Organoid as alternative to study food-related host responses

Public awareness for food products has risen in recent years. Clinical observations correlated dietary habits with adverse health effects such as low-grade inflammation and documented how food intake influences drug absorption efficiency in patients. The rapid increase of available food products requires vigorous evaluation of their safety. Animal models are still the golden standard for this process. However, they have different dietary requirements than humans and often do not recapitulate human- related diseases. The use of an alternative, physiologically relevant model is of utmost importance and will guide the design of clinical studies in patients. Ingested food first interacts with gastrointestinal (GI) epithelial cells within our body. We hypothesize that GI organoids are an ideal model system to investigate metabolite or food additive host interactions in vitro. Organoids are easily scalable, amenable to genetic perturbation and compatible with screening approaches. Here, we investigate their suitability to address food safety concerns and to study metabolite-drug-epithelial cell interaction dynamics. In objective 1, we generate a healthy human organoid reference biobank which includes gastric, small intestinal and colonic cultures established from the same healthy patient donors. The mutational landscape of every culture will be analysed to identify potential genetic predispositions or disease-driving mutations. To study the effect of luminal-delivered compounds, organoid-derived monolayers will be established and optimized to obtain cultures enriched for progenitors, enterocytes, foveolar cells or enteroendocrine cells or to model an inflammatory environment. Well characterized organoids from 3 donors will be used as replicates to screen in objective 2 how food additives influence epithelial cell dynamics such as barrier function, cytokine and hormone secretion behaviour and the acquisition of DNA damages or in objective 3 how human metabolites affect the cellular uptake of autofluorescent drugs or their transport across the epithelial barrier. For each objective, the mode-of- action in epithelial cells for the two strongest hits will be investigated by performing RNA-seq experiments and engineering single gene knockouts for selected signalling pathways. This project investigates how food additives and metabolites affect human GI organoids. The proposed experiments illustrate how they could be used for massive parallel screening of hundred different conditions and how mechanistic insights can be obtained in follow-up experiments. We describe thus a platform that is compatible with future food safety tests and may help in the formulation of diet recommendations for specific patient groups.