Small intestine lamina propia iNKT cells in comparison to iNKT cells residing in lymphoid tissues

Intestinal homeostasis is maintained through the combined functions of epithelial and immune cells that collaborate to preserve the integrity of the intestinal barrier. However, the mechanisms by which immune cell populations regulate intestinal epithelial cell (IEC) homeostasis remain unclear. Here, we use a multi-omics approach to study the immune-epithelial crosstalk and identify CD1d-restricted Natural Killer T (NKT) cells as regulators of IEC biology. We find that NKT cells are abundant in the proximal small intestine and show hallmarks of activation at steady state. Subsequently, NKT cells regulate the survival and the transcriptional and cellular composition landscapes of IECs in intestinal organoids, through mechanisms dependent on IFN-? and IL-4 secretion by NKT cells but independent of the expression of CD1d on IECs. In vivo, lack of NKT cells results in an increase in IEC turnover, while NKT cell activation leads to IFN-?-dependent epithelial apoptosis. Our findings propose NKT cells as potent producers of cytokines that contribute to the regulation of IEC homeostasis. Overall design: 4 samples were sequenced across 2 individual experiments. Small intestinal lamina propia iNKT cells were sorted in a BD FACS Aria Fusion into RLT buffer before proceeding to mRNA isolation. Samples were frozen at –80°C before RNA extraction.