Fig. 3. IIOs recapitulate clinically manifested intestinal inflammation associated with TCB.
a, Representative images examining induction of green caspase 3/7 signal within IIO co-cultures 24 h following supplementation with EpCAM TCB. b, Quantification of caspase 3/7 signal from a. Two-way analysis of variance (ANOVA) with Sidak’s multiple-comparisons test. Triplicate IIO cultures representative of experiments performed with three independent biological donors. MFI, mean fluorescence intensity. c, Quantification of caspase 3/7 signal in IIO co-cultures treated for 72 h across a range of EpCAM TCB. Two independent IIO cultures were run across a six-dose titration of EpCAM TCB; mean (black line) and s.d. (grey shading). d, Single-cell transcriptomic profiles of gut-derived immune cells from IIO model were integrated and grouped into 14 distinct cell states as represented by colours in the UMAP embedding. Organoid schematic adapted with permission from ref. 60. e, Dotplot summarizing the expression patterns of representative genes across the clusters identified in d. f, Integrated UMAP embedding (left) and proportional distribution (right) of gut-derived immune cells from IIO model, coloured by treatment and profiling time. g, Barplot showing significantly enriched Gene Ontology biological processes for activated cell states (top) and heatmap showing average expression profiles of corresponding associated genes (bottom). h, Dotplot summarizing the expression pattern of representative genes involved in proliferation, signalling and cytotoxicity in activated T cell populations, as captured by scRNA-seq snapshots at different time points and under various treatment conditions. i, Flow cytometry plots visualizing expression of TNF, IFNγ, Gzmb and Ki67 across different time points within CD4+ and CD8+ TRM cells isolated from IIO cultures. Representative of five biologically independent experiments. Scale bars, 1 mm.