Germ-free and microbiota-associated mice yield intestinal organoids with robust transcriptome/proteome phenotypes
Intestinal organoids derive from stem cells isolated from the mucosa. It remained unclear how microbiota exposure of those stem cells influences organoid phenotypes. In a recent study from the Hardt lab, Annika Hausmann et al. address whether littermate control organoids are needed and how well organoids represent their tissue of origin, in comparison to cell lines.
Intestinal epithelial organoids have become a widely used research tool. However, it remains unclear how environmental cues, divergent microbiota composition and other sources of variation confound organoid properties, and how these properties relate to the original tissue. Here, we probed the effect of donor microbiota differences, previously identified as a confounding factor in murine in vivo studies, on organoids. We analyzed the proteomes and transcriptomes of primary organoid cultures established from two colonized and one germ-free mouse colony of C57BL/6J genetic background, and compared them to their tissue of origin and commonly used cell lines. While an imprint of microbiota-exposure was observed on the proteome of epithelial samples, the long-term global impact of donor microbiota on organoid expression patterns was negligible. Integration of transcriptome and proteome datasets revealed an organoid-typic expression signature comprising 14 transcripts and 10 proteins that distinguished organoids across all donors from murine epithelial cell lines and closely mimicked expression patterns in the gut epithelium. This included the inflammasome components ASC, Naip1-6, Nlrc4, and Caspase-1, which were highly expressed in all organoids compared to the reference cell line m-ICc12. Taken together, these results reveal that the donor microbiota has little effect on the organoid phenotype and suggest that organoids represent a more suitable culture model than immortalized cell lines, in particular for studies of intestinal epithelial inflammasomes.
Link to the publication in external page Cellular Microbiology.