Project description:To globally define methylation-âproneâ and -âprotectedâ CpG islands in colorectal carcinoma we analyzed the methylation status of 23,000 CpG islands of the human genome in ten coleorectal carcinoma samples as well as normal colon using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. Keywords: MCIp-on-Chip; comparative genomic hybridization CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from colorectal carcinoma samples was compared to the enriched material from normal colon to identify aberrantly methylated regions.
Project description:To globally define methylation-M-bM-^@M-^YproneM-bM-^@M-^Y and -M-bM-^@M-^YprotectedM-bM-^@M-^Y CpG islands in cancer, we analyzed the methylation status of 23,000 CpG islands of the human genome in 19 colorectal carcinoma samples as well as normal colon using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from colorectal carcinoma samples was compared to the enriched material from normal colon to identify aberrantly methylated regions.
Project description:The concept of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) is widely accepted, though the timing of its occurrence and its interaction with other genetic defects are not fully understood. Our aim in this study was to unravel the molecular development of CIMP cancers by dissecting their genetic and epigenetic signatures in precancerous and malignant colorectal lesions. A total of 88 samples (16 normal colon tissues taken from adjacent tumor tissue, 70 colorectal tumor tissues and 2 cell lines) was analyzed using MCA microarray. Aberrant DNA methylation was compared with clinicopathological features and copy number.
Project description:We used Illumina Infinium 27k Human DNA Methylation BeadChip v1.2 to assess genome-wide DNA methylation profiling of normal colon epithelial, adenomas and colorectal adenocarcinomas across approximately 27,000 CpGs in fresh frozen colorectal tissue samples. We found that cancer-associated methylation changes with impact on transcription occur nearly as frequent at non-CpG island as CpG island promoters in colorectal cancer (CRC). Samples included 6 normal colon epithelial tissue samples, 6 adenomas, and 30 colorectal adenocarcinomas. Bisulfite-converted DNA from the 42 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.
Project description:We used Illumina Infinium 27k Human DNA Methylation BeadChip v1.2 to assess genome-wide DNA methylation profiling of normal colon epithelial, adenomas and colorectal adenocarcinomas across approximately 27,000 CpGs in fresh frozen colorectal tissue samples. We found that cancer-associated methylation changes with impact on transcription occur nearly as frequent at non-CpG island as CpG island promoters in colorectal cancer (CRC).
Project description:Transcription profiling of human colon biopsy samples from healthy individuals and patients with colon adenomas, colorectal cancer or inflammatory bowel disease
