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Genome-wide CpG methylation analysis of human white blood cells in obese patients under a weight loss treatment.

ABSTRACT: Genome wide DNA methylation profiling of white blood cells in obese patients under two different diets (The American Heart Association's Diet and RESMENA diet (Zulet MA et al., Nutr Hosp. 2011 Jan-Feb;26(1):16-26. )) in order to reduce weight. The Illumina infinium HumanMethylation450 beadchip kit was used, which assayed 450,000 potential methylation sites. Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip.

ORGANISM(S): Homo sapiens

SUBMITTER: Maria Mansego

PROVIDER: E-MTAB-2372 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide DNA methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis

Project description:Ductal carcinoma in situ (DCIS) of the breast is a precursor of invasive breast carcinoma (IBC). DNA methylation alterations are thought to be an early event in progression of cancer, and may prove valuable as a tool in clinical decision making and for understanding neoplastic development. Genome-wide DNA methylation profiles of 285 breast tissue samples representing progression of cancer were generated using Illumina HumanMethylation450. Validation of methylation changes between normal and DCIS was performed in an independent dataset of 15 normal and 40 DCIS samples, and validation of a prognostic signature was performed on 583 breast cancer samples from The Cancer Genome Atlas. Using two independent datasets of normal breast tissue and DCIS revealed that DNA methylation profiles of DCIS were radically altered compared to normal breast tissue, involving almost 7000 genes (including CUL7 and ICAM2). Changes between DCIS and IBC involved around 1000 genes. In tumors, DNA methylation was associated with gene expression of almost 3000 genes (p<0.05, Bonferroni corrected) including both negative and positive correlations. A prognostic signature based on methylation level of 18 CpGs (representing genes such as IRF6, TBX5, ZNF259, KCTD21, EPN3, MACF1 and CSNK1G2) was associated to survival of breast cancer patients with invasive tumors, as well as to survival of patients with DCIS and mixed lesions of DCIS and IBC. This work demonstrates that changes in the epigenome occurs early in the neoplastic progression, provide evidence for the possible utilization of DNA methylation based markers of progression in the clinic, and highlights the importance of epigenetic changes in carcinogenesis. Bisulphite converted DNA from the 285 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

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DNA methylation data from primary neuroblastoma tumors

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Interplay between promoter methylation and chromosomal loss in gene silencing at 3p11-p14 in cervical cancer

Project description:We performed integrative methylation, gene dosage and expression profiling to explore the interplay between promoter methylation and loss in gene silencing at 3p11-p14 in cervical cancer. Totally 26 hypermethylated genes were identified by comparing the methylation level of individual CpG sites with corresponding data of normal cervical tissue. Candidate methylation regulated genes in tumors were proposed from the correlation between methylation and gene expression. Integrated analysis of methylation, gene dosage and expression revealed three significant regulation patterns encompassing 8 hypermethylated genes; a methylation driven pattern, a gene dosage driven pattern, and a combined methylation and gene dosage driven pattern. For the LRIG1 gene, patients with both hypermethylation and loss had a worse outcome compared to those harboring only hypermethylation or none of the events. C3orf14 emerged as a novel methylation regulated suppressor gene, for which knockdown was found to promote invasive growth in human papilloma virus (HPV)-transformed keratinocytes. Methylation levels from Illumina 450K methylation arrays were correlated with Illumina gene expression data in cohort 1 and validated in cohort 2.

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Integrative analysis of methylome and transcriptome in human blood identifies extensive sex and immune cell-specific differentially methylated regions [methylation]

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Primary neuroblastoma tumors

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Array-based profiling of the lymphoma cell DNA methylome does not unequivocally distinguish primary lymphomas of the central nervous system from non-CNS diffuse large B-cell lymphomas

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Epigenome analysis of glioma patient surgical samples and corresponding xenotransplants and cell lines

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