Using Transcriptomic data to access the similarity between intestinal organoids and the tissue they dervied from

Intestinal organoids of livestock animals are increasingly used as an in vitro research tool to investigate gut health and functioning and to unravel complex phenotypes. The transcriptomic resemblance of organoids with the original in vivo intestinal tissue and variability within cultured organoids has previously been studied for jejunum, but for colon and ileum such comparisons are still missing. Furthermore, for ileal organoids the sampling location might have an effect considering the presence or absence of Peyer's Patches (PP). The aims of this study were 1) investigate similarities between tissue and organoid transcriptomic profiles at four different locations (ileum PP, ileum nonPP, mid colon and distal colon) and 2) investigate the variability within sampling site of these four locations. From six pigs, we harvested tissue samples from each location. These tissue samples were used to develop 3D organoids and we compared the transcriptomic RNA profiles of the original tissue and derived organoid samples. The results showed that tissue and organoid samples formed separate clusters based on their general gene expression profiles. This could be explained since tissue contain more diverse cell types compared to organoids. Average Pearson correlations of general gene expression profiles within ileum PP, ileum nonPP, mid colon and distal colon organoids were respectively, 0.97 ± 0.03, 0.98 ± 0.02, 0.94 ± 0.06 and 0.97 ± 0.02 suggesting low variability within location. Future work will focus on between and within variability of the four locations. Our results suggest that derived organoids resemble their original tissue quite well and at least for colonic organoids the exact sampling location has limited influence, and thus organoids could be a promising practical application to investigate colon function.