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Analysis of epigenetic changes in human colorectal cancer and matching mucosa tissues

ABSTRACT: We used NimbleGen human CpG/promoter microarrays for profiling epigenetic changes (DNA methylation, H3K27me3 and H3K4me3 marks) in colon tumors (Duke's stage II) and matching mucosa samples from patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE47075 | GEO | 2013/12/31

SECONDARY ACCESSION(S): PRJNA203426

REPOSITORIES: GEO

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Analysis of epigenetic changes in human colorectal cancer and matching mucosa tissues

Project description:We used NimbleGen human CpG/promoter microarrays for profiling epigenetic changes (DNA methylation, H3K27me3 and H3K4me3 marks) in colon tumors (Duke's stage II) and matching mucosa samples from patients. Analysis of DNA methylation was done by using the methylated CpG island recovery assay (MIRA) technique with further hybridization versus input on NimbleGen human CpG/promoter microarrays. For profiling of H3K27me3 and H3K4me3 marks, we performed chromatin immunoprecipitation with H3K27me3 (#07-449, Millipore) and H3K4me3 (#39159, Active Motif) antibodies and further hybridized versus input on NimbleGen human CpG/promoter microarrays. All experiments were performed simultaneously for matching tissue samples.

2013-12-31 | E-GEOD-47075 | biostudies-arrayexpress

Expression data for 4 colon tumor (Duke's stage II) /matching mucosa tissue pairs

Project description:Analysis of expression changes between colon tumors (Duke's stage II) and matching colon mucosa tissues using Affymetrix GeneChip® Human Gene 2.0 ST arrays.

2013-12-31 | GSE47074 | GEO

Expression data for 4 colon tumor (Duke's stage II) /matching mucosa tissue pairs

Project description:Analysis of expression changes between colon tumors (Duke's stage II) and matching colon mucosa tissues using Affymetrix GeneChipÂ® Human Gene 2.0 ST arrays. All experiments were performed simultaneously for matching tissue samples.

2013-12-31 | E-GEOD-47074 | biostudies-arrayexpress

ColoCare Project: Gene expression analysis in colorectal cancer and adjacent mucosa tissues

Project description:Within the ColoCare Project we obtained gene expression profiles from 77 tumor and 117 mucosa tissues using Illumina HumanHT12v4 gene chips. Including GSE101764, there are 77 tumor and 108 mucosa samples with matching DNA methylation profiles. The complex interplay between DNA methylation and gene expression was analysed by using both data sets.

2018-12-01 | GSE106582 | GEO

Normal human colorectal mucosa, cecum, ascending, transverse, sigmoid and rectum

Project description:Normal human colorectal mucosa was sampled at points along the colon. Keywords: normal human tissue

2007-12-01 | GSE9254 | GEO

Histone ChIP-seq from mucosa of descending colon (ENCSR869XBX)

Project description:H3K4me3 ChIP-seq on mucosa of descending colon tissue male adult (40 years) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

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gasric mucosa tissues

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Comparative study of gene expression in human colorectal cancer tissues and normal mucosa

Project description:The purpose of our study was to better understand the genetic mechanism of oncogenesis for human colorectal cancer and to identify potential new tumour markers of use in clinical practice. Results: Comparing cancerous tissues with normal colonic mucosa we identified 584 known genes (3%) differentially expressed to a significant degree (p<0.001). Many of the transcripts that were more abundant in tumours than in non-neoplastic tissues appear to reflect important events for colon carcinogenesis. For example, a significant number of these genes serve as apoptotic inhibitors (e.g. BFAR, BIRC1, BIRC6). Furthermore, we observed the simultaneous upregulation of HLA-E and the downregulation of b2-microglobulin; these genes strongly support a potential tumour escape strategy from immune surveillance in colon cancer tissues. Conclusions: Our study provides new gene candidates in the pathogenesis of human CRC disease. From our results we hypothesise that CRC cells escape immune surveillance through a specific gene expression alteration; moreover, overexpression of several survival genes seems to confer a more anti-apoptotic phenotype. These genes are involved in pathways not previously implicated in CRC pathogenesis and they may provide new targets for therapy. Keywords: disease state analysis

2006-03-01 | GSE3294 | GEO

Epigenome analysis of normal colon mucosa samples

Project description:To investigate whether lifestyle factors modulate the stability of gene promoter methylation in the normal aging colonic mucosa, we performed genome-scale DNA methylation profiling of 178 normal colon biopsies 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 Aspirin use and hormonal replacement therapy (HRT) suppress, whereas a high body mass index (BMI) and smoking promote age-related hyermethylation. Many of these loci modulated by lifestyle in the healthy colon mucosa coincide with loci hypermethylated in colorectal cancers and down-regulated in adenomas. The data show that lifestyle modulates the stability of DNA methylation in the aging colonic epithelium and thereby impacts the rate of evolution of cancer methylomes.

2014-07-01 | GSE48988 | GEO

Epigenome analysis of normal colon mucosa samples

2014-07-01 | E-GEOD-48988 | biostudies-arrayexpress

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