Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood

ABSTRACT: Inter-individual DNA methylation variations were frequently hypothesized to alter individual susceptibility to Type 2 Diabetes Mellitus (T2DM). Sequence-influenced methylations were described in T2DM-associated genomic regions, but evidence for direct, sequence-independent association with disease risk is missing. Here we explore disease-contributing DNA methylation through a stepwise study design: first, a pool-based, genome-scale screen among 1,169 case and control individuals revealed an excess of differentially methylated sites in genomic regions that were previously associated with T2DM through genetic studies. Next, in-depth analyses were performed at selected top-ranked regions. A CpG site in the first intron of the FTO gene showed small (3.35%) but significant (p=0.000021) hypomethylation of cases relative to controls. The effect was independent of the sequence polymorphism in the region and persists among individuals carrying the sequence risk alleles. The odds of belonging to the T2DM group increased by 6.1% for every 1% decrease in methylation (OR=1.061, 95% CI: 1.032-1.090), and the sensitivity (AUC = 0.638, 95% CI: 0.586-0.690), (Males=0.675, Females=0.609), was better than of the strongest known sequence variant. Furthermore, a prospective study in an independent population cohort revealed significant hypomethylation of young individuals that later progressed to T2DM, relative to the individuals that stayed healthy. Further genomic analysis revealed co-localization with gene enhancers and with binding sites for methylation-sensitive transcriptional regulators. The data showed that low methylation level at the analyzed sites is an early marker of T2DM, and suggest a novel mechanism by which early-onset, inter-individual methylation variation at isolated non-promoter genomic sites predisposes to T2DM. Five pools of DNA samples consist of 710 T2DM patients and 459 control individuals were analyzed for average methylation levels at 1,461,753 DNA genomic fragments containing 3,359,645 CpG methylation sites using four SNP arrays for each sample, two 'genomic' (before treatment) replicates and two MSRE (treatment with a cocktail of five methyl-sensitive-restriction-enzyme) replicates. The analysis was done using the Affymetrix SNP 6.0 array.

ORGANISM(S): Homo sapiens

SUBMITTER: Asaf Hellman

PROVIDER: E-GEOD-33032 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood.

Toperoff Gidon G Aran Dvir D Kark Jeremy D JD Rosenberg Michael M Dubnikov Tatyana T Nissan Batel B Wainstein Julio J Friedlander Yechiel Y Levy-Lahad Ephrat E Glaser Benjamin B Hellman Asaf A

Human molecular genetics 20111012 2

Inter-individual DNA methylation variations were frequently hypothesized to alter individual susceptibility to Type 2 Diabetes Mellitus (T2DM). Sequence-influenced methylations were described in T2DM-associated genomic regions, but evidence for direct, sequence-independent association with disease risk is missing. Here, we explore disease-contributing DNA methylation through a stepwise study design: first, a pool-based, genome-scale screen among 1169 case and control individuals revealed an exce ...[more]

PMID: 21994764

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Project description:Genome wide methylation profiling of gliomas is likely to provide important clues to improving treatment outcomes. Restriction enzyme based approaches have been widely utilized for methylation profiling of cancer genomes and will continue to have importance in combination with higher density microarrays. With the availability of the human genome sequence and microarray probe sequences, these approaches can be readily characterized and optimized via in silico modeling. We adapted the previously described HpaII/MspI based Methylation Sensitive Restriction Enzyme (MSRE) assay for use with two-color Agilent 244K CpG island microarrays. In this assay, fragmented genomic DNA is digested in separate reactions with isoschizomeric HpaII (methylation-sensitive) and MspI (methylation-insensitive) restriction enzymes. Using in silico hybridization, we found that genomic fragmentation with BfaI was superior to MseI, providing a maximum effective coverage of 22,362 CpG islands in the human genome. In addition, we confirmed the presence of an internal control group of fragments lacking HpaII/MspI sites which enable separation of methylated and unmethylated fragments. We used this method on genomic DNA isolated from normal brain, U87MG cells, and a glioblastoma patient tumor sample and confirmed selected differentially methylated CpG islands using bisulfite sequencing. Along with additional validation points, we performed a receiver operating characteristics (ROC) analysis to determine the optimal threshold (p â¤ 0.001). Based on this threshold, we identified ~2400 CpG islands common to all three samples and 145 CpG islands unique to glioblastoma. These data provide general guidance to individuals seeking to maximize effective coverage using restriction enzyme based methylation profiling approaches. Five samples: normal human brain DNA, U87MG cell line, glioblastoma tumor, human DNA treated with SssI enzyme used as positive control, and Genomiphied human DNA used as negative control. Two technical replicates were performed on all samples except the negative control.

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Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood

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Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood.

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