Biology subjects

Zheng, S.-Y.

Publications and source records attributed to Zheng, S.-Y..

4 recordsLinked to original sources

bioRxiv2026

Interstitium-mimicking porous alveolar membranes enable physiologic aerosol transport and distinct acute-chronic lung injury responses

Barrier membranes govern transport and mechanochemical coupling in lung-on-chip systems but typically exhibit low open porosity, limited pore interconnectivity, and diffusion distances exceeding native thin septal regions. An interstitium-mimicking, alveolus-shaped poly({varepsilon}-caprolactone) membrane is developed using dual-templated nonsolvent-induced phase separation followed by controlled enzymatic pore enlargement. The resulting architecture achieves [~]40% total porosity with 97% pore interconnectivity and incorporates a locally thinned dome region ([~]2.5 {micro}m). This structure sustains cyclic deformation while increasing oxygen diffusivity fivefold compared with conventional Transwell(R) membranes under both acellular and epithelial-endothelial co-culture conditions. Integrated into an air-liquid interface platform, the membrane enables direct aerosol deposition and quantitative interrogation of cross-barrier mass transfer. Using carbonaceous nanoscale particulate matter as a model inhaled aerosol, controlled exposure induces dose-dependent oxidative, inflammatory, and genotoxic responses. Matched cumulative dose studies reveal distinct biological trajectories: acute high-dose exposure produces rapid cytotoxic stress and barrier disruption, whereas chronic low-dose exposure preserves viability yet promotes sustained DNA repair and genome-maintenance programs. Compartment-resolved analysis and therapeutic intervention further demonstrate the platforms utility for spatial and translational interrogation of lung injury. By restoring physiologically relevant diffusion distance, interconnectivity, and strain responsiveness, the interstitium-mimicking membrane advances lung-on-chip design toward functional replication of alveolar transport dynamics for studying lung injury and barrier dysfunction.

bioengineering↗

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

Droplet-compatible single-cell DNA methylation sequencing with PreTIC

Single-cell DNA methylation sequencing has remained technically specialized due to challenges of interfacing conversion chemistry with droplet microfluidics. We introduce pre-tagmentation in situ conversion (PreTIC), which enables whole-methylome profiling on a commercial droplet platform using off-the-shelf reagents. With PreTIC, we produce over 13,000 single-cell methylomes from fixed frozen cells in two days and resolve cell-specific epigenetic variation in human peripheral blood mononuclear cells.

genomics↗

bioRxiv2023

Rapid and unbiased enrichment of extracellular vesicles via meticulously engineered peptide

Extracellular vesicles (EVs) have garnered significant attention in biomedical applications, particularly as biomarkers and therapeutic agents for cancer diagnosis and treatment. However, the rapid, efficient, and unbiased separation of EVs from complex biological fluids remains a challenge due to their heterogeneity and low abundance concentration in biofluids. Herein, we report a novel approach to reconfigure and modify an artificial insertion peptide for the rapid isolation of EVs in 20 min with [~] 80% recovery. By inserting the peptide into the phospholipid bilayer of EVs, our method enables the unbiased isolation of EVs. Moreover, our approach demonstrates exceptional anti-interference capability and achieves a high purity of EVs comparable to standard ultracentrifugation and other methods. Importantly, we show that the isolated EVs could be directly applied for downstream protein and nucleic acids analyses, including proteomics analysis, exome sequencing analysis, as well as the detection of EGFR and KRAS gene mutation in clinical plasma samples. Our approach offers new possibilities for utilizing EVs in cancer diagnostics through liquid biopsy, as well as in various other biomedical applications.

bioengineering↗