway.

pathology↗