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Methylated CpG island amplification (MCA) microarray analysis of human gastric mucosa and cancer

ABSTRACT: Aberrant DNA methylation is implicated in the epigenetic field defect seen in gastric cancer (GC). Our aim in this study was to identify predictive biomarkers by screening for DNA methylation in noncancerous background gastric mucosa from GC patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE39175 | GEO | 2012/09/01

SECONDARY ACCESSION(S): PRJNA170141

REPOSITORIES: GEO

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Methylated CpG island amplification (MCA) microarray analysis of human gastric mucosa and cancer

Project description:Aberrant DNA methylation is implicated in the epigenetic field defect seen in gastric cancer (GC). Our aim in this study was to identify predictive biomarkers by screening for DNA methylation in noncancerous background gastric mucosa from GC patients. A total of 46 endoscopically obtained human gastric mucosa, 10 gastric cancer and 5 cell lines were analyzed using MCA microarray. Aberrant DNA methylation was compared with clinicopathological features. Healthy individuals were divided into two groups based on the types of chronic gastritis; A: antrum-predominant gastritis P or C: pangastritis or corpus-predominant gastritis

2012-09-01 | E-GEOD-39175 | biostudies-arrayexpress

Methylated CpG island amplification (MCA) microarray analysis of human colorectal tumors

Project description:The concept of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) is widely accepted, though the timing of its occurrence and its interaction with other genetic defects are not fully understood. Our aim in this study was to unravel the molecular development of CIMP cancers by dissecting their genetic and epigenetic signatures in precancerous and malignant colorectal lesions. A total of 88 samples (16 normal colon tissues taken from adjacent tumor tissue, 70 colorectal tumor tissues and 2 cell lines) was analyzed using MCA microarray. Aberrant DNA methylation was compared with clinicopathological features and copy number.

2012-08-31 | E-GEOD-35508 | biostudies-arrayexpress

Methylated CpG island amplification (MCA) microarray analysis of human colorectal tumors

2012-08-31 | GSE35508 | GEO

Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

Project description:CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumour suppressors. Currently, for most cancers including gastric cancer [GC], mechanisms underlying CIMP remain poorly understood. We sought to discover molecular contributors to CIMP in GC, by performing global DNA methylation, gene expression, and proteomics profiling across 14 gastric cell lines, followed by similar integrative analysis in 50 GC cell lines and 467 primary GCs. We identify the cystathionine beta-synthase enzyme (CBS) as a highly recurrent target of epigenetic silencing in CIMP GC. Likewise, we show that CBS epimutations are significantly associated with CIMP in various other cancers, occurring even in premalignant gastroesophageal conditions and longitudinally linked to clinical persistence. Of note, CRISPR deletion of CBS in normal gastric epithelial cells induces widespread DNA methylation changes that overlap with primary GC CIMP patterns. Reflecting its metabolic role as a gatekeeper interlinking the methionine and homocysteine cycles, CBS loss in vitro also causes reductions in the anti-inflammatory gasotransmitter hydrogen sulphide (H2S), with concomitant increase in NF-κB activity. In a murine genetic model of CBS-deficiency, preliminary data indicate upregulated immune-mediated transcriptional signatures in the stomach. Our results implicate CBS as a bi-faceted modifier of aberrant DNA methylation and inflammation in GC and highlights H2S donors as a potential new therapy for CBS-silenced lesions.

2021-04-19 | GSE149411 | GEO

Deoxyribonucleic acid methylation profiling of single human blastocysts by methylated CpG-island amplification coupled with CpG-island microarray.

Project description: Not available

| S-EPMC4449363 | biostudies-literature

ONECUT2 is a putative oncogene associated with CpG hypomethylation at promoter-proximal DNA in gastric cancer and triggers ACSL5, a member of the ACS family

Project description:To access methylation change during gastric carcinogenesis in this study, we performed RRBS analysis with LCM-derived normal gastric mucosa and gastric tumor tissue [GSE55159]. Among a set of genes hypomethylated and upregulated in GC, ONECUT2 was identified as a hypomethylated target in GC. Upregulated ONECUT2 expression significantly increased the proliferation, colony formation, migration and invasion in GC cells. To identify target genes regulated by ONECUT2, we performed ChIP-seq and RNA-seq.

2020-02-16 | GSE113045 | GEO

Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array

Project description:Methylated DNA enrichment is a key step in a microarray based genome-wide methylation profiling study, and even for future high-throughput sequencing based methylome analysis. In order to evaluate the sensitivity and accuracy of methylated DNA enrichment, we investigated and optimized a number of important parameters to improve the performance of several enrichment assays, including differential methylation hybridization (DMH), microarray-based methylation assessment of single samples (MMASS), and methylated DNA immunoprecipitation (MeDIP). With advantages and disadvantages unique to each approach, we found that assays based on methylation-sensitive enzyme digestion and those based on immunoprecipitation detected different methylated DNA fragments, indicating that they are complementary in their relative ability to detect methylation differences. Our study provides the first comprehensive evaluation for widely used methodologies for methylated DNA enrichment, and could be helpful for developing a cost effective approach for DNA methylation profiling.

2010-01-22 | GSE19974 | GEO

Effect of DNMT3A polymorphisms on CpG island hypermethylation in gastric mucosa.

Project description: Not available

| S-EPMC7562764 | biostudies-literature

CpG island methylation

Project description:We compare the methylation status of CpG island clones by MeDIP in SW48 colon cancer cells relative to normal colon mucosa and WI38 primary fibroblasts. Keywords: ordered

2005-07-03 | GSE2653 | GEO

CpG island methylation

Project description:We compare the methylation status of CpG island clones by MeDIP in SW48 colon cancer cells relative to normal colon mucosa and WI38 primary fibroblasts.

2010-06-09 | E-GEOD-2653 | biostudies-arrayexpress

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