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Genome-wide DNA methylation analysis in early-stage colorectal cancer

ABSTRACT: Genome-wide DNA methylation analysis in early-stage colorectal cancer

PROVIDER: PRJNA489460 | ENA |

REPOSITORIES: ENA

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Genome-wide DNA methylation analysis in early-stage colorectal cancer

Project description:The current risk stratification system defined by clinicopathological features do not accurately identify the risk of disease recurrence in patients with stage I-II colorectal cancer (CRC). We aimed to investigate whether the CpG sites from newly established genome-wide methylation profiles could serve as biomarkers to improve prognosis prediction.

2023-04-19 | GSE119526 | GEO

Genome-Wide DNA Methylation Profiles of Low- and High-Grade Adenoma Reveals Potential Biomarkers for Early Diagnosis of Colorectal Carcinoma

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

Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation [Methylation]

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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

Transcriptome-wide characterization of m6A methylation in colorectal cancer

Project description:Transcriptome-wide characterization of m6A methylation in colorectal cancer

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A Genome-wide DNA Methylation Study in Colorectal Carcinoma

2012-05-22 | E-GEOD-29490 | biostudies-arrayexpress

Gene expression data from very early stage lesions (T1) of colorectal cancer

Project description:Gene expression data from very early stage lesions (T1) of colorectal cancer

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Genome-wide DNA methylation analysis of colorectal cancer and polyp

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

Epigenome-wide association study of differential DNA-methylation in background mucosa among adults with colorectal adenoma

Project description:Background: Colorectal adenoma is the primary precursor in colorectal cancer development, partially driven by epigenetic alteration occurring at a very early stage. While aberrant DNA-methylations have been observed in mucosa adjacent to primary tumors, this study aimed to investigate whether such alterations exist in distant background mucosa as global defect rather than local transition, and identify adenoma-related CpG sites which may serve as potential targets for early intervention. Methods: DNA methylation in normal rectal mucosal biopsies from 24 individuals with colorectal adenoma and 20 normal controls were profiled utilizing the Illumina Infinium MethylationEPIC v2.0 BeadChip (935K). Linear regression model was employed to investigate the relationship between adenoma incidence and DNA methylation at each CpG site, adjusted for demographic characteristics. GO and KEGG enrichment analysis were conducted using genes containing CpG sites significantly associated with adenoma. A sensitivity analysis was conducted with individuals who had one or more known risk factors for colorectal adenoma. Results: Twenty-seven CpG sites with aberrant DNA-methylation were significantly correlated with the incidence of adenoma (P<1×10-5, |Δβ|≧0.2). Through GO and KEGG enrichment analysis and lookups in EWAS atlas, a group of CpG sites and genes were identified as potential intervention targets. Conclusions: A group of adenoma-related CpG sites and genes with aberrant DNA-methylation was identified in normal-appearing rectal mucosa. Further extensive validation of the adenoma-related loci as targets for molecular intervention could pave the way for colorectal cancer prevention.

2025-12-31 | GSE284238 | GEO

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