Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenome analysis of normal colon mucosa samples

ABSTRACT: To investigate whether lifestyle factors modulate the stability of gene promoter methylation in the normal aging colonic mucosa, we performed genome-scale DNA methylation profiling of 178 normal colon biopsies using the Illumina Infinium DNA methylation assay, which assesses the DNA methylation status of 27,578 CpG sites located at the promoter regions of 14,495 protein-coding genes. We identified Aspirin use and hormonal replacement therapy (HRT) suppress, whereas a high body mass index (BMI) and smoking promote age-related hyermethylation. Many of these loci modulated by lifestyle in the healthy colon mucosa coincide with loci hypermethylated in colorectal cancers and down-regulated in adenomas. The data show that lifestyle modulates the stability of DNA methylation in the aging colonic epithelium and thereby impacts the rate of evolution of cancer methylomes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE48988 | GEO | 2014/07/01

SECONDARY ACCESSION(S): PRJNA212703

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Epigenome analysis of normal colon mucosa samples

Project description:To investigate whether lifestyle factors modulate the stability of gene promoter methylation in the normal aging colonic mucosa, we performed genome-scale DNA methylation profiling of 178 normal colon biopsies using the Illumina Infinium DNA methylation assay, which assesses the DNA methylation status of 27,578 CpG sites located at the promoter regions of 14,495 protein-coding genes. We identified Aspirin use and hormonal replacement therapy (HRT) suppress, whereas a high body mass index (BMI) and smoking promote age-related hyermethylation. Many of these loci modulated by lifestyle in the healthy colon mucosa coincide with loci hypermethylated in colorectal cancers and down-regulated in adenomas. The data show that lifestyle modulates the stability of DNA methylation in the aging colonic epithelium and thereby impacts the rate of evolution of cancer methylomes. Bisulphite converted DNA from the 178 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2014-07-01 | E-GEOD-48988 | biostudies-arrayexpress

Racial Disparities in Epigenetic Aging of the Right versus the Left Colon

Project description:Here, we present the first study showing race and side-specific differences in the trajectories of epigenetic aging in normal colonic mucosa. The cohort conisted of matched biopsies of left/right colon from healthy individuals (n=129). The majority of individuals were African American (n=89). Methylation arrays (Illumina EPIC) were performed on DNA extracted from fresh frozen biopsies taken at the time of colonoscopy. Our results provide novel insight of epigenetic aging underlying racial disparities in CRC. Side-specific colonic epigenetic aging may be a promising marker to guide interventions to reduce CRC burden.

2020-10-16 | GSE151732 | GEO

Genome-wide analysis of gene expression in partial Dnmt3a deleted colon mucosa cells of APC(Min/+) mice

Project description:Analysis of gene expression in partial Dnmt3a deleted colon mucosa cells of APC(Min/+) mice. In the present study the influence of Dnmt3a deletion on colonic tumorigenesis, gene expression and DNA methylation was analyzed. Results provide important information about the role of Dnmt3a in colonic tumorigenesis.

2015-06-01 | GSE48115 | GEO

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

Project description:To characterize DNA methylation-based subgroups in colorectal cancer, we performed genome-scale DNA methylation profiling of 125 colorectal tumor samples and 29 histologically normal-adjacent colonic tissue samples using the Illumina Infinium DNA methylation assay, which assesses the DNA methylation status of 27,578 CpG sites located at the promoter regions of 14,495 protein-coding genes. We identified four DNA methylation-based subgroups of CRC using model-based cluster analyses. Each subtype shows characteristic genetic and clinical features, indicating that they represent biologically distinct subgroups.

2011-06-03 | GSE25062 | GEO

The Microbiome Modulates DNA Methylation in Mouse Colonic Mucosa

Project description:DNA methylation is an epigenetic mark that is altered in cancer and aging tissues. The effects of extrinsic factors on DNA methylation remain incompletely understood. Microbial dysbiosis is a hallmark of colorectal cancer, and infections have been linked to aberrant DNA methylation in cancers of the GI tract. To determine the microbiota’s impact on DNA methylation, we studied the DNA methylation of colorectal mucosa in germ-free (GF, no microbiome) and specific pathogen free (SPF, controlled microbiome) mice, as well as in interleukin 10 KO mice (Il10-/-) which are prone to inflammation and tumorigenesis in the presence of a microbiome. We compared DNA methylation changes to those seen in aging, and after exposure to the colon carcinogen azoxymethane (AOM). DNA methylation changes associated with aging were accelerated in the Il10-/- /SPF mice. By contrast, AOM induced profound hypomethylation that was distinct from the effects of aging or of the microbiome. CpG sites modified by the microbiome were over-represented among DNA methylation changes in colorectal cancer. Thus, the microbiome affects the DNA methylome of colorectal mucosa in patterns reminiscent of what is observed in colorectal cancer.

2023-05-09 | GSE150333 | GEO

ColoCare Project: Epigenome-wide analysis of DNA methylation in colorectal cancer and adjacent mucosa tissues

Project description:Within the ColoCare Project we obtained genome-wide DNA methylation profiles from 149 mucosa and 112 colorectal cancer tissues using Illumina HumanMethylation450k BeadChips. DNA methylation profiles were analysed by patient characteristics, lifestyle and exposures.

2017-09-13 | GSE101764 | GEO

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

2011-06-03 | E-GEOD-25062 | biostudies-arrayexpress

DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [tumor, paired normal]

Project description:Promoter hypermethylation divides colon cancers into subtypes with and without a CpG island methylator phenotype (CIMP). Here, we performed genome-wide DNA methylation profiling of colonic normal and tumor tissues to dissect development of CpG hypermethylation in colon carcinogenesis. This identified age-environment related versus genetically driven CpG hypermethylation, the latter being associated with CIMP cancers. We found a strong association between BRAFV600E mutation and downregulation of the DNA demethylases TET1 and TET2. Expression of BRAFV600E in CIMP cancer cells suppressed TET1 transcription, which was sufficient to establish hypermethylation at CIMP genes promoters, including that of TET2. This phenotype was reverted by the BRAFV600E inhibitor vemurafenib. Thus, BRAFV600E, via impairment of cytosine de-methylation, is a genetic driver of CIMP in colon tumorigenesis. Genome-wide DNA methylation profiling of adjacent non-tumor colon tissue and colon adenocarcinoma samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 8 colon cancer tissues and their associated healthy mucosa (CAM).

2019-12-18 | GSE98531 | GEO

A Genome-wide DNA Methylation Study in Colorectal Carcinoma

Project description:Genome wide DNA methylation profiling of tumor and surrounding healthy colonic mucosa from patients with colorectal carcinoma. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across 27,578 CpG loci covering 14,475 genes.

2012-05-23 | GSE29490 | GEO

Genome-wide mRNA expression profiling for Wild Type and Itch-/- colonic mucosa Transcriptomes by RNA sequencing

Project description:To test the hypothesis that defects in the termination of inflammatory signaling led to colon inflammation, we isolated RNA from the colonic mucosa of Itch-/- mice and from the colonic mucosa of wild-type mice treated with DSS and performed genome-wide mRNA expression profiling by RNA sequencing.

2016-06-20 | GSE81066 | GEO

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