2-D organoids demonstrate specificity in the interactions of parasitic nematodes and their secreted products at the basal or apical intestinal epithelium

The intestinal epithelium is a selectively permeable barrier that absorbs water and nutrients, senses the luminal environment, and orchestrates submucosal immune responses. Some gastrointestinal nematodes occupy both submucosal and luminal niches and can cause profound changes in epithelial cells. Yet, there is little understanding of the specificity of parasite-host interactions with epithelial cells and the differential responses at the apical or basal sides. Organoids enable uncoupling of parasite-driven responses from immune-driven effects on the epithelium, and two-dimensional (2-D) organoids allow for controlled access to both sides. Here we used 2-D enteroids to model in vivo localisation of Heligmosomoides bakeri ( H. bakeri ) fourth-larval (L4) and adult stages and identify localisation-specific effects on gene expression. Using bulk RNA sequencing, we found an enhanced upregulation of IFN-stimulated genes (ISGs) during basal co-culture and an overall stronger response to L4 parasites than adults. Further, H. bakeri live worms induced much stronger effects on gene expression than their isolated excretory-secretory (ES), but cells that internalised H. bakeri extracellular vesicles (EVs) displayed up-regulation of ISGs, repair genes, and YAP/TAZ signalling. Our results demonstrate that nematodes and their products, including EVs, modify the host epithelium in a localisation-dependent and cell-specific manner.