IEL ORGANOIDE Transcriptome

Intraepithelial lymphocytes (IELs) are the first immune cells to contact and fight intestinal pathogens such as Cryptosporidium, a widespread parasite which infects the gut epithelium. IFN-g producing CD4+ T IELs provide an efficient and a long-term protection against cryptosporidiosis while intraepithelial type 1 innate lymphoid cells limits pathogen spreading during the early stages of infection and in immunodeficient individuals. Yet, the role of T-cell like innate IELs, the most frequent subset of innate lymphocytes in the gut, remains unknown. To better define functions of innate IELs in cryptosporidiosis, we then developed a co-culture model with innate IELs isolated from Rag2-/- mice and 3D intestinal organoids infected with C parvum using microinjection. Thanks to this original model, we demonstrated that innate IELs control parasite proliferation. We further showed that although innate IELs secrete IFN-g in response to C parvum, the cytokine was not sufficient to inhibit parasite proliferation at early stages of the infection. The rapid protective effect of innate IELs was in fact mediated by a cytotoxic, granzyme-dependent mechanism. Moreover, transcriptomic analysis of the cryptosporidium-infected organoids revealed that epithelial cells down regulated serpinb9b, a granzyme inhibitor, which may increase their sensitivity to cytolytic attack by innate IELs.