Project description:Intestinal epithelial cells (IECs) serve as critical interfaces between the host immune system and enteric pathogens, yet their role in orchestrating mucosal immune responses remains incompletely understood. Major histocompatibility complex class II (MHCII) expression on IECs has been proposed to contribute to antigen presentation and T cell priming during intestinal infection, but the cell type-specific transcriptional programs influenced by epithelial MHCII remain unclear. Here, we performed single-cell RNA sequencing (10x Genomics) to comprehensively profile intestinal epithelial and immune cell populations during Citrobacter rodentium infection. We analyzed colonic tissues from H2-Ab1^fl/fl (wild-type) and H2-Ab1^Villin (IEC-specific conditional knockout) mice at naïve baseline and days 9, 14, and 42 post-infection, capturing acute infection, peak response, and memory phases. This dataset enables dissection of MHCII-dependent and -independent transcriptional responses across diverse epithelial lineages and immune cell subsets, providing insights into how IEC-intrinsic MHCII expression shapes mucosal immunity and tissue-resident memory formation during bacterial infection.
Project description:Small RNAs are emerging as important molecules for cross-species communication. Thanks to available and affordable sequencing technologies it is now possible to sequence small RNAs (sRNA-Seq) present in samples of interacting organisms. A first step when analyzing sRNA-Seq of two interacting species is to determine which sequences are being produced by which organism. Due to their small size (18-30), small RNAs could easily map to both host and parasite genomes. Here we produced data for Mus musculus intestinal epithelial cells treated with Extracellular Vesicles (EV) produced by the parasitic nematode Heligmosomoides bakeri.
Project description:Inflammatory injury to the intestine triggers a reprogramming of the intestinal epithelium to a fetal-like state, facilitating rapid restoration of the epithelial barrier. Although the intestinal microbiota is a key modulator of inflammation, its role in driving epithelial fetal-like reversion and promoting restitution remains unclear. Using irradiation (IR) injury as a model for small intestinal epithelium restitution, we found that the intestinal microbiota accelerated epithelial restitution by amplifying a repair-associated inflammatory response that promoted the emergence of fetal-like intestinal epithelial cells (IECs), marked by Ly6a and Clu. NOD2, the strongest genetic link to the development of Crohn’s disease, was expressed in fetal-like IECs following injury. Notably, stimulation of NOD2 by its peptidoglycan ligand in an ileal organoid model potentiated an inflammatory gene signature characterized by interferon (IFN) signaling, coinciding with enterocyte recovery. NOD2 deficiency exacerbated epithelial apoptosis following IR injury, while epithelial-specific NOD2 signaling promoted the emergence of fetal-like IECs and enhanced epithelial proliferation. Together, these results identify a critical role for microbiota and microbial sensing by NOD2 in controlling the fate of fetal-like IECs following injury, thereby contributing to the protective effect of this microbial sensor during intestinal inflammation.
