DNA Methylation Analysis in Human Chorionic Villus and Maternal Blood Cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Tianjiao Chu
PROVIDER: E-GEOD-23311 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:We present a detailed structural and functional analysis of the placental epigenome at its maternal interface. Specifically, we analyzed the DNA methylation pattern of chromsomes 13, 18, and 21 in samples of chorionic villus (CVS) and maternal blood cells (MBC) using custom designed microarrays. We then compared these data with transcription data for the same tissues. In addition to the discovery that CVS genomes are significantly more hypomethylated than their MBC counterparts, we identified numerous tissue-specific differentially methylated regions (T-DMRs). We further discovered that these T-DMRs are clustered spatially along the genome and are enriched for genes with tissue-specific biological functions. We identified unique patterns of DNA methylation associated with distinct genomic structures such as gene bodies, promoters and CpG islands and identified both direct and inverse relationships between DNA methylation levels and gene expression levels in gene bodies and promoters respectively. Furthermore, we found that these relationships were significantly associated with CpG content. We conclude that the early gestational placental DNA methylome is highly organized and is significantly associated with transcription. These data provide a unique insight into the structural and regulatory characteristics of the placental epigenome at its maternal interface and will drive future analyses of the role of placental dysfunction in gestational disease. Two-condition experiment, CVS vs. MBC cells. Biological replicates: 2 pooled CVS samples, 2 pooled MBC samples, collected from different patients. Each sample is divided into two parts, one part treated with HpaII enzyme, one part without. The two parts then are hybridized to the two channels of the same array. Two arrays for each sample, with dye swap to remove dye bias.
2010-08-27 | E-GEOD-23835 | biostudies-arrayexpress
Project description:Placental gene expression is a finely controlled process, yet little is known about the factors that regulate it, including epigenetic factors such as DNA methylation. In this study, we quantified the effects of DNA methylation on placental gene expression. Using targeted high throughput sequencing, we generated methylation profiles of 3.7 million CpG dinucleotides from 6 karyotypically normal CVS samples and compared these to gene expression data obtained from a publically available database. We found a broad association between methylation and gene expression at both the chromosome and individual gene levels. At the chromosome level, we found alternating domains of high and low methylation. Within each gene, we found distinct methylation patterns at different regulatory genetic elements. For example, the promoters of highly expressed genes were neither highly methylated, nor completely unmethylated. Rather, they had < 50% of the CG dinucleotides in their sequences in the methylated state. In contrast, promoters of unexpressed genes tended to be either highly methylated or fully unmethylated. Similarly, patterns of methylation in exons and introns differed between highly expressed and unexpressed genes. Our data show that the relationship between DNA methylation and gene expression is nuanced: highly expressed and unexpressed genes differ, not only by their extent of methylation, but also by minute changes in the locations of their methylation sites. DNA methylation analysis of placental genes may help predict abnormal placental gene expression and pregnancy complications, making it a possible tool for prenatal diagnosis. DNA from 6 chorionic villus samples from the 1st trimester (from 3 male and 3 female fetuses) as well as 3 maternal blood cell samples was extracted, hybridized to probes in the Agilent SureSelectXT Methyl-Seq Target Enrichment kit, targeting 84Mb of the genome and then bisulfite converted before sequencing.
2016-06-25 | E-GEOD-58826 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of normal and trisomic placentas, and maternal blood cell DNA. The aim of this study was to search for methylation differences between maternal and fetal(placenta) cell free DNA, and between normal and trisomic placentas for an optimized methylation based noninvasive prenatal diagnosis of fetal chromosomal aberations. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in DNA samples from Chorionic villus samples(CVS) and DNA samples from whole blood. Samples included 12 Maternal blood cell samples from normal pregnancies, 12 normal CVS, 12 Trisomy 21 CVS, 12 trisomy 18 CVS and 6 trisomy 13 CVS samples.
2015-03-31 | GSE66210 | GEO
Project description:Episodes of chronic stress can result in psychic disorders like post-traumatic stress disorder, but also promote the development of metabolic syndrome and type 2 diabetes. We hypothesize that muscle, as main regulator of whole-body energy expenditure, is a central target of acute and adaptive molecular efects of stress in this context. Here, we investigate the immediate efect of a stress period on energy metabolism in Musculus gastrocnemius in our established C57BL/6 chronic variable stress (Cvs) mouse model. Cvs decreased lean body mass despite increased energy intake, reduced circadian energy expenditure (EE), and substrate utilization. Cvs altered the proteome of metabolic components but not of the oxidative phosphorylation system (OXPHOS), or other mitochondrial structural components. Functionally, Cvs impaired the electron transport chain (ETC) capacity of complex I and complex II, and reduces respiratory capacity of the ETC from complex I to ATP synthase. Complex I-OXPHOS correlated to diurnal EE and complex II-maximal uncoupled respiration correlated to diurnal and reduced nocturnal EE. Bioenergetics assessment revealed higher optimal thermodynamic efciencies (ƞ-opt) of mitochondria via complex II after Cvs. Interestingly, transcriptome and methylome were unafected by Cvs, thus excluding major contributions to supposed metabolic adaptation processes. In summary, the preclinical Cvs model shows that metabolic pressure by Cvs is initially compensated by adaptation of mitochondria function associated with high thermodynamic efciency and decreased EE to manage the energy balance. This counter-regulation of mitochondrial complex II may be the driving force to longitudinal metabolic changes of muscle physiological adaptation as the basis of stress memory.
2023-03-31 | PXD035798 | Pride
Project description:Episodes of chronic stress can result in psychic disorders like post-traumatic stress disorder, but also promote the development of metabolic syndrome and type 2 diabetes. We hypothesize that muscle, as main regulator of whole-body energy expenditure, is a central target of acute and adaptive molecular effects of stress in this context. Here, we investigate the immediate effect of a stress period on energy metabolism in Musculus gastrocnemius in our established C57BL/6 chronic variable stress (Cvs) mouse model. Cvs decreased lean body mass despite increased energy intake, reduced circadian energy expenditure (EE), and substrate utilization. Cvs altered the proteome of metabolic components but not of the oxidative phosphorylation system (OXPHOS), or other mitochondrial structural components. Functionally, Cvs impaired the electron transport chain (ETC) capacity of complex I and complex II, and reduces respiratory capacity of the ETC from complex I to ATP synthase. Complex I-OXPHOS correlated to diurnal EE and complex II-maximal uncoupled respiration correlated to diurnal and reduced nocturnal EE. Bioenergetics assessment revealed higher optimal thermodynamic efficiencies (ƞ-opt) of mitochondria via complex II after Cvs. Interestingly, transcriptome and methylome were unaffected by Cvs, thus excluding major contributions to supposed metabolic adaptation processes. In summary, the preclinical Cvs model shows that metabolic pressure by Cvs is initially compensated by adaptation of mitochondria function associated with high thermodynamic efficiency and decreased EE to manage the energy balance. This counter-regulation of mitochondrial complex II may be the driving force to longitudinal metabolic changes of muscle physiological adaptation as the basis of stress memory.Chronic stress targets mitochondrial respiratory efficiency in the skeletal muscle of C57BL/6 mice.Nikolic A, Fahlbusch P, Wahlers N, Riffelmann NK, Jacob S, Hartwig S, Kettel U, Dille M, Al-Hasani H, Kotzka J, Knebel B. Cell Mol Life Sci. 2023 Mar 29;80(4):108. doi: 10.1007/s00018-023-04761-4.PMID: 36988756
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Project description:Genome wide DNA methylation profiling of normal and trisomic placentas, and maternal blood cell DNA. The aim of this study was to search for methylation differences between maternal and fetal(placenta) cell free DNA, and between normal and trisomic placentas for an optimized methylation based noninvasive prenatal diagnosis of fetal chromosomal aberations. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in DNA samples from Chorionic villus samples(CVS) and DNA samples from whole blood. Samples included 12 Maternal blood cell samples from normal pregnancies, 12 normal CVS, 12 Trisomy 21 CVS, 12 trisomy 18 CVS and 6 trisomy 13 CVS samples. Bisulphite converted DNA from the 54 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.
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Project description:DNA methylation profiling of whole blood using Illumina's Infinium HumanMethylation27 Beadchip array. The dataset encompasses profiles of 12 non-diabetic control blood donors and 12 type-2 diabetic (T2D) individuals. Bisulfite converted DNA from 24 blood samples were hybridised to the Illumina Infinium HumanMethylation27 Beadchip
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Project description:Comparison of DNA methylation levels of chromosome 18 between placentas and blood cells of pregnant women Extracted DNA from 5 cases of placental tissues and 5 cases of maternal blood cell was subjected to MeDIP (methylated DNA immunoprecipitation) and hybridized to Affymetrix GeneChip® Human Tiling 2.0R Array sets. A control without immunoprecipitation (IP) was also processed in parallel with the immunoprecipitated DNA samples. The results were validated with bisulfite sequencing and mass spectrometry-based analysis
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Project description:In this study, we expand on this major advancement in O-GlcNAc enrichment protocols by adapting this approach to human-banked samples, which often presents their significant challenges. Indeed, patient samples are often banked without proper washing, thus contaminating cells with abundant O-glycosylated blood protein. These glycoproteins, such as human serum albumin, antibodies, and hemoglobin, pollute MS acquisition, masking the less abundant intracellular proteins and, even more, their O-GlcNAcylated forms. Thus, using freshly banked placentas, we present an adapted method to prepare human placental samples with naturally high blood content (13). We then enriched for O-GlcNAcylated protein using the PTMscan antibodies previously mentioned (12). However, our adapted protocol yielded over 60% of HexNAc peptide on total peptides. Per sample, we obtained up to 2,600 HexNAc-containing PSMs, 1,090 unique HexNAc peptides, and more than 1,000 unique HexNAc proteins using 45mg of starting placenta. Furthermore, we present a bioinformatic workflow to sort these HexNAc PSMs and extract the most confident O-GlcNAcylated proteins and sites. Thus, we confidentially identified 641 O-GlcNAcylated proteins, including up to 146 new proteins and 730 new sites within the 2 placental samples analyzed. Furthermore, we enriched for over 50 placenta-enriched O-GlcNAcylated proteins, such as RPA4, representing a new biomarker of the placental O-GlcNAcylation.
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