DNA Methylation profiles of colorectal cancer samples
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ABSTRACT:
PROVIDER: EGAD00010001888 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:We report the RNA-seq data of 40 advanced colorectal adenoma patients form Dongguk University Ilsan International Hospital. The polyps with a diameter of 1cm or greater were regarded as advenced colorectal adenoma and obtained through colonoscopy. The data consist of 22 tublar adenoma, 6 tublovillous adenoma, 5 sessile serrated adenoma/polyp, 1 traditional serrated adenoma, intramucosal adenocarcinoma, neuroendocrine tumor, hyperplastic polyp, inflammatory polyp, high grade dysplasia, and atypical glands with adjacent hyperplastic mucosa.
2023-08-07 | GSE154548 | GEO
Project description:Background: Duodenal adenoma/adenocarcinomas are rare, and the global gene expression changes associated with the initial stages of carcinogenesis of these neoplasms have not been elucidated. Results: To comprehensively analyze genetic markers and pathways specific to early-stage duodenal adenoma/adenocarcinomas, transcriptional profiles of 4 fresh-frozen non-ampullary duodenal adenoma/adenocarcinomas and surrounding duodenal normal mucosa were compared. Key features of gene expression analysis demonstrated a strong correlation between these tumors and colorectal adenomas, as well as the Wnt/β-catenin pathway. These results shed new light on the transcriptional changes that occur during the early stages of duodenal tumorigenesis. All samples were obtained prior to treatment in order to minimize effects of cauterization, and immediately fresh-frozen.
2018-08-06 | GSE102208 | 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:A study to evaluate techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples by direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched fresh frozen (FF) tissues. Formalin-fixed paraffin-embedded tissue from three colon adenocarcinoma samples were subjected to different FFPE-oriented DNA repair approaches and sequences, then compared with corresponding fresh frozen tissues. All samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip.
2014-12-17 | E-GEOD-59038 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of normal and tumoral tissues of the breast. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450 thousand CpGs in fresh frozen tissue samples (40 primary breast tumours and 17 normal breast tissues). Samples included morphologically normal samples of each tissue and tumor samples.
2015-02-04 | GSE52865 | GEO
Project description:We evaluated the profile of miRNA expression in 6 colorectal adenoma (CRA), 6 colorectal adenocarcinoma (CRC) and 6 matched normal mucosa (NOR) using the Exiqon miRCURY LNA microRNA array,7th generation. We found that global dysregulated miRNAs between colorectal lesions and normal mucosa. Our findings implicates that dysregulation of miRNAs may play important role in the carcinogenesis and present therapeutic targets for CRC.
2018-08-23 | GSE72281 | GEO
Project description:Aberrant methylation of DNA is supposed to be a major and early driver of colonic adenoma development and may also lead to colorectal cancer (CRC) formation. While gene methylation assays are used already for CRC screening, differential epigenetic alterations of recurring and non-recurring colorectal adenomas have yet not been systematically investigated. Here, we collected a sample set (n=72) of formalin-fixed paraffin-embedded (FFPE) primary colorectal adenomas without recurrence (n=30), primary adenomas with recurrence at the same location (n=19), so-called “matched pair samples” (n=10; comprising the primary adenoma and the recurrent adenoma) and normal mucosa specimens (n=3). We aimed to unveil differentially methylated CpG positions (DMPs) across the methylome of the selected samples using the Illumina HumanMethylation 450K BeadChip array. Unsupervised hierarchical clustering exhibited a significant association of methylation patterns with the histological subtypes. No significant DMPs were identified comparing primary adenomas with and without recurrence. Despite that, a total of 5,094 DMPs (FDR<0.05, fold change>10%) were identified in the comparisons of recurrent adenomas vs. (non-) matched primary adenomas with recurrence (674; 98% hypermethylated), recurrent adenomas vs. primary adenomas with and without recurrence (241; 99% hypermethylated) and adenomas vs. normal mucosae (4,179; 46% hypermethylated). DMPs in CpG islands were frequently hypermethylated whereas open sea and shelves exhibited hypomethylation. Gene ontological analysis demonstrated enrichment of genes associated with the immune system, inflammatory processes, and cancer-pathways. We conclude that methylation data is helpful to contribute to a more stable and reproducible histological adenoma classification which is a prerequisite to establishing profound surveillance guidelines
2019-06-01 | GSE129364 | 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:We searched the database of the Department of Pathology at The University of Texas MD Anderson Cancer Center and selected 21 patients who had invasive microsatellite-stable colorectal adenocarcinoma arising from a pre-existing adenoma and adjacent non-neoplastic mucosa in a resection specimen to permit pairwise analyses, and who had informed consent for research use of their residual tissue. A hematoxylin and eosin (H&E)-stained slide from each formalin-fixed paraffin-embedded tissue block was used to select one block that had invasive adenocarcinoma and adenoma with low- and high-grade dysplasia with minimal contamination by stromal and inflammatory cells, and adjacent full thickness non-neoplastic mucosa including the surface epithelium and proliferative zone. Unstained recut slides with 5-micrometer sections and no coverslip were laid over the marked slide, and the corresponding demarcated areas were manually microdissected.
2012-08-17 | E-MTAB-813 | biostudies-arrayexpress
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. We conducted genome-wide array-based studies and comprehensive data analyses of aberrantly methylated loci in 41 normal colon samples, 42 colon adenomas, and 64 colorectal cancers. Supplementary file 'GSE48684_Matrix_signal_intensities_1.txt.gz': includes the unmethylated and methylated signal intensities from Samples GSM1183439-GSM1183561. Supplementary file 'GSE48684_Matrix_signal_intensities_2.txt.gz': includes the unmethylated and methylated signal intensities from Samples GSM1235135-GSM1235158.
2014-09-08 | E-GEOD-48684 | biostudies-arrayexpress