Similar Datasets
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:Colorectal laterally spreading tumors (LSTs) are rare comparing to adenomas but are becoming more prevalent. Unlike many neoplasms in colons, LST grows to extremely large size, usually greater than 10mm in diameter while rarely invades deeply. Also, there is a low tendency for LSTs to become cancerous. The epigenetic landscape of LST has not been defined. In this study, we used a genome-wide methylation profiling technology, i.e. the Illumina Human Methylation 450K array, to query the main epigenetic difference between LST and para-cancerous samples. Our results suggest that LST displays significant decrease in DNA methylation, especially in some intergenic regions (IGR). By integration of public data for adenomas and colorectal cancers, we defined the commonality and specific epigenetic signatures for these three types of neoplasms in colon, in particular LST and adenomas which represent precancerous conditions. These three diseases shared little specific DNA methylation abnormalities. However, our pathway-level analysis revealed that certain pathways were common targets of epimutation. More interestingly, different diseases seem to employ distinct epigenetic insult to disturb these pathways. Between LST and adenoma, we found eight pathways were commonly targeted but the epi-mutation patterns were opposite between the two diseases. Comparison between precancerous conditions and invasive states revealed the key pathways governing the progression to malignancy, including CAMs and PI3K-Akt pathways.
2019-01-01 | GSE106556 | GEO
Project description:Colorectal polyp is known a precursor of colorectal cancer (CRC) that holds an increased risk for progression to CRC. Circulating cell-free DNA(cfDNA) methylation has shown favorable performance in the detection and monitoring the malignant progression in a variety of cancers. Here, we conducted a study to discovery cfDNA methylation markers for the diagnosis of CRC. We first performed a genome-wide analysis using the Infinium HumanMethylationEPIC BeadChip array to identify differentially methylated CpGs (DMCs) between 8 CRC and 8 polyp tissues. Then, we validated DMCs in a larger tissue cohort and four methylation markers (cg04486886, cg06712559, cg13539460 and cg27541454) were selected as the methylation markers in tissue by LASSO and random forest models. A diagnosis prediction model was bulit based on the four markers and the methylaion diagnosis score (md-score) can effectively discriminate patients with CRC from polyp tissues. Finally, a single cfDNA methylation marker, cg27541454, was confirmed hypermethylated in CRC in the plasma validation cohort. Together, our findings suggested that the md-score derived from tissue could robustly detect CRC from polpy patients, and cg27541454 may be a promising candidate non-invasive biomarker for CRC early diagnosis.
2024-01-01 | GSE220160 | GEO
Project description:Colorectal Cancer DNA Methylation
| PRJNA699596 | ENA
Project description:Identification of molecular subtypes of colorectal signet ring cell carcinoma based on differences in DNA methylation.
2017-07-21 | GSE79740 | GEO
Project description:Colorectal cancer stem cells (CR-CSCs) are implicated in tumor development, metastasis, and therapy resistance, however little is known about their epigenetic features. Here we describe the DNA methylation profiles of eight CR-CSC lines and their distinctive patterns, which are maintained following in vivo passages in immune-compromised mice.
2020-01-15 | GSE123367 | GEO
Project description:Abnormal DNA methylation is a hallmark of human cancers and may be a promising biomarker for early diagnosis of human cancers1. However, the majority of DNA methylation biomarkers that have been identified are based on the hypothesis that early differential methylation regions (DMRs) are maintained throughout carcinogenesis and could be detected at all stages of cancer. In this study, we identified potential early biomarkers of colorectal cancer (CRC) development by genome-wide DNA methylation assay (Illumina infinium450, 450K) to normal (N=20) and pre-colorectal cancer samples including 18 low-grade adenoma (LGA) and 22 high-grade adenoma (HGA).
2020-04-23 | GSE139404 | GEO
Project description:Colorectal tumorigenesis proceedes through well defined clinical stages assoicated with charateristic mutations. Besides genetic alterations, epi-driver genes that are aberrantly expressed in cancers in a fashion that confers a seletive growth advantage can also contribute to tumor evolution. To gain a global view of methylation patterns in normal and maliganant colorectal epithelia, we performed genome-wide DNA methylation analysis on DNAs from 48 fresh frozen CRC samples at different stages of CRC progression. We used IlluminaHumanMethylation450 Beadchip to get a broad view of genome-wide DNA methylationdata during CRC progression and identified significantly differentially methylated genes during CRC progression
2016-05-13 | GSE77954 | 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