A human autoimmune organoid model reveals IL-7 function in celiac disease

In vitro models of autoimmunity are constrained by an inability to culture affected epithelium alongside the complex tissue-resident immune microenvironment. Celiac disease (CeD) is an autoimmune disease where dietary gluten-derived peptides bind the MHC- II molecules HLA-DQ2 or -DQ8 to initiate immune-mediated duodenal mucosal injury. Here, we generated air-liquid interface (ALI) duodenal organoids from endoscopic biopsies that preserve epithelium alongside native mesenchyme and tissue-resident immune cells as a unit without requiring reconstitution. The ALI organoid immune diversity spanned T, B, plasma, NK and myeloid cells with extensive T and B cell receptor repertoires. HLA-DQ2.5-restricted gluten peptides selectively instigated epithelial destruction in HLA-DQ2.5-expressing CeD patient organoids, which was antagonized by MHC-II or NKG2C/D blockade. Gluten epitopes stimulated a CeD organoid network response in lymphoid and myeloid subsets alongside anti-TG2 autoantibody production. Functional studies in CeD organoids revealed IL-7 as a novel gluten-inducible pathogenic modulator which regulated CD8+ T cell-NKG2C/D expression and was necessary and sufficient for epithelial destruction. Further, endogenous IL-7 was markedly induced in patient biopsies from active CeD versus remission disease, predominantly in lamina propria mesenchyme. By preserving epithelium alongside diverse immune populations, this human in vitro CeD model recapitulates gluten-dependent pathology, facilitates mechanistic investigation, and establishes proof-of-principle for organoid modeling of autoimmunity. CeD organoid cultures were dissociated (as described above) 2 days after gliadin or CLIP treatment. Fresh tissues were dissociated on the same day of receiving the sample. Single live CD45+ or EPCAM+ cells from dissociated organoids or fresh tissues were sorted by FACS into WENR media and subjected to droplet based scRNA-seq with the 10X Genomics Chromium single cell 5? platform, with or without single-cell TCR/Ig V(D)J library, per the manufacturer?s protocol using Chromium Next GEM Single Cell 5' Kit v2 (PN-1000263), Library Construction Kit (PN-1000190), Chromium Single Cell Human TCR Amplification Kit (PN-1000252) and Chromium Single Cell Human BCR Amplification Kit (PN-1000253). Cell capture, library construction, and sequencing were performed as previously described