Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [Neuron SmartSeq2]

Enteric neurons are essential regulators of intestinal physiology, yet their responses to varying microbial and immune environments along the intestinal tract and or during challenges remain poorly understood. Here, we regionally profile enteric neurons across gnotobiotic, allergic and parasite-infected mice. We demonstrate that timing and complexity of microbial perturbations and type 2 inflammation result in motor neuron state shifts and alter multiple functionally distinct sensory neurons, including IL-13- and leukotriene-responsive Nmu-hi cells and Grp-hi neurons, which expand in germ-free colonic tissue and interact with Grpr+ interstitial cells of Cajal. Leveraging AAV-based Perturb-seq to define genetic controllers of inhibitory motor neuron state transition, we identified Edf1 and Mitf as controllers of this program and of gastrointestinal transit time, directly linking enteric neuron states to physiology. Overall design: Enteric neurons were isolated from submucosal and myenteric plexuses of duodenal-jejunal segments, ileum and colon from either germ free (GF), Bacteroides thetaiotaomicron (BT) colonized, altered Schaedler flora (ASF) rederived or specific-pathogen free (SPF) mice. In addition, we also examined the ENS response to a spectrum of type 2 inflammatory responses induced by food allergy or by infection with an enteric parasite. For food allergy, mice were sensitized with ovalbumin (OVA) in alum administered intraperitoneally, and subsequently challenged by intragastric OVA. To examine responses to a parasite, we studied animals at 14 days post infection with the exclusively enteric parasite Heligmosomoides polygyrus (H. polygyrus), a helminth. We utilized the neuron-specific Uchl1 (also known as PGP9.5) reporter mouse Uchl1-H2B-mCherry/GFPgpi.