High-Throughput DNA Barcoding Identifies Lipid Nanoparticles for Lung Delivery of TRAIL-mRNA to Induce Tumor Cell Death in Experimental Metastasis Model

Abstract

Introduction Lipid nanoparticles (LNPs) have enabled the clinical translation of nucleic acid therapeutics, and their composition plays a critical role in organ targeting and route-specific delivery. Intranasal (IN) administration offers direct access to the lungs, while reducing systemic exposure. However, designing LNPs capable of overcoming respiratory tract barriers remains a challenge. Methods We used DNA barcoding (b-DNA) for high-throughput in vivo screening of an LNP library following IN administration to investigate the impact of helper lipid identity and changes in the relative helper lipid/cholesterol composition on lung delivery. Following physicochemical characterization, pooled LNPs were administered intranasally to C57BL/6 mice, and their biodistribution was quantified by next-generation sequencing. Lead formulations were further evaluated for lung transfection in vivo and pulmonary cell transfection in vitro, cell viability, concentration-response relationships, and membrane-disruptive properties were also assessed. To better understand the discrepancies between the in vivo and in vitro performance, LNP stability was investigated in simulated nasal fluid and cell culture media. Results DOPE-based LNPs exhibited uniform diameters of approximately 90–110 nm, whereas DSPC- and DOTAP-based formulations showed greater variability in size. While DOPE- and DSPC-LNPs displayed slightly negative zeta potential values, DOTAP-formulations exhibited positive values. DSPC-LNP6 has emerged as the lead formulation for lung delivery and transfection in vivo, despite exhibiting limited transfection efficiency in pulmonary cells in vitro. Notably, the impact of simulated nasal fluid on the physicochemical properties of LNPs was comparable across formulations, suggesting that intrinsic membrane properties contribute to enhanced pulmonary transfection after IN administration. Finally, DSPC-LNP6 successfully mediated TRAIL mRNA delivery and induced tumor cell death in an experimental lung metastasis model. Conclusion Collectively, our findings provide critical insights into the development of RNA therapeutics that target the respiratory tract.