Methylation profiling in colorectal cancer
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE36380 | GEO | 2012/03/10
SECONDARY ACCESSION(S): PRJNA153263
REPOSITORIES: GEO
Similar Datasets
Project description:Methylation profiling in colorectal cancer : adjacent normal tissue vs colon tumor tissue indirect comparison experiment : CRD(common reference DNA) vs tumor-adjacent normal, CRD vs Colon tumor
2012-03-10 | E-GEOD-36380 | biostudies-arrayexpress
Project description:DNA methylation in colorectal cancer diagnosis. The Illumina GoldenGate Methylation Cancer Panel I was used to select a set of candidates markers informative of colorectal cancer diagnosis from 807 cancer-related genes. In the discovery phase, tumor tissue and paired adjacent normal mucosa from 92 colorectal patients were analyzed.
2013-05-27 | GSE43369 | GEO
Project description:Genetic and epigenetic alterations are a fundamental aspect of colorectal cancer formation. There is considerable heterogeneity between colorectal cancers regarding the mutations and methylated genes they carry, and this heterogeneity may arise early in the polyp-cancer sequence. However, our understanding of the epigenetic alterations and gene mutations in colon adenomas and their relation to colorectal cancer is incomplete. Thus, we have assessed the methylome in normal colon mucosa, tubular adenomas, and colorectal adenocarcinomas and have determined the relationship of these findings between adenomas and cancer in the colon. Genome-wide alterations in DNA methylation were found in the normal colon mucosa adjacent to colorectal cancer, tubular adenomas, and colorectal cancer. Three subgroups of CRCs and two subgroups of adenomas were identified on the basis of their DNA methylation patterns. The adenomas separated into a high-frequency methylation class (Adenoma-H) and a low-frequency methylation class. The adenoma-H polyps have a methylated DNA signature similar to non-CIMP CRCs, whereas those of the Adenoma-L class have a similar methylation pattern to normal colon mucosa. The CpGs that account for these signatures are located in intragenic/intergenic regions, which suggests that these two groups of adenomas arise from different stem cell populations.
2014-09-08 | GSE48684 | GEO
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
Project description:Genome-wide DNA methylation of colorectal cancer patients with lymph node metastases showed global loss of DNA methylation in CG-poor, non-CpG island (CGI) regions. Overall CGI methylation was increased in tumour samples. Differential methylation analysis of CGIs identified 60 putative biomarkers, with >20% increase in DNA methylation in both primary tumour and metastasis samples compared to normal adjacent tissue.
2020-11-02 | GSE151318 | GEO
Project description:Dysregulation of cellular metabolism is one of the hallmarks of cancer. Tumor cells would enhance glycolysis to fuel the phenotypes of rapid proliferation and invasion. This study aims to explore epigenetic reprogramming of glycolysis pathway in colorectal cancer (CRC). CRCs and the adjacent normal colon tissues were profiled by using a comprehensive methylation array (Illumina Methylation EPIC Beadchips) to comprehensively analyze the methylation alterations in the glycolysis pathway. Differentially methylated genes (DMGs) were identified by using β value difference (≧ 0.2 or ≦ -0.2) and Wilcoxon rank-sum test (p < 0.05), and the common DMG in open datasets (GSE42752, GSE25062 and TCGA). Pyrosequencing was executed to validate the DMGs. Hexokinase domain containing 1 (HKDC1), the major hypomethylated gene we found, was overexpressed in colon cancer cells. Cells were treated with an HKDC1 inhibitor to elucidate the role of HKDC1. We found hypomethylation of HKDC1 was the only shared hypomethylated DMG in glycolysis pathway after comparing our methylation profiles of CRC to 3 public datasets. The RT-qPCR study in our cohort supported HDKC1 expression is methylation-regulated. Overexpression of HKDC1 in colon cancer cells resulted in increased proliferation of colon cancer cells and decreased cytotoxicity by an HKDC1 inhibitor. RNA sequencing revealed significant up-regulation of glycolysis and cell cycle pathways and their targets in HKDC1 overexpressed cells. In summary, hypomethylation of HKDC1 is common in CRC and may regulate cellular metabolism to promote proliferation of colon cancer cells through upregulation of glycolysis and cell cycle pathways.
2026-09-25 | GSE309002 | GEO
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. Bisulfite converted DNA from fresh frozen 125 colorectal tumors and 29 adjacent normal tissues were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2
2011-06-03 | E-GEOD-25062 | biostudies-arrayexpress
Project description:Project was focused on methylation profiling of colorectal carcinoma progression from pre-cancerous adenoma, through primary tumor to metastatic sites. Together with comparison with methylation profiles of healthy colon and liver tissue.
2026-09-07 | E-MTAB-16230 | biostudies-arrayexpress
Project description:Methylation profiling in Bladder cancer : adjacent normal tissue vs bladder tumor tissue
2021-04-03 | GSE171369 | GEO
Project description:Methylation profiling in prostate cancer: adjacent normal tissue vs prostate tumor tissue
2025-09-03 | GSE306933 | GEO