Relevance of porcine intestinal organoids as a surrogate for animal experimentation: application to the investigation of host–virus interactions during porcine coronavirus infection

The small intestine, a part of the digestive system, absorbs nutrients and plays a role in immune protection against viruses that can disrupt its activity. Currently, to analyse these functions, studies rely on in vivo (animals) or in vitro (most often immortalized cell lines) experiments. However, these models have ethical and methodological concerns. Organoids, an ex vivo model, consisting of 3D self-organized cell complexes to recapitulate the cellular diversity, structure, and functionality of an evaluated organ, represent an alternative system. However, to infect organoids, the apical pole containing viral receptors, which are localized in the lumen of the 3D organoids, must be accessible. For this purpose, 2D organoids, corresponding to dissociated and plated 3D organoids, are typically used. This study aimed to characterize the robustness and fidelity of 3D and 2D organoids in terms of gene expression in jejunum tissue and the contribution of 2D organoids in comparison to those of swine testicular cells (ST cells) and piglet jejunums to decipher host-virus interactions with transmissible gastroenteritis virus (TGEV). Our study revealed that our culture and differentiation procedures enabled the production of 3D and 2D organoids that reproduced intestinal epithelial organization with high repeatability. Similar to infected piglets and ST cells, infected 2D organoids expressed genes involved in innate and antiviral immune responses, with a variety of genes activated as a function of viral load. Organoids, which maintain the cellular diversity of the intestinal epithelium, therefore offer the possibility to decipher the host-virus interactions involved in enteric infections.