Genome-Wide Analysis of DNA Methylation Differences in Muscle and Fat from Monozygotic Twins Discordant for Type 2 Diabetes
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE38291 | GEO | 2012/12/10
SECONDARY ACCESSION(S): PRJNA167625
REPOSITORIES: GEO
Similar Datasets
Project description:Monozygotic twins discordant for type 2 diabetes constitute an ideal model to study environmental contributions to type 2 diabetic traits. We aimed to examine whether global DNA methylation differences exist in major glucose metabolic tissues from twelve 53–80 year-old monozygotic discordant twin pairs. DNA methylation was measured by the Illumina HumanMethylation27 BeadChip in 22 (11 pairs) skeletal muscle and 10 (5 pairs) subcutaneous adipose tissue biopsies. No replicates were included.
2012-12-10 | E-GEOD-38291 | biostudies-arrayexpress
Project description:The exploration of copy number variation (CNV), notably of somatic cells, is an understudied aspect of genome biology. Any differences in the genetic make-up between twins derived from the same zygote represent an extreme example of somatic variation. We studied 19 pairs of monozygotic twins with either concordant or discordant phenotype using two platforms for genome-wide CNV analyses and show that CNVs exist within pairs in both groups. These findings impact our views of genotypic and phenotypic diversity in monozygotic twins, and suggest that CNV analysis in phenotypically discordant monozygotic twins may provide a powerful tool in identifying disease predisposition loci. Our results also imply that caution should be exercised with the interpretation of disease causality of de novo CNVs found in patients based on analysis of a single tissue in routine disease-related DNA diagnostics Analysis of copy number variability in concordant healthy monozygotic twin pairs as well as three monozygostic twin pairs discordant a Parkinsons disease (PD) phenotype using the Illumina HumanHap 300 dead chips. Keywords: SNP data
2007-12-11 | GSE9608 | GEO
Project description:Schizophrenia affects approximately 1% of the world population. Genetics, epigenetics, and environmental factors are known to play a role in this psychiatric disorder. While there is a high concordance in monozygotic twins, about half of twin pairs are discordant for schizophrenia. To address the question of how and when concordance in monozygotic twins occur, we have obtained fibroblasts from two pairs of schizophrenia discordant twins (one sibling with schizophrenia while the second one is unaffected by schizophrenia) and three pairs of healthy twins (both of the siblings are healthy). We have prepared iPSC models for these 3 groups of patients with schizophrenia, unaffected co-twins, and the healthy twins. When the study started the co-twins were considered healthy and unaffected but both the co-twins were later diagnosed with a depressive disorder. The reprogrammed iPSCs were differentiated into hippocampal neurons to measure the neurophysiological abnormalities in the patients. We found that the neurons derived from the schizophrenia patients were less arborized, were hypoexcitable with immature spike features, and exhibited a significant reduction in synaptic activity with dysregulation in synapse-related genes. Interestingly, the neurons derived from the co-twin siblings who did not have schizophrenia formed another distinct group that was different from the neurons in the group of the affected twin siblings but also different from the neurons in the group of the control twins. Importantly, their synaptic activity was not affected. Our measurements that were obtained from schizophrenia patients and their monozygotic twin and compared also to control healthy twins point to hippocampal synaptic deficits as a central mechanism in schizophrenia
2024-05-06 | GSE263672 | GEO
Project description:To identify genes dysregulated in bipolar disorder (BD1) we carried out global gene expression profiling using whole-genome microarrays. To minimize genetic variation in gene expression levels between cases and controls we compared expression profiles in lymphoblastoid cell lines from monozygotic twin pairs discordant for the disease. We identified 82 genes that were differentially expressed by ≥ 1.3-fold in 3 BD1 cases compared to their co-twins, and which were statistically (p ≤ 0.05) differentially expressed between the groups of BD1 cases and controls. Using qRT-PCR we confirmed the differential expression of some of these genes, including: KCNK1, MAL, PFN2, TCF7, PGK1, and PI4KCB, in at least 2 of the twin pairs. In contrast to the findings of a previous study by Kakiuchi and colleagues with similar discordant BD1 twin design1 our data do not support the dysregulation of XBP1 and HSPA5. From pathway and gene ontology analysis we identified up-regulation of the WNT signalling pathway and the biological process of apoptosis. The differentially regulated genes and pathways identified in this study may provide insights into the biology of BD1. Keywords: Bipolar Disorder, Monozygotic Twins, Discordant, Trasnsformed Lymphocytes
2007-03-31 | GSE7036 | GEO
Project description:The exploration of copy number variation (CNV), notably of somatic cells, is an understudied aspect of genome biology. Any differences in the genetic make-up between twins derived from the same zygote represent an extreme example of somatic variation. We studied 19 pairs of monozygotic twins with either concordant or discordant phenotype using two platforms for genome-wide CNV analyses and show that CNVs exist within pairs in both groups. These findings impact our views of genotypic and phenotypic diversity in monozygotic twins, and suggest that CNV analysis in phenotypically discordant monozygotic twins may provide a powerful tool in identifying disease predisposition loci. Our results also imply that caution should be exercised with the interpretation of disease causality of de novo CNVs found in patients based on analysis of a single tissue in routine disease-related DNA diagnostics Analysis of copy number variability in concordant healthy monozygotic twin pairs as well as three monozygostic twin pairs discordant a Parkinsons disease (PD) phenotype using the Illumina HumanHap 300 dead chips. Genotyping using the HumanHap300-duo bead chip from Illumina, GEO accession GPL5711
2010-06-25 | E-GEOD-9608 | biostudies-arrayexpress
Project description:Human intelligence demonstrates one of the highest heritabilities among human quantitative traits. Phenotypically discordant monozygotic twins provide a way to identify loci reponsible for the phenotypical differences. We performed comprehensive DNA methylation analysis in monozygotic twins manifesting differences in IQ scores. Genes with significantly different methylation status are considered as candidates related to human intelligence. Methylation profiling was conducted using methylated DNA enriched fraction by MethylMiner. Subjects were compared with their co-twins by MAT software and bed files were generated. Significantly high methyalted regions with MAT score p value < 0.000001 in each twin pairs were extracted as candidates.
2012-10-20 | E-GEOD-33477 | biostudies-arrayexpress
Project description:To identify genes dysregulated in bipolar disorder (BD1) we carried out global gene expression profiling using whole-genome microarrays. To minimize genetic variation in gene expression levels between cases and controls we compared expression profiles in lymphoblastoid cell lines from monozygotic twin pairs discordant for the disease. We identified 82 genes that were differentially expressed by ⥠1.3-fold in 3 BD1 cases compared to their co-twins, and which were statistically (p ⤠0.05) differentially expressed between the groups of BD1 cases and controls. Using qRT-PCR we confirmed the differential expression of some of these genes, including: KCNK1, MAL, PFN2, TCF7, PGK1, and PI4KCB, in at least 2 of the twin pairs. In contrast to the findings of a previous study by Kakiuchi and colleagues with similar discordant BD1 twin design1 our data do not support the dysregulation of XBP1 and HSPA5. From pathway and gene ontology analysis we identified up-regulation of the WNT signalling pathway and the biological process of apoptosis. The differentially regulated genes and pathways identified in this study may provide insights into the biology of BD1. Experiment Overall Design: Three pairs of Monozygotic Twins which were discordant for Bipolar Disorder with psychotic features were examined. (n=6)
2008-06-15 | E-GEOD-7036 | biostudies-arrayexpress
Project description:We aim to investigate circulating genome-wide microRNA (miRome) profiles in Moyamoya disease (MMD)-discordant monozygotic (MZ) twins with the RNF213 founder mutation (rs112735431).A disease discordant monozygotic twin-based study design may unmask potential confounders from previously published circulating microRNA signature in MMD. Circulating genome-wide microRNA (miRNome) profiling was performed in MMD-discordant monozygotic twins, non-twin-MMD patients, and non-MMD healthy volunteers by microarray followed by qPCRvalidation, using blood samples. Differential plasma-microRNAs were further quantified in endothelial cells differentiated from iPS cell lines (iPSECs) derived from another independent non-twin cohort. Lastly, their target gene expression in the iPSECs was analyzed. Microarray detected 309 plasma-microRNAs in MMD-discordant monozygotic twins that were also detected in the non-twin cohort. Principal component analysis of the plasma-microRNA expression level demonstrated distinct 2 groups separated by MMD and healthy control in the twin- and non-twin cohorts. Of these, differential up-regulations of hsa-miR-6722-3p/-328-3p were validated in the plasma of MMD (Imposed threshold: absolute log2 expression fold change (logFC) > 0.26 for the twin cohort; absolute logFC > 0.26, p < 0.05, and q < 0.15 for the non-twin cohort). In MMD derived iPSECs, hsa-miR-6722-3p/-328-3p showed a trend of up-regulation with a 3.0- or higher expression fold change. Bioinformatics analysis revealed that 41 target genes of miR- 6722-3p/-328-3p were significantly down-regulated in MMD derived iPSECs and were involved in STAT3, IGF-1-, and PTEN-signaling, suggesting a potential microRNA- gene expression interaction between circulating plasma and endothelial cells. In conclusion, our MMD-discordant monozygotic twin-based study confirmed a novel circulating microRNA signature in MMD as a potential diagnostic biomarker minimally confounded by genetic heterogeneity. The novel circulating microRNA signature can contribute for the future functional microRNA analysis to find new diagnostic and therapeutic target of MMD.
2018-08-02 | GSE100488 | GEO
Project description:Human intelligence demonstrates one of the highest heritabilities among human quantitative traits. Phenotypically discordant monozygotic twins provide a way to identify loci responsible for normal-range intelligence. We conducted array-based genome-wide gene expression analysis aiming to identify genes displaying significant difference among monozygotic twin pairs manifesting between-co-twins IQ differences.
2012-10-20 | GSE33476 | GEO
Project description:DNA methylation appears to play an essential mechanistic role in the pathogenesis of ALL, thereby potentiate its use as a biomarker for diagnosis and prognosis (Milani, Lundmark et al. 2010; Geng, Brennan et al. 2012; Sandoval, Heyn et al. 2013), and even a potential target of novel therapeutic approaches in ALL. In present study, we collected blood specimens for 4 pairs of monozygotic twins (MZ) and 1 pair of dizygotic twin (DZ) that are discordant for ALL. We sought to comprehensively assess the magnitude of genetic and epigenetic differences between ALL-affected and unaffected twins. we conducted whole genome and whole methylome sequencing on these five pairs of ALL-discordant twins. We also examined both the MZ and DZ twins using whole-genome bisulfite sequencing (WGBS). At first, the methylation differences across the genome were addressed globally by Circos software. And then tried to characterize the co-twin methylation divergence in specific genomic regions between ALL-discordant twin pairs. These patterns of dynamic co-twin methylation changes in these discordant ALL samples were generally consistent among MZ and DZ twins, indicating similarities of methylation abnormalities. As a result, 780, 566, 309, 293 and 2110 DMRs were identified, with a similar distribution pattern across different genomic elements among the five twin pairs.Then we annotate whether these DMRs were located in regulatory elements and identification of genes with recurring methylation alterations in a cohort of ALL patients. We collected blood specimens from 4 pairs of MZ twins and 1 pair of DZ twin that are discordant for ALL. At first, the methylation differences across the genome were addressed globally by Circos software. And then tried to characterize the co-twin methylation divergence in specific genomic regions and differentially methylated gene regions (DMRs) were identified between ALL-discordant twin pairs. Then we annotate whether these DMRs were located in regulatory elements and identification of genes with recurring methylation alterations in a cohort of ALL patients.
2015-01-01 | E-GEOD-59869 | biostudies-arrayexpress