Relating the transcriptome and microbiome by paired terminal ileal Crohn disease

Cai, Chenwen; Zhu, Sibo; Tong, Jinlu; Wang, Tianrong; Feng, Qi; Qiao, Yu; Shen, Jun

doi:10.1016/j.isci.2021.102516

Cited by 4 publications

(2 citation statements)

References 48 publications

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“…Coherently, the study of RNAseq data from 10 CD patients (GEO database, GSE171244 [ 30 ]) shows a positive correlation between the expression levels of CD44 and Wnt target genes, PCs, and stem cell markers (Fig. 5e ).…”

Section: Resultsmentioning

confidence: 99%

Wnt signaling is boosted during intestinal regeneration by a CD44-positive feedback loop

et al. 2022

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Enhancement of Wnt signaling is fundamental for stem cell function during intestinal regeneration. Molecular modules control Wnt activity by regulating signal transduction. CD44 is such a positive regulator and a Wnt target gene. While highly expressed in intestinal crypts and used as a stem cell marker, its role during intestinal homeostasis and regeneration remains unknown. Here we propose a CD44 positive-feedback loop that boosts Wnt signal transduction, thus impacting intestinal regeneration. Excision of Cd44 in Cd44fl/fl;VillinCreERT2 mice reduced Wnt target gene expression in intestinal crypts and affected stem cell functionality in organoids. Although the integrity of the intestinal epithelium was conserved in mice lacking CD44, they were hypersensitive to dextran sulfate sodium, and showed more severe inflammation and delayed regeneration. We localized the molecular function of CD44 at the Wnt signalosome, and identified novel DVL/CD44 and AXIN/CD44 complexes. CD44 thus promotes optimal Wnt signaling during intestinal regeneration.

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Section: Resultsmentioning

confidence: 99%

Wnt signaling is boosted during intestinal regeneration by a CD44-positive feedback loop

et al. 2022

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“…The selection of datasets was based on the following criteria: 1. they contain RNA-sequencing raw data; 2. they include patients with CD and/or UC and/or healthy individuals (HIs); and 3. the data are derived from intestinal mucosa biopsy samples. In total, 5 datasets that matched our criteria were retrieved, 2 consisting of both patients with CD and UC, as well as healthy individuals (PRJNA797175 [ 75 ], PRJNA565216 [ 76 ]), 1 containing samples from CD patients and healthy individuals (PRJNA276116 [ 77 ]), 1 with samples from only patients with CD (PRJNA718848 [ 78 ]), and 1 with samples from only UC patients (PRJNA420681). The total amount of biopsy samples pooled from these datasets was 2785.…”

Section: Methodsmentioning

confidence: 99%

Exploring Microbial Metabolite Receptors in Inflammatory Bowel Disease: An In Silico Analysis of Their Potential Role in Inflammation and Fibrosis

Spathakis,

Dovrolis,

Filidou

et al. 2024

Pharmaceuticals

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Metabolites produced by dysbiotic intestinal microbiota can influence disease pathophysiology by participating in ligand–receptor interactions. Our aim was to investigate the differential expression of metabolite receptor (MR) genes between inflammatory bowel disease (IBD), healthy individuals (HIs), and disease controls in order to identify possible interactions with inflammatory and fibrotic pathways in the intestine. RNA-sequencing datasets containing 643 Crohn’s disease (CD) patients, 467 ulcerative colitis (UC) patients and 295 HIs, and 4 Campylobacter jejuni-infected individuals were retrieved from the Sequence Read Archive, and differential expression was performed using the RaNA-seq online platform. The identified differentially expressed MR genes were used for correlation analysis with up- and downregulated genes in IBD, as well as functional enrichment analysis using a R based pipeline. Overall, 15 MR genes exhibited dysregulated expression in IBD. In inflamed CD, the hydroxycarboxylic acid receptors 2 and 3 (HCAR2, HCAR3) were upregulated and were associated with the recruitment of innate immune cells, while, in the non-inflamed CD ileum, the cannabinoid receptor 1 (CNR1) and the sphingosine-1-phospate receptor 4 (S1PR4) were downregulated and were involved in the regulation of B-cell activation. In inflamed UC, the upregulated receptors HCAR2 and HCAR3 were more closely associated with the process of TH-17 cell differentiation, while the pregnane X receptor (NR1I2) and the transient receptor potential vanilloid 1 (TRPV1) were downregulated and were involved in epithelial barrier maintenance. Our results elucidate the landscape of metabolite receptor expression in IBD, highlighting associations with disease-related functions that could guide the development of new targeted therapies.

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Impact of exposure to arsenic on the bacterial microbiota associated with river biofilms in the Pampas region

deDiego

Steinhardt²,

Ferro³

et al. 2022

Aquatic Toxicology

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Relating the transcriptome and microbiome by paired terminal ileal Crohn disease

Cited by 4 publications

References 48 publications

Wnt signaling is boosted during intestinal regeneration by a CD44-positive feedback loop

Wnt signaling is boosted during intestinal regeneration by a CD44-positive feedback loop

Exploring Microbial Metabolite Receptors in Inflammatory Bowel Disease: An In Silico Analysis of Their Potential Role in Inflammation and Fibrosis

Impact of exposure to arsenic on the bacterial microbiota associated with river biofilms in the Pampas region

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