Similar Datasets
Project description:Methylation profiling in Bladder cancer : adjacent normal tissue vs bladder tumor tissue
2021-04-03 | GSE171369 | GEO
Project description:High-throughput analyses of concordant gene methylation and expression events were carried out for 91 human prostate specimens, including prostate cancer (T), matched normal adjacent to tumor (AT), and organ donor (OD). Methylated DNA in genomic DNA was immunoprecipitated with anti-methylcytidine antibodies and detected by Affymetrix human whole genome SNP 6.0 chips. Methylated genomic DNA was purified by 5-hmc antibodies and Affymetrix SNP arrays were performed according to the manufacturer's manual.
2013-08-01 | GSE45000 | GEO
Project description:Archival formalin-fixed paraffin-embedded tissues were collected. The slides were reviewed by a pathologist to identify representative tumor tissue blocks. Enrichment of tumor cells was performed by tissue macro-dissection of predetermined areas, as outlined by Haemotoxylin and Eosin staining. Seven-micron thick sections in isolated areas of interest with at least 50% tumor cellularity were dissected to be used as tumor samples. Normal prostate samples were obtained from the adjacent tissues demonstrating no tumor involvement. Genomic DNA extraction was conducted using the Illumina FFPE DNA recovery kit. Following bisulfite conversion, DNA methylation analysis of the samples was performed using the Illumina Infinium methylation 450k bead chip array (San Diego, CA), according to the manufacturer’s protocol. Both tumor and normal samples were assayed in one experiment to avoid batch effect. The resulting methylated and unmethylated signal intensity data were imported into R 3.4.2 for analysis. Normalization was performed using Illumina normalization method with background correction using the minfi package in R 3.4.2.
2018-03-20 | GSE112047 | GEO
Project description:Men with African ancestry have the highest incidence and mortality rates of prostate cancer (PCa) worldwide. This study aimed to identify differentially methylated genes between tumor vs. adjacent normal and aggressive vs. indolent PCa in 121 African American patients. Epigenome-wide DNA methylation patterns in tumor DNA were assessed using the human Illumina Methylation EPIC V1 array. Around 5,139 differentially methylated CpG-sites (q<0.01, lΔβl>0.2) were identified when comparing normal vs. tumor, with an overall trend of hypermethylation in prostate tumors. Multiple representatives differentially methylated regions (DMRs), including immune-related genes, such as CD40, Galectin3, OX40L, and STING, were detected in prostate tumors when compared to adjacent normal tissues. Based on an epigenetic clock model, we observed that tumors' total number of stem cell divisions and the stem cell division rate were significantly higher than adjacent normal tissues. Regarding aggressiveness, 2,061 differentially methylated CpG-sites (q<0.05, lΔβl>0.05) were identified when the grade group (GG)1 was compared with GG4/5. Among these 2,061 CpG sites, 155 probes were consistently significant in more than one comparison. Among these genes, several immune system genes, such as COL18A1, S100A2, ITGA4, HLA-C, and ADCYAP1, have previously been linked to tumor progression in PCa. Several differentially methylated genes involved in immune-oncologic pathways associated with disease risk or aggressiveness were identified. In addition, 261 African American-specific differentially methylated genes related to the risk of PCa were identified. These results can shed light on potential mechanisms contributing to PCa disparities in the African American population.
2024-08-01 | GSE269244 | GEO
Project description:Methylation profiling in colorectal cancer : adjacent normal tissue vs colon tumor tissue
2012-03-10 | GSE36380 | GEO
Project description:Genome-Wide DNA methylation analysis of tumor and adjacent normal prostate tissues
| PRJNA439005 | ENA
Project description:Genome wide DNA methylation profiling of normal and tumor prostate samples, as well as cultured primary prostate cells overexpressing DNA Methyltransferases (DNMTs) and EZH2 Candidate gene based studies have identified a handful of aberrant CpG DNA methylation events in prostate cancer. However, DNA methylation profiles have not been compared on a large scale between prostate tumor and normal prostate, and the mechanisms behind these alterations are unknown. In this study, we quantitatively profiled 95 primary prostate tumors and 86 healthy prostate tissue samples for their DNA methylation levels at 26,333 CpGs representing 14,104 gene promoters by using the Illumina HumanMethylation27 platform. A 2-class Significance Analysis of this dataset revealed 5,912 CpG sites with increased DNA methylation and 2,151 CpG sites with decreased DNA methylation in tumors (FDR < 0.8%). Prediction Analysis of this dataset identified 87 CpGs that are the most predictive diagnostic methylation biomarkers of prostate cancer. By integrating available clinical follow-up data, we also identified 69 prognostic DNA methylation alterations that correlate with biochemical recurrence of the tumor. To identify the mechanisms responsible for these genome-wide DNA methylation alterations, we measured the gene expression levels of several DNA methyltransferases (DNMTs) and their interacting proteins by TaqMan qPCR and observed increased expression of DNMT3A2, DNMT3B, and EZH2 in tumors. Subsequent transient transfection assays in cultured primary prostate cells revealed that DNMT3B1 and DNMT3B2 overexpression resulted in increased methylation of a substantial subset of CpG sites that also showed tumor-specific increased methylation.
2011-04-19 | GSE26126 | GEO
Project description:The Illumina Infinium HumanMethylation450 BeadChip arrays were performed on a collection of primary gastric cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM) as well as unrelated normal tissue myofibroblasts (NTM). CAM and ATM samples were obtained from patients undergoing gastric cancer surgery; whereas NTM samples were generated from deceased transplant donors with normal morphology.
2019-01-10 | GSE97686 | GEO
Project description:The Illumina Infinium HumanMethylation450 BeadChip arrays were performed on a collection of primary oesophageal cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM). CAM and ATM samples were obtained from patients with oesophageal adenocarcinomas undergoing cancer surgery.
2019-01-10 | GSE97687 | GEO
Project description:Lung cancer occurs in never-smokers. Epigenetic changes in lung cancer potentially represent important diagnostic, prognostic, and therapeutic targets. We compared DNA methylation profiles of 28 adenocarcinomas of the lungs of never-smokers with paired adjacent nonmalignant lung tissue. We correlated differential methylation changes with gene expression changes from the same 28 samples. We observed a distinct separation in methylation profiles between tumor and adjacent nonmalignant lung tissue using principal component analysis. Tumors were generally hypomethylated compared with adjacent nonmalignant tissue. Of 1,906 differentially methylated CpG sites between tumor and nonmalignant tissue, 1,198 were within classically defined CpG islands where tumors were hypermethylated compared with nonmalignant tissue. A total of 708 sites were outside CpG islands where tumors were hypomethylated compared with nonmalignant tissue. There were significant differences in expression of 351 genes (23%) of the 1,522 genes matched to the differentially methylated CpG sites. Genes that were not significantly differentially expressed and were hypermethylated within CpG sites were enriched for homeobox genes. These results suggest that the methylation profiles of lung adenocarcinomas of never-smokers and adjacent nonmalignant lung tissue are significantly different. Despite the differential methylation of homeobox genes, no significant changes in expression of these genes were detected.
2015-02-03 | GSE62948 | GEO