ScRNA sequencing of the small intestine lamina propria of laboratory and rewilded mice
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE282735 | GEO | 2024/11/29
REPOSITORIES: GEO
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Project description:Innate lymphoid cells (ILCs) in the lamina propria of the small intestine (siLP) are essential for maintaining intestinal immune homeostasis; however, their isolation remains challenging. Here, we present a protocol for the rapid isolation of siLP ILCs. We describe steps for small intestine collection and trimming, epithelial cell dissociation, lamina propria digestion, and ILC analysis by flow cytometry. For complete details on the use and execution of this protocol, please refer to Zheng et al.1.
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Project description:Intestinal resident macrophages (M?s) regulate gastrointestinal homeostasis via production of an anti-inflammatory cytokine interleukin (IL)-10. Although a constant replenishment by circulating monocytes is required to maintain the pool of resident M?s in the colonic mucosa, the homeostatic regulation of M? in the small intestine (SI) remains unclear. Here, we demonstrate that direct stimulation by dietary amino acids regulates the homeostasis of intestinal M?s in the SI. Mice that received total parenteral nutrition (TPN), which deprives the animals of enteral nutrients, displayed a significant decrease of IL-10-producing M?s in the SI, whereas the IL-10-producing CD4(+) T cells remained intact. Likewise, enteral nutrient deprivation selectively affected the monocyte-derived F4/80(+) M? population, but not non-monocytic precursor-derived CD103(+) dendritic cells. Notably, in contrast to colonic M?s, the replenishment of SI M?s and their IL-10 production were not regulated by the gut microbiota. Rather, SI M?s were directly regulated by dietary amino acids. Collectively, our study highlights the diet-dependent, microbiota-independent regulation of IL-10-producing resident M?s in the SI.
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2022-04-15 | GSE171330 | GEO
Project description:Phagocytes such as dendritic cells and macrophages, which are distributed in the small intestinal mucosa, play a crucial role in maintaining mucosal homeostasis by sampling the luminal gut microbiota. However, there is limited information regarding microbial uptake in a steady state. We investigated the composition of murine gut microbiota that is engulfed by phagocytes of specific subsets in the small intestinal lamina propria (SILP) and Peyer's patches (PP). Analysis of bacterial 16S rRNA gene amplicon sequences revealed that: 1) all the phagocyte subsets in the SILP primarily engulfed Lactobacillus (the most abundant microbe in the small intestine), whereas CD11bhi and CD11bhiCD11chi cell subsets in PP mostly engulfed segmented filamentous bacteria (indigenous bacteria in rodents that are reported to adhere to intestinal epithelial cells); and 2) among the Lactobacillus species engulfed by the SILP cell subsets, L. murinus was engulfed more frequently than L. taiwanensis, although both these Lactobacillus species were abundant in the small intestine under physiological conditions. These results suggest that small intestinal microbiota is selectively engulfed by phagocytes that localize in the adjacent intestinal mucosa in a steady state. These observations may provide insight into the crucial role of phagocytes in immune surveillance of the small intestinal mucosa.
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Project description:Background & aimsEsophageal biopsies in children with eosinophilic esophagitis (EoE) are often inadequate for assessment of lamina propria and lamina propria fibrosis (LPF). For children with EoE, little is known about the factors associated with adequate lamina propria (aLP) sampling or the relationship among epithelial features in esophageal biopsies with and without LPF. We aimed to evaluate aLP in esophageal biopsies from children with and without EoE, identify factors associated with aLP and LPF, and examine the relationship among epithelial features in biopsies with and without LPF in children with EoE.MethodsIn a retrospective study, we analyzed clinical, endoscopic, and histologic data from 217 children (124 with EoE and 94 without EoE [controls]) using descriptive statistics, logistic regression, Spearman's correlation, and receiver operating characteristic curve analysis. Active and inactive EoE were defined per the 2011 consensus guidelines.ResultsaLP was observed in biopsies from higher proportion of children with EoE (69%) than controls (31%) (P = .0001). Active EoE was independently associated with aLP (adjusted odds ratio [aOR], 4.23; 95% CI, 1.00-18.13; P = .05). Patient sex (aOR for boys, 8.37; 95% CI, 1.23-56.74; P = .03) and peak eosinophil count (aOR, 1.02; 95% CI, 1.01-1.04; P = .01) were independently associated with LPF. Epithelial features were strongly interrelated in biopsies with LPF, and the presence of specific epithelial features was associated with LPF.ConclusionsaLP was observed in a higher proportion of esophageal biopsies from children with EoE than controls. EoE status, patient sex, and peak eosinophil count were associated with aLP sampling and LPF. Given the intricate relationship between epithelial features and LPF, computational models can be developed to identify children with esophageal biopsies without aLP who are at risk for LPF.
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Project description:To maintain immune homeostasis, the intestinal immune system has evolved redundant regulatory strategies. In this regard, the gut is home to a large number of regulatory T (T reg) cells, including the Foxp3(+) T reg cell. Therefore, we hypothesized that the gut environment preferentially supports extrathymic T reg cell development. We show that peripheral conversion of CD4(+) T cells to T reg cells occurs primarily in gut-associated lymphoid tissue (GALT) after oral exposure to antigen and in a lymphopenic environment. Dendritic cells (DCs) purified from the lamina propria (Lp; LpDCs) of the small intestine were found to promote a high level of T reg cell conversion relative to lymphoid organ-derived DCs. This enhanced conversion by LpDCs was dependent on TGF-beta and retinoic acid (RA), which is a vitamin A metabolite highly expressed in GALT. Together, these data demonstrate that the intestinal immune system has evolved a self-contained strategy to promote T reg cell neoconversion.
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Project description:Dendritic cells play a vital role in initiating robust immunity against pathogens as well as maintaining immunological tolerance to self antigens, food antigens and intestinal commensals. However, the intracellular signaling networks that program DCs to become tolerogenic are largely unknown. To address this, we analyzed gene expression profiles using microarray analysis of purified intestinal lamina propria DCs (CD11c+ CD11b+ DCs and CD11c+ CD11b- DCs) from mice. Keywords: Lamina propria, DCs, cell type comparison
2010-06-05 | GSE22127 | GEO
Project description:The intestinal immune system must elicit robust immunity against harmful pathogens but restrain immune responses directed against commensal microbes and dietary antigens. The mechanisms that maintain this dichotomy are poorly understood. Here we describe a population of CD11b+F4/80+CD11c– macrophages in the lamina propria (LP) that express several anti-inflammatory molecules including interleukin 10 (IL-10), but little or no pro-inflammatory cytokines, even upon stimulation with Toll-like receptor (TLR) ligands. These macrophages induced, in a manner dependent on IL-10, retinoic acid and exogenous transforming growth factor-β, differentiation of FoxP3+ regulatory T cells. In contrast, LP CD11b+ dendritic cells elicited IL-17 production. This IL-17 production was suppressed by LP macrophages, indicating that a dynamic interplay between these subsets may influence the balance between immune activation and tolerance. Splenic or small intestine lamina propria CD11b+11c- cells were isolated for RNA extraction and hybridization on Affymetrix microarrays. We sought to determine the unique genetic profile of small intestine lamina propria CD11b+11c- cells. Keywords: cell type comparison
2007-08-24 | GSE8868 | GEO
Project description:CX(3)CR1(+) and CD103(+) dendritic cells (DCs) in intestinal lamina propria play a key role in mucosal immunity. However, the origin and the developmental pathways that regulate their differentiation in the lamina propria remain unclear. We showed that monocytes gave rise exclusively to CD103(-)CX(3)CR1(+) lamina propria DCs under the control of macrophage-colony-stimulating factor receptor (M-CSFR) and Fms-like thyrosine kinase 3 (Flt3) ligands. In contrast, common DC progenitors (CDP) and pre-DCs, which give rise to lymphoid organ DCs but not to monocytes, differentiated exclusively into CD103(+)CX(3)CR1(-) lamina propria DCs under the control of Flt3 and granulocyte-macrophage-colony-stimulating factor receptor (GM-CSFR) ligands. CD103(+)CX(3)CR1(-) DCs but not CD103(-)CX(3)CR1(+) DCs in the lamina propria constitutively expressed CCR7 and were the first DCs to transport pathogenic Salmonella from the intestinal tract to the mesenteric lymph nodes. Altogether, these results underline the diverse origin of the lamina propria DC network and identify mucosal DCs that arise from pre-DCs as key sentinels of the gut immune system.
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Project description:Dendritic cells play a vital role in initiating robust immunity against pathogens as well as maintaining immunological tolerance to self antigens, food antigens and intestinal commensals. However, the intracellular signaling networks that program DCs to become tolerogenic are largely unknown. To address this, we analyzed gene expression profiles using microarray analysis of purified intestinal lamina propria DCs (CD11c+ CD11b+ DCs and CD11c+ CD11b- DCs) from mice. Keywords: Lamina propria, DCs, cell type comparison We sought to determine the expression profile of small intestine lamina propria CD11c+ cells. RNA was extracted from DCs sorted from mouse small intestine (CD11c+CD11b- and CD11c+CD11b+ cells) and hybridized on Affymetrix microarrays.
2010-06-16 | E-GEOD-22127 | biostudies-arrayexpress