Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Intestinal N-glycomics in pediatric ulcerative colitis

ABSTRACT: This project used glycomics approach to study the N-glycan present at the intestinal mucosal-luminal interface of pediatric UC patients.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Xu Zhang

LAB HEAD: Daniel Figeys

PROVIDER: PXD026327 | Pride | 2022-03-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions

Project description:Background and Aims: Individuals with ulcerative colitis (UC) are at increased risk for colorectal cancer, although underlying mechanisms are incompletely understood. We sought to identify a potential gene expression signature in non-dysplastic distal mucosa that as a “genetic field effect” could be a marker for remote neoplastic lesions. Results: 468 genes were significantly up-regulated and 541 genes were significantly down-regulated >2-fold in UC patients with neoplasia compared to UC patients without neoplasia. Nine genes (ACSL1, BIRC3, CLC, CREM, ELTD1, FGG, S100A9, THBD, and TPD52L1) were progressively and significantly up-regulated from controls to quiescent non-dysplastic UC to UC with neoplasia. Immunostaining of proteins revealed increases in tissue expression of S100A9 and REG1 in UC-associated cancer and in non-dysplastic tissue from UC patients harboring remote neoplasia, compared to UC patients without dysplasia and normal controls. Conclusions: Gene expression changes occur as a field effect in UC patients without active inflammation who harbor a remote dysplastic lesion. Further characterization of these genes and proteins might elucidate pathways of carcinogenesis in IBD and lead to the development of more accurate, less invasive markers of dysplasia in those at increased risk. Microarray assay were conducted on 20 RNA samples isolated from colon mucosa of 20 patients. Of these patients, 5 were normal controls, 4 had quiescent UC, and 11 had UC with neoplasia. Patients were included if they had a previous clinical diagnosis of UC confirmed by an expert GI pathologist, a disease duration > 7 years, and an extent of disease >20 cm proximal to the anal verge.

2012-04-19 | E-GEOD-37283 | biostudies-arrayexpress

Gene expression profiling of mucosal biopsies from pediatric patients with moderately to severely active ulcerative colitis

Project description:To acquire a better understanding of the molecular pathogenesis of pediatric UC with different disease extent, we performed mRNA microarray studies to compare gene expression of patients with extensive UC vs. that of patients with limited UC. No significant difference was observed in mRNA expression between extensive and limited UC in pediatric patients.

2018-12-01 | GSE87465 | GEO

Transcription profiling of human ulcerative colitis colonic mucosa to define an ulcerative colitis preinflammatory state

Project description:The samples are a part of a study aiming at diagnosing ulcerative colitis from genome-wide gene expression analysis of the colonic mucosa. Colonic mucosal samples were collected as endoscopic pinch biopsies from ulcerative colitis patients and from control subjects. Samples with and without macroscopic signs of inflammation were collected from the patients. Experiment Overall Design: The series contain eight UC samples with macroscopic signs of inflammation, 13 UC smaples without macroscopic signs of inflammation, five control subjects.

2008-06-20 | E-GEOD-9452 | biostudies-arrayexpress

Transcriptional signatures that define Ulcerative Colitis in remission

Project description:Background: This study addresses whether existing specific transcriptional profiles can improve and support the current status of the definition of ulcerative colitis (UC) remission apart from the existing endoscopic, histologic, and laboratory scoring systems. For that purpose, a well-stratified UC patient population in remission was compared to active UC and control patients and was investigated by applying the next-generation technology RNA-Seq. Methods: Mucosal biopsies from patients in remission (n = 14), patients with active UC (n = 14), and healthy control patients (n = 16) underwent whole-transcriptome RNA-Seq. Principal component analysis, cell deconvolution methods, gene profile enrichment, and pathway enrichment methods were applied to define a specific transcriptional signature of UC in remission. Results: Analyses revealed specific transcriptional signatures for UC in remission with increased expression of genes involved in O-glycosylation (MUC17, MUC3A, MUC5AC, MUC12, SPON1, B3GNT3), ephrin-mediated repulsion of cells (EFNB2E, EFNA3, EPHA10, EPHA1), GAP junction trafficking (TUBA1C, TUBA4A, TUBB4B, GJB3, CLTB), and decreased expression of several toll-like receptors (TLR1, TLR3, TLR5, TLR6). Conclusions: This study reveals specific transcriptional signatures for remission. Partial restoration and improvement of homeostasis in the epithelial mucus layer and revival of immunological functions were observed. A clear role for bacterial gut flora composition can be implied. The results can be useful for the development of treatment strategies for UC in remission and may be useful targets for further investigations aiming to predict the outcome of UC in the future.

2020-01-18 | GSE128682 | GEO

Expression data from Ulcerative Colitis subjects

Project description:We used microarrays to detail the global gene expression of inflamed vs non-inflamed colon tissue from UC subjects

2018-04-01 | GSE107499 | GEO

Control (IBS) & Ulcerative colitis (UC) subjects

Project description:IBS: Patients who have undergone a diagnostic program for gastrointestinal symptoms and where the diagnosis irritable bowel syndrome was reached. UC: Patients with well-diagnosed ulcerative colitis Keywords: other

2005-04-01 | GSE2461 | GEO

Genome-wide analysis of Crohn's disease and ulcerative colitis biopsy samples.

Project description:Gene expression patterns of Crohn's disease (CD) and ulcerative colitis (UC) colonic specimens were analyzed using whole-genome microarrays. Healthy control samples were included in order to detect gene expression changes associated with CD or UC. CD and UC samples were also compared in order to identify the molecular mechanisms that distinguish both fenotypes of inflammatory bowel disease. Total RNA obtained from intestinal biopsies were analyzed using whole-genome microarrays.

2013-09-23 | E-GEOD-36807 | biostudies-arrayexpress

Transcription profiling of human ulcerative colitis samples to develop a molecular marker

Project description:Samples were taken from either surgically resected specimens or during surveillance colonoscopic examination. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for predicting development of cancer and/or dysplasia in ulcerative colitis, and to characterize potential diagnostic markers in UC-associated neoplasm. Experiment Overall Design: 43 UC-NonCa, 10 UC-Ca, 60 sporadic-Ca and 6 UC-associated Ca were analyzed

2008-06-12 | E-GEOD-3629 | biostudies-arrayexpress

Ulcerative colitis biopsies analyzed by PCT-SWATH mass spectrometry

Project description:Ulcerative colitis (UC) is an idiopathic chronic inflammatory disorder of the colonic mucosa with rising incidence. Despite numerous known genetic risk loci environmental factors seem to be crucial in the pathogenesis of this complex disease with suboptimal treatment options. Approaches utilizing methods of systemic biology have been started to use in the analysis of mucosal biopsies in order to get a more comprehensive view of the changes related to the disorder. Our aim was to test the capability of a new mass spectrometry (MS) -based assay (PCT-SWATH mass spectrometry) to characterize host proteomes both in inflamed and non-inflamed colon tissues of an UC patient cohort.

2017-06-12 | PXD004907 | Pride

Genome-wide analysis of Crohn's disease and ulcerative colitis biopsy samples.

2013-09-23 | GSE36807 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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