DNA methylation landscape and signature of CD4+ lymphocytes of lamina propria in Crohn's patients by reduced representation and bisulfite sequencing [RNA-seq]
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ORGANISM(S): Homo sapiens
PROVIDER: GSE184307 | GEO | 2023/09/01
REPOSITORIES: GEO
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Project description:A genome-wide DNA methylation study was conducted using base resolution bisulfite sequencing for purified intestinal CD4+ cells (resected or biopsied mucosa of a terminal ileum) from 21 patients with Crohn’s disease and 12 age/sex matched controls. The sequencing data was analyzed for differentially methylated CpGs (DMCs) and differentially methylated regions (DMRs). Integration was performed with RNA-sequencing data for the same set of samples to verify the functional impact of DNA methylation changes.
2023-09-01 | GSE184312 | GEO
Project description:BackgroundAbnormal handling of E. coli by lamina propria (LP) macrophages may contribute to Crohn's disease (CD) pathogenesis. We aimed to determine LP macrophage phenotypes in CD, ulcerative colitis (UC) and healthy controls (HC), and in CD, to compare macrophage phenotypes according to E. coli carriage.MethodsMucosal biopsies were taken from 35 patients with CD, 9 with UC and 18 HCs. Laser capture microdissection was used to isolate E. coli-laden and unladen LP macrophages from ileal or colonic biopsies. From these macrophages, mRNA was extracted and cytokine and activation marker expression measured using RT-qPCR.ResultsE. coli-laden LP macrophages were identified commonly in mucosal biopsies from CD patients (25/35, 71 %), rarely in UC (1/9, 11 %) and not at all in healthy controls (0/18). LP macrophage cytokine mRNA expression was greater in CD and UC than healthy controls. In CD, E. coli-laden macrophages expressed high IL-10 & CD163 and lower TNFα, IL-23 & iNOS irrespective of macroscopic inflammation. In inflamed tissue, E. coli-unladen macrophages expressed high TNFα, IL-23 & iNOS and lower IL-10 & CD163. In uninflamed tissue, unladen macrophages had low cytokine mRNA expression, closer to that of healthy controls.ConclusionIn CD, intra-macrophage E. coli are commonly found and LP macrophages express characteristic cytokine mRNA profiles according to E. coli carriage. Persistence of E. coli within LP macrophages may provide a stimulus for chronic inflammation.
| S-EPMC4490755 | biostudies-literature
Project description:To investigate the global DNA methylation changes in mouse hematopoietic stem cell aging, we performed whole-genome bisulfite sequencing (WGBS). We generated 1,494 million (4mo HSCs), and 1,493 million (24mo HSCs) raw reads; about 82.6% and 84.3%, respectively, were successfully aligned to either strand of the reference genome (mm9). Of all the cytosines present in the reference genome sequence, about 93% of Cs and 99% of CGs were covered in both datasets, with an average coverage of 46-fold (4mo) and 50-fold (24mo). In contrast to the age-associated hypomethylation observed in studies of somatic cells, mentioned above, HSCs showed an increase of methylation with age. The average methylation level over all 16 million covered CpGs increased from 83.5% in young (4mo) HSC to 84.6% in old (24mo) HSC. We observed a total of 448,166 differentially methylated CpGs (DMCs), defined as those having a 20% or more difference in methylation ratio, of which 38.5% (172,609) were hypomethylated (hypo-DMCs) and 61.5% (275,557) were hypermethylated (hyper-DMCs) with aging. For different genomic features, a slightly greater DNA methylation ratio increase was observed for the gene body, LINEs and SINEs, while CGIs and promoters showed balanced increases and decreases. Localization analysis of DMCs indicates that DNA encoding for ribosome RNA (rDNA) is primarily a hotspot for hypo-DMCs, while promoters without CpG islands, CpG island shores and LINE repetitive elements exhibit both hypo- and hyper-DMCs. Mouse hematopoietic stem cell DNA methylation profiles of 4 month and 24 month old WT mice were generated generated by deep sequencing, in duplicate, using Illumina Hiseq 2000.
2014-04-30 | E-GEOD-47815 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-09-01 | GSE184314 | GEO
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.
| S-EPMC8033509 | biostudies-literature
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.
| S-EPMC2778256 | biostudies-literature
Project description:BackgroundThe aetiology of Crohn's disease [CD] involves immune dysregulation in a genetically susceptible individual. Genome-wide association studies [GWAS] have identified 200 loci associated with CD, ulcerative colitis, or both, most of which fall within non-coding DNA regions. Long non-coding RNAs [lncRNAs] regulate gene expression by diverse mechanisms and have been associated with disease activity in inflammatory bowel disease. However, disease-associated lncRNAs have not been characterised in pathogenic immune cell populations.MethodsTerminal ileal samples were obtained from 22 CD patients and 13 controls. RNA from lamina propria CD4+ T cells was sequenced and long intergenic non-coding RNAs [lincRNAs] were detected. Overall expression patterns, differential expression [DE], and pathway and gene enrichment analyses were performed. Knockdown of novel lincRNAs XLOC_000261 and XLOC_000014 was performed. Expression of Th1 or Th17-associated transcription factors, T-bet and RORγt, respectively, was assessed by flow cytometry.ResultsA total of 6402 lincRNAs were expressed, 960 of which were novel. Unsupervised clustering and principal component analysis showed that the lincRNA expression discriminated patients from controls. A total of 1792 lincRNAs were DE, and 295 [79 novel; 216 known] mapped to 267 of 5727 DE protein-coding genes. The novel lincRNAs were enriched in inflammatory and Notch signalling pathways [p <0.05]. Furthermore, DE lincRNAs in CD patients were more frequently found in DNA regions with known inflammatory bowel disease [IBD]-associated loci. The novel lincRNA XLOC_000261 negatively regulated RORγt expression in Th17 cells.ConclusionsWe describe a novel set of DE lincRNAs in CD-associated CD4+ cells and demonstrate that novel lincRNA XLOC_000261 appears to negatively regulate RORγt protein expression in Th17 cells.
| S-EPMC6930003 | biostudies-literature
Project description:Background & aimsIntestinal lymphoepithelial interactions occur in the epithelium and the subepithelial space. We asked whether normal, Crohn's disease (CD), or ulcerative colitis (UC) lamina propria lymphocytes (LPL) could promote intestinal epithelial cell (IEC) growth and differentiation.MethodsT84 cells were cocultured with isolated LPL. IECs were then lysed and subjected to measurement of intestinal alkaline phosphatase (IAP) activity; Western blot analysis for MAPK and Akt activation; and real-time polymerase chain reaction to assess caudal-related homeoprotein 2 (CDX2) messenger RNA (mRNA) levels. Tissue sections were immunostained for evidence of mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K) activation, CDX2, and IAP; and CDX2 mRNA expression was assessed in human colonic biopsy specimens.ResultsIAP activity was increased in T84 cells cocultured for 8 days with normal LPL (P < .05) and even greater with CD LPL (P < .001). Crypt IECs in active CD mucosa expressed IAP ex vivo. Phospho-MAPK (extracellular signal-regulated kinase 1/2, p38, and c-Jun-N-terminal kinase) and phospho-Akt were seen as early as 30 minutes after coculture. MAPK activation was greatest in T84 cells cocultured with CD LPL. There was a specific increase in Phospho-p38 MAPK and Phospho-Akt staining in the nuclei of crypt IECs in active vs inactive CD, normal mucosa, and UC mucosa. CDX2 mRNA expression was increased in CD LPL cocultured T84 cells, which did not correlate with CDX2 protein localization ex vivo.ConclusionsThere is cross talk between LPL and IECs, which leads to IEC differentiation. The differentiation is accelerated in CD mucosa.
| S-EPMC2975902 | biostudies-literature
Project description:The physiological process of defecation is directly controlled by colorectal motility. The transient receptor potential ankyrin 1 (TRPA1) channel is expressed in small intestine enterochromaffin cells and is involved in gastrointestinal motility via serotonin release. In the colorectum, however, enterochromaffin cell localization is largely distinct from that in the small intestine. Here, we investigated the role of lower gastrointestinal tract TRPA1 in modulating colorectal motility. We found that in colonic tissue, TRPA1 is predominantly expressed in mesenchymal cells of the lamina propria, which are clearly distinct from those in the small intestine. These cells coexpressed COX1 and microsomal prostaglandin E synthase-1. Intracolonic administration of TRPA1 agonists induced colonic contraction, which was suppressed by a prostaglandin E2 (PGE2) receptor 1 antagonist. TRPA1 activation induced calcium influx and PGE2 release from cultured human fibroblastic cells. In dextran sulfate sodium-treated animals, both TRPA1 and its endogenous agonist were dramatically increased in the colonic lamina propria, accompanied by abnormal colorectal contractions. Abnormal colorectal contractions were significantly prevented by pharmacological and genetic inhibition of TRPA1. In conclusion, in the lower gastrointestinal tract, mesenchymal TRPA1 activation results in PGE2 release and consequently promotes colorectal contraction, representing what we believe is a novel physiological and inflammatory bowel disease-associated mechanism of gastrointestinal motility.
| S-EPMC6538323 | biostudies-literature
Project description:This RNA seq experiment was designed to identify a gene signature of a CCR5-expressing subset of human intestinal Th17-cells. T helper-cells from peripheral blood of healthy donors and from the lamina propria of Crohn’s Disease patients were FACS-purified according to the expression of the chemokine receptors CCR6, CCR5 and CXCR3. Four CCR6+Th- subsets were isolated according to CXCR3 and CCR5 expression: two CXCR3- Th17 subsets (CCR5-: “cTh17” or CCR5+: “pTh17”) and two subsets of CXCR3+ Th1/17-cells (CCR5+ or CCR5-)
2023-07-27 | E-MTAB-13178 | biostudies-arrayexpress