Comprehensive transcriptional atlas of intestinal immune cells reveals that neuropeptide α-CGRP orchestrates ILC2 responses

We combine single-cell RNA sequencing (scRNA-seq) with physiological and genetic perturbations to dissect the cellular circuit of type 2 intestinal inflammation. To uncover key responding cellular components, we profiled individual immune cells in the lamina propria (LP) and Peyer’s patches (PPs), regions of the small intestine enriched for immune cells, in homeostasis and in an intestinal type 2 inflammatory model. We obtained 36,797 and 21,270 high-quality cells passing initial filtering from PP and LP regions, respectively. To understand the small intestine in homeostasis, untreated cells from wild-type mice were collected; while to investigate the impacts of type 2 inflammation on intestinal immune cells, cells from mice after induction of an inflammatory reaction to ovalbumin were used. Cells were profiled using both 3'-droplet-based single-cell RNA sequencing, obtained 30,723 cells from wild-type mice and 27,344 cells from treated mice. To study the functions of the alpha-calcitonin gene-related peptide (α-CGRP) in ILC2s, flow sort-purified intestinal KLRG1+ ILC2s were stimulated in vitro with IL-25 and/or α-CGRP for 3 hours.