Biology subjects

Yang, S. W.

Publications and source records attributed to Yang, S. W..

4 recordsLinked to original sources

bioRxiv2026

Comparison of Techniques for Isolating Small Extracellular Vesicles from Drosophila Larval Hemolymph

Extracellular vesicles (EVs) are membrane-delimited nanoparticles, secreted by virtually all tested cell types to mediate intercellular and interorgan communication by transporting biomolecules, such as proteins, nucleic acids, and lipids, to recipient cells. Many EV isolation techniques have been developed for mammalian EVs and exploit specific EV properties, such as size, density, and solubility. Although Drosophila has emerged as a simple yet robust animal model for studying fundamental EV biology in its native context, it remains unclear whether commonly used EV isolation techniques can be applied to hemolymph (Drosophila blood). In this study, we first provide an in-depth characterization of particles in hemolymph using two complementary particle analysis techniques: dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA). We then evaluate the performance of three commonly used small EV isolation methods--solvent precipitation, ultracentrifugation, and size-exclusion chromatography--for their ability to isolate small EVs from Drosophila larval hemolymph. All three methods can enrich small EVs from hemolymph to varying degrees, but none completely remove circulating proteins and lipoproteins. In particular, size-exclusion chromatography yields the purest small EV fractions, as evidenced by the enrichment of Drosophila orthologs of human small EV markers, including Tetraspanin 42Ee (Tsp42Ee), Tetraspanin 42Ed (Tsp42Ed), Tetraspanin 96F (Tsp96F), and Annexin B11 (AnxB11), although it produces the lowest protein yield. Altogether, our study provides practical guidance on both selecting an appropriate small EV isolation method and rigorously characterizing isolated small EV fractions according to specific research needs. More broadly, the knowledge gained from this study provides a framework for the isolation and characterization of small EVs in other insects, thereby facilitating future EV research across diverse insect species.

cell biology↗

bioRxiv2026

Structure-guided design of a CD81-binding mini-protein that blocks hepatitis C virus entry

Despite the success of direct-acting antivirals, preventing hepatitis C virus (HCV) reinfection remains a critical global challenge. To address this, we leveraged deep learning-based de novo protein design to engineer mini-proteins targeting the large extracellular loop (LEL) of the HCV co-receptor CD81. These mini-proteins are predicted to precisely dock into CD81-LEL, occluding the critical binding interface required for the HCV E2 glycoprotein. Through biophysical screening, we identified mini-19, a lead candidate with sub-nanomolar affinity (KD = 0.5 nM) and high thermostability up to 95{degrees}C. Flow cytometry and super-resolution imaging confirmed that mini-19 specifically recognizes the native topology of CD81 on cells and extracellular vesicles. Functionally, mini-19 neutralized HCVcc infection (IC50 = 1.2 nM). Molecular dynamics simulations demonstrated that mini-19 acts as a structural clamp, restricting the fusogenic conformational plasticity of the receptor. By targeting a conserved host factor rather than the rapidly mutating viral envelope, mini-19 provides a high genetic barrier to resistance. Beyond offering a prophylactic strategy against HCV, our findings establish a stable biologic platform for targeting tetraspanin-enriched microdomains and modulating host-pathogen interactions.

bioengineering↗

bioRxiv2026

Induction and regulation of a reversible form of suspended animation in C. elegans

Suspended animation, a state of extreme quiescence with microscopically invisible movement and development, is a remarkable yet poorly understood stress resilience strategy in animals. Here, we describe a newly discovered form of suspended animation inducible by high-population density in isosmotic liquids in C. elegans throughout larval development and adulthood. Transcriptomic, metabolomic and live-cell activity reporter imaging analyses reveal striking molecular and cellular landscape changes by such liquid-induced suspended animation (LISA), including remodeling of gene expression programs, energy metabolites, lysosomal and mitochondrial morphology. Genetic screens identify mutants with altered stress responses and survival against LISA. While key endo-lysosomal regulators promote survival during LISA, organelle remodeling and a neuronal axis via downstream neuropeptide and cAMP/PKA signaling orchestrate behavioral awakening from LISA. Our findings define a facile paradigm for reversible SA, providing a powerful model system to uncover key molecular and cellular mechanisms governing an extreme case of reversible life arrest and dormancy.

developmental biology↗

bioRxiv2024

VIPER-TACs leverage viral E3 ligases for disease-specific targeted protein degradation

In targeted protein degradation (TPD) a protein of interest is degraded by chemically induced proximity to an E3 ubiquitin ligase. One limitation of using TPD therapeutically is that most E3 ligases have broad tissue expression, which can contribute to toxicity via target degradation in healthy cells. Many pathogenic and oncogenic viruses encode E3 ligases (vE3s), which de facto have strictly limited expression to diseased cells. Here, we provide proof-of-concept for Viral E3 Pan-Essential Removing Targeting Chimeras (VIPER-TACs) that are bi-functional molecules that utilize viral E3 ubiquitin ligases to selectively degrade pan-essential proteins and eliminate diseased cells. We find that the human papillomavirus (HPV) ligase E6 can degrade the SARS1 pan-essential target protein in a model of HPV-positive cervical cancer to selectively kill E6 expressing cancer cells. Thus, VIPER-TACs have the capacity to dramatically increase the therapeutic window, alleviate toxicity concerns, and ultimately expand the potential target space for TPD.

cancer biology↗