Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transkingdom network analysis reveals role of IgA and Acinetobacter in immunometabolic alterations leading to CVID enteropathy

ABSTRACT: this work combines newly developed methods of host gene expression analysis in duodenal tissues with unique approaches to the identification of specific pathobiont bacteria in the duodenal microbiome to elucidate mechanisms of GI dysfunction in Common Variable Immunodeficiency (CVID). As such it provides new insights into how the mucosal immune response controls gut function in general.

PROVIDER: PRJEB18593 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2984740.fastq.gz	Fastqsanger.gz
	ERR2985250.fastq.gz	Fastqsanger.gz
	ERR2984741.fastq.gz	Fastqsanger.gz
	ERR2985251.fastq.gz	Fastqsanger.gz
	ERR2984742.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 303

Similar Datasets

Gene expression in duodenal biopsy samples from CVID enteropathy patients and healthy controls

Project description:A subgroup of CVID patients presents with gastrointestinal complications (enteropathy), which manifests in the duodenum as celiac like-diese ase. CVID enteropathy patients can present with severe histopathology in form of villous atrophy (CVID VA) or without VA (CVID noVA). RNAseq data from CVID VA and CVID noVA derived duodenal tissues were compared to each other and to healthy controls.

2023-02-10 | GSE189820 | GEO

Duodenal inflammation in Common variable immunodeficiency has altered transcriptional response to viruses

Project description:To elucidate the role of duodenal microenvironment in Common variable immunodeficiency pathogenesis (CVID), we sought to explore the transcriptome regulation in duodenal biopsies.

2022-11-03 | GSE207243 | GEO

Gastrointestinal symptoms and pathology in patients with Common variable immunodeficiency

Project description:Based on the findings of increased IEL in duodenal biopsies in CVID, an overlap with celiac disease has been suggested. In the present study, increased IEL, in particular in the pars descendens of the duodenum, was one of the most frequent histopathological finding. We therefore examined the gene expression profile in pars descendens of duodenum in CVID patients with increased IEL (n=13, IEL mean 34 [range 22-56] IEL/100 EC), CVID with normal levels of IEL (n=7), celiac disease (n=10, Marsh grade 3a or above) and healthy controls (n=17) by gene expression microarray GI histopathological findings in 53 CVID patients that underwent upper and lower endoscopic examination were addressed. For the microarray analysis 20 CVID (7 CVID_normal and 13 CVID with incresed IEL), 10 patients with celiac diseases and 17 healthy controls were included.

2015-09-02 | E-GEOD-72625 | biostudies-arrayexpress

Gene expression in duodenal biopsy samples from CVID enteropathy patients and healthy controls

Project description:Gene expression in duodenal biopsy samples from CVID enteropathy patients and healthy controls

| PRJNA784599 | ENA

Gene expression in CD21low and CD21pos B cells from CVID patients

Project description:A subgroup of CVID patients presents with a loss of switched memory B cells and an accumulation of CD21low B cells.RNAseq data from CVID derived CD21low and CD21pos B cells were compared to naive CD21pos B cells in Healthy controls. The data reveal a distinct gene expression profile in CD21low B cells compared to HD.

2021-08-05 | GSE148163 | GEO

HIF2 regulates intestinal Wnt5a expression

Project description:Radiation therapy for abdominal tumors is challenging because the small intestine is exquisitely radiosensitive. Unfortunately, there are no FDA-approved therapies to prevent or mitigate GI radiotoxicity. The EGLN protein family are oxygen sensors that regulate cell survival and metabolism through the degradation of hypoxia-inducible factors (HIFs). Our group has previously shown that stabilization of HIF2 through genetic deletion or pharmacologic inhibition of the EGLNs mitigates and protects against GI radiotoxicity in mice by improving intestinal crypt stem cell survival. Here we aimed to elucidate the molecular mechanisms by which HIF2 confers GI radioprotection. We developed duodenal organoids from mice, transiently overexpressed non-degradable HIF2, and performed bulk RNA sequencing. Interestingly, HIF2 upregulated known radiation modulators and genes involved in GI homeostasis, including Wnt5a. Non-canonical Wnt5a signaling has been shown by other groups to improve intestinal crypt regeneration in response to injury. Here we show that HIF2 drives Wnt5a expression in multiple duodenal organoid models. Luciferase reporter assays performed in human cells showed that HIF2 directly activates the WNT5A promoter via a hypoxia response element. We then evaluated crypt regeneration using spheroid formation assays. Duodenal organoids that were pre-treated with recombinant Wnt5a had a higher cryptogenic capacity after irradiation, compared to vehicle-treated organoids. Conversely, we found that Wnt5a knockout decreased the cryptogenic potential of intestinal stem cells following irradiation. Treatment with recombinant Wnt5a prior to irradiation rescued the cryptogenic capacity of Wnt5a knockout organoids, indicating that Wnt5a is necessary and sufficient for duodenal radioprotection. Taken together, our results.txt suggest that HIF2 radioprotects the GI tract by inducing Wnt5a expression.

2021-12-15 | GSE186927 | GEO

Gastrointestinal symptoms and pathology in patients with Common variable immunodeficiency

2015-09-02 | GSE72625 | GEO

Identification of IVIg regulated genes in human peripheral blood monocytes from Common Variable Immunodeficiency patients (CVID) [CD14+]

Project description:Identification of IVIg regulated genes in human peripheral blood monocytes by gene expression analysis before and after IVIg infusion in CVID patients

2022-05-03 | GSE133907 | GEO

Identification of IVIg regulated genes in human peripheral blood mononuclear cells from Common Variable Immunodeficiency patients (CVID) [PMBC]

Project description:Identification of IVIg regulated genes in human PBMC by gene expression analysis before and after IVIg infusion in CVID patients.

2022-05-03 | GSE133835 | GEO

Transcription profiling of human T lymphocytes from patients with hypogammaglobulinemia of unknown cause (CVID) vs. hypogammaglobulinemia of known cause (XLA) and vs. healthy controls

Project description:Comparison of gene expression in T lymphocytes from patients with hypogammaglobulinemia of unknown cause (CVID), patients with hypogammaglobulinemia of known cause (XLA) and healthy controls

2004-07-18 | E-MEXP-76 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data