Apical-Out Ileal Organoids: A Versatile Platform for Probing Gut-Nanomaterial Interactions

Abstract

The human ileal epithelium forms a critical interface governing interactions with luminal microorganisms and nanomaterials, yet physiologically relevant in vitro models with accessible apical surfaces remain limited. Here, human apical-out ileoids derived from healthy ileal biopsies are established as a platform that recapitulates the architecture and complexity of the native ileal epithelium. Assessment of donor- and passage-dependent variability identifies a representative ileoid line and a robust culture window. Integrated proteomic, imaging, ultrastructural, and functional analyses demonstrate preservation of key epithelial features, including brush-border organization, barrier integrity, absorptive capacity, and multiple endocytic pathways. Intact ileoids internalize nanoparticles of distinct surface charge, including empty lipid nanoparticles compositionally matched to approved mRNA vaccine formulations, establishing that uptake can be quantified across an unperturbed apical surface. This uptake is restrained by a retained mucin-rich glycocalyx. Cleavage of surface-attached mucins selectively enhances uptake of negatively charged nanoparticles, leaving near-neutral and positively charged nanoparticles unchanged, and increasing entry of Salmonella bacteria. These findings reveal the glycocalyx as a charge-selective regulator of epithelial uptake. In conclusion, our study provides a foundation for nanoparticle-epithelium investigations using human apical-out ileoids, and a versatile, translationally relevant platform for nanomedicine delivery, host-microbe interactions, and epithelial transport.