Adult porcine intestinal organoids as models for regional epithelial identity and individual regulatory variation

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Abstract Background Organoids offer controlled epithelial systems for functional follow-up of candidate genes and variants in farm animals, but their usefulness for genotype-to-phenotype research depends on whether they retain intestinal regional identity and animal-specific molecular signatures. We profiled 32 RNA-seq libraries from matched tissues and organoids derived from duodenum, jejunum, ileum and colon of four slaughter-age Large White pigs. Results Organoids were transcriptionally distinct from native tissues but remained within the intestinal transcriptional space and retained regional structure, particularly when epithelial cell signature genes were considered. Most expressed genes were shared between tissues and organoids (81.2% of all detected genes and 81.8% of epithelial cell signature genes). Innate immune genes were also largely detected in organoids (79.6% shared), but with a lower regional organisation. Projection of ileal organoids onto an in vivo developmental reference positioned them closer to foetal or newborn samples than to slaughter-age ileum tissue, consistent with a comparatively immature transcriptional state. Differential expression and enrichment analyses showed attenuation of gene-level segment differences in organoids but partial preservation of regional markers and Gene Ontology terms linked to intestinal development and regionalisation, absorption, metabolism, epithelial signalling, mucosal immune responses and transport. Animal-associated differences were retained for selected epithelial signatures, notably the glycosylation-related genes FUT2 and B4GALNT2 . FUT2 expression was strongly reduced in one animal and associated with linked intronic variants, whereas B4GALNT2 separated two pairs of animals and segregated with candidate variants affecting protein expression or transcript processing. Conclusions Adult porcine intestinal organoids retain a substantial epithelial component of regional identity and preserve selected animal-specific regulatory signatures, while showing reduced immune spatial patterning and immature transcriptional features. Standardised organoid biobanks from genotyped and phenotyped pigs may support functional follow-up of candidate genes, variants and pathways when intestinal epithelial mechanisms are implicated.

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