Transcriptome profiling of organoids from the human and murine gastrointestinal tract

The epithelial layer of the gastrointestinal tract is the body’s first line of defense against gut pathogens. However, our current understanding of the innate immune response of the epithelial layer is limited. For this study, we used gastrointestinal organoids which have the advantage of being primary, non-transformed epithelium that retains organ-specific characteristics in culture, and also that they lack any confounding immune cells. We systematically profiled the transcriptomes of gastrointestinal epithelial cells using a newly generated biobank of human and murine GI organoids grown from tissue-resident stem cells, providing an atlas of gene expression along the GI tract of both species. RNA sequencing of all lines confirmed the preservation of tissue identity, and in addition revealed extensive organization of innate immune signaling components along the cephalocaudal axis, endowing a specific innate immune profile to each segment. We generated a biobank of 18 human, 18 adult murine organoid lines, comprised of 3 lines each for the individual gastrointestinal segments of corpus, pylorus, duodenum, jejunum, ileum and colon. Additionally, organoids were generated from E16 embryonic mice and 2 organoid lines generated from embryonic stomach and 3 lines generated from proximal intestine.