The development of a recent stem cell based organoid model can be used to culture intestinal epithelium in vitro. Intestinal organoids have a crypt-villus architecture and consist of all cell types that are present in the native intestinal epithelium. The organoid system enables us to address one of the enigmas of the pathogenesis of IBD: How do the various subsets of epithelial cells regulate responsiveness upon chronic microbial exposure?Methods:
The epithelial responsiveness to microbial antigens was systematically studied by using human intestinal organoids and exposing them to bacterial lysates. We have profiled transcriptomes and active DNA regulatory elements, thereby elucidating the processes that are involved in the epithelial response to microbes and their kinetics. Furthermore, we determined the location specific responses (i.e., duodenum, ileum and colon) and we discriminated between the effect of apical and basolateral exposure. The responses of the different epithelial cell types were determined by the use of both single cell RNA-sequencing and culturing methods that alter cell type composition of the organoids.Results:
Expression profiling of the kinetics of the epithelial response shows that the exposure of organoids to bacterial lysate results in an acute inflammatory response including upregulation of the NF-kB pathway and downregulation of cell cycle processes. Furthermore, the upregulated genes are highly enriched for genes that are associated with IBD. The inflammatory response is downregulated upon chronic exposure, resulting in a state that is featured by the upregulation of a distinctive set of genes including HNF4α. Duodenum-, ileum- and colon-derived organoids show location specific responses upon basolateral versus apical exposure. Furthermore, we show that responsiveness decreases upon differentiation of the epithelium and that the cell types involved in the response to microbial antigens are Wnt-dependent.Conclusions:
We used a human intestinal organoid model to characterize the responsiveness of the intestinal epithelium. The expression patterns and DNA regulatory elements were profiled upon acute and chronic exposure to microbial antigens. Finally, we delineated the anatomy of the response by identifying cell types that are involved and we characterized differences in responsiveness between different parts of the intestine.