Location-specific cell identity rather than exposure to GI microbiota defines many innate immune signalling cascades in the gut epithelium

Abstract

ObjectiveThe epithelial layer of the GI tract is equipped with innate immune receptors to sense invading pathogens. Dysregulation in innate immune signalling pathways is associated with severe inflammatory diseases, but the responsiveness of GI epithelial cells to bacterial stimulation remains unclear.DesignWe generated 42 lines of human and murine organoids from gastric and intestinal segments of both adult and fetal tissues. Genome-wide RNA-seq of the organoids provides an expression atlas of the GI epithelium. The innate immune response in epithelial cells was assessed using several functional assays in organoids and two-dimensional monolayers of cells from organoids.ResultsResults demonstrate extensive spatial organisation of innate immune signalling components along the cephalocaudal axis. A large part of this organisation is determined before birth and independent of exposure to commensal gut microbiota. Spatially restricted expression of Toll-like receptor 4 (Tlr4) in stomach and colon, but not in small intestine, is matched by nuclear factor kappa B (NF-κB) responses to lipopolysaccharide (LPS) exposure. Gastric epithelial organoids can sense LPS from the basal as well as from the apical side.ConclusionWe conclude that the epithelial innate immune barrier follows a specific pattern per GI segment. The majority of the expression patterns and the function of TLR4 is encoded in the tissue-resident stem cells and determined primarily during development.

Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut

“…4b, 4G). This compartmentalization of response along the GI tract is consistent with previous reports describing that different sections of the GI tract respond differently to microbial challenges [44]. Most importantly, our results reveal that production of ISGs is mostly restricted to bystander cells, while production of IFN is detected mostly in infected cells (Fig.…”

Interleukin-37 Regulates Innate Immune Signaling in Human and Mouse Colonic Organoids

“…The low or lack of innate response of human colonoids to IL-1β stimulation is not caused by the ineffectiveness of IL-1β, as IL-1β, even at a concentration of 5 times less, was able to induce higher levels of IL-8 and CCL20 secretion by Caco2 cells (Supp 1F). LPS also failed to induce the secretion of IL-8 and CCL20 by human colonoids, similar to a recent finding 3 (Fig 1B).…”

“…Since IL-37 typically acts under inflammatory conditions, expression of various innate receptors was evaluated in human colonoids to determine their capacity to respond to pro-inflammatory stimuli. Recently published studies have demonstrated site specific innate receptor expression as well as human specific innate responses by IEC to host or microbial products 2,3,28 . By real-time qPCR analysis, both pediatric and adult colonoids were confirmed to transcribe mRNA for several innate immune receptors including TLR4, TLR5 IL-1R and IL-18R1 (Supp 1B).…”

“…For experiments, colonoids were passaged using TrypLE techniques as already described but with modifications 3,28,36 . First, Matrigel domes were disrupted by adding ice-cold PBS containing 5 mM EDTA and incubating on ice for 15 min.…”

“…In this location, IEC play a central role in coordinating mucosal immunity, including promoting host defense by being responsive to luminal threats such as bacterial pathogens 1 . IEC accomplish this by expressing various pattern recognition receptors such as toll-like-receptors (TLR) [2][3][4] . These TLR enable IEC to sense those microbial pathogens that are able to escape the gut lumen and reach them, triggering IEC intrinsic pro-inflammatory and anti-microbial response, as well as signaling the presence of the invading microbes to underlying immune cells [4][5][6] .…”