Homo sapiens
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PROVIDER: PRJNA227180 | ENA |
REPOSITORIES: ENA
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Project description:Borderline personality disorder (BPD) is a complex psychiatric disease with an increased impact in the last years. While the diagnosis and therapy are well established, little is known on the pathogenesis of borderline personality disorder. Previously, a significant increase in DNA methylation of relevant neuropsychiatric genes in BPD patients has been reported. In our study we performed genome wide methylation analysis and revealed specific CpG sites that exhibited increased methylation in 26 BPD patients compared to 11 healthy controls. Bead chip technology and quantitative bisulfite pyrosequencing showed a significantly increased methylation at CpG sites of APBA2 (1.1 fold) and APBA3 (1.1 fold), KCNQ1 (1.6 fold), MCF2 (1.1 fold) and NINJ2 (1.2 fold) in BPD patients. For the CpG sites of GATA4 an increase in DNA methylation was observed, but was only significant in the bead chip assay. Moreover genome wide methylation levels of blood samples of BPD patients and control samples are similar. In summary, our results show a significant 1.26 fold average increase in methylation at the analyzed gene associated CpG sites in the blood of BPD patients compared to controls samples (p<0.001). This data may provide new insights into epigenetic mechanisms underlying the pathogenesis of BPD.
2014-02-01 | GSE52222 | GEO
Project description:Borderline personality disorder (BPD) is a complex psychiatric disease with an increased impact in the last years. While the diagnosis and therapy are well established, little is known on the pathogenesis of borderline personality disorder. Previously, a significant increase in DNA methylation of relevant neuropsychiatric genes in BPD patients has been reported. In our study we performed genome wide methylation analysis and revealed specific CpG sites that exhibited increased methylation in 26 BPD patients compared to 11 healthy controls. Bead chip technology and quantitative bisulfite pyrosequencing showed a significantly increased methylation at CpG sites of APBA2 (1.1 fold) and APBA3 (1.1 fold), KCNQ1 (1.6 fold), MCF2 (1.1 fold) and NINJ2 (1.2 fold) in BPD patients. For the CpG sites of GATA4 an increase in DNA methylation was observed, but was only significant in the bead chip assay. Moreover genome wide methylation levels of blood samples of BPD patients and control samples are similar. In summary, our results show a significant 1.26 fold average increase in methylation at the analyzed gene associated CpG sites in the blood of BPD patients compared to controls samples (p<0.001). This data may provide new insights into epigenetic mechanisms underlying the pathogenesis of BPD. Whole blood samples for 26 BPD patients and 11 controls were obtained from the Psychiatric Hospital in Münsterlingen, Switzerland. All patients signed informed consent at initial clinical investigation. The study was approved by the local ethic committee. Diagnosis of BPD was established by an experienced psychiatrist (Dr. G. W. Dammann). Clincopathological parameter of the patients and controls are summarized in table S1 (for details see (Dammann et al, 2011)). Genomic DNA from whole blood was isolated by Nucleo Spin XL Blood (Macherey and Nagel, Düren, Germany). For the bead chip array 500 ng of genomic DNA was treated with bisulfite (Dammann et al, 2011).
2014-02-01 | E-GEOD-52222 | biostudies-arrayexpress
Project description:DNA methylation changes at CpG and non-CpG sites are associated with development and clinical behavior in neuroblastoma [methylation]
| PRJNA237498 | ENA
Project description:We examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared to non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands. These results demonstrate the significance of aberrant DNA methylation in HCC tumorigenesis.
2014-01-30 | GSE54503 | GEO
Project description:Serous borderline tumours (SBOT) are a challenging group of ovarian tumours positioned between benign and malignant disease. We have profiled the DNA methylomes of 12 low grade serous carcinoma (LGSC), 19 SBOT and 16 benign serous tumours (BST) across 27,578 CpG sites to further characterise the epigenomic relationship between these subtypes of ovarian tumours. Unsupervised hierarchical clustering of DNA methylation levels showed that LGSC differ distinctly from BST, however, not from SBOT. Gene ontology analysis of genes showing differential methylation at linked CpG sites between LGSC and BST revealed significant enrichment of gene groups associated with cell adhesion, cell-cell signalling and the extracellular region consistent with a more invasive phenotype of LGSC as compared to BST. Consensus clustering highlighted differences between SBOT methylomes and returned subgroups with malignant-like or benign-like methylation profiles. Furthermore, a two loci DNA methylation signature can distinguish between these SBOT subgroups with benign-like and malignant-like methylation characteristics. Our findings indicate striking similarities between SBOT and LGSC methylomes which supports a common origin and the view that LGSC may arise from SBOT. A subgroup of SBOT can be classified into tumours with a benign-like or a malignant-like methylation profile which may help in identifying tumours more likely to progress into LGSC. Array-based methylation profiling was performed using the Infinium HumanMethylation27 BeadChip in 12 low grade serous carcinoma, 19 serous borderline tumours and 16 benign serous tumours. The reproducibility of the Infinium HumanMethylation27 BeadChips was evaluated using four biological replicates of the high grade serous ovarian cancer cell line PEO1. Differential methylation cutoff was estimated from four biological replicates by bootstrap resampling and set at Δβ ≥ 0.25 corresponding to a FDR ≤ 0.09.
2012-12-31 | E-GEOD-40105 | biostudies-arrayexpress
Project description:Abstract: Noncoding variants of presumed regulatory function contribute to neuropsychiatric disease heritability. 4442 noncoding variants connected to risk for 10 neuropsychiatric disorders, including autism spectrum disorder, attention deficit hyperactivity disorder, bipolar disorder, borderline personality disorder, major depression, generalized anxiety disorder, panic disorder, post-traumatic stress disorder, obsessive-compulsive disorder, and schizophrenia, were studied within developing human neural cells. Integrating epigenomic and transcriptomic data with massively parallel reporter assays identified 637 disease-associated single-nucleotide variants (daSNVs) with altered transcription-regulating activity. Expression-gene mapping, network analyses, and chromatin looping identified 619 candidate disease-relevant target genes modulated by these daSNVs. Specific daSNV-associated molecular pathways mapped to prevalent mental health symptoms. These data provide a framework resource to study inherited pathogenic risk for human neuropsychiatric disorders. Purpose: To place disease-associated single nucleotide variants (daSNVs) in genomic context within human neural cells, matched RNA-seq, chromatin accessibility profiling via ATAC-seq, and enhancer-promoter looping via H3K27ac HiChIP was performed in ES cells and at day 2 (N-D2), 10 (N-D10), and 28 (N-D28) of neuronal differentiation. Additionally, anterior (A-NPC) and posterior (P-NPC) neuronal stem cells were generated and studied. Matched sequencing was also performed on primary human astrocytes from adult brains. Processed and raw data for all cell types can be found in this repository. All biological replicates (n=2) are merged using the ENCODE pipeline.
2022-12-16 | GSE182093 | GEO
Project description:We examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared to non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands. These results demonstrate the significance of aberrant DNA methylation in HCC tumorigenesis. Bisulfite modification of 1µg DNA was conducted using an EZ DNA Methylation Kit (Zymo Research, Irvine, CA) according to the manufacturer’s procedure. The Infinium Methylation 450K assay was performed according to Illumina’s standard protocol. Six HCC tumor/adjacent non-tumor tissue pairs were processed on the same chip to avoid chip-to-chip variation.
2014-01-30 | E-GEOD-54503 | biostudies-arrayexpress
Project description:There is a growing realization that some aging-associated phenotypes/diseases have an epigenetic basis. Here we report the first genome-scale study of epigenomic dynamics during normal human aging. We identify aging-associated differentially methylated regions (aDMRs) in whole blood in a discovery cohort, and then replicate these aDMRs in sorted CD4+ T-cells and CD14+ monocytes in an independent cohort, suggesting that aDMRs occur in precursor haematopoietic cells. Further replication of the aDMRs in buccal cells, representing a tissue that originates from a different germ-layer compared with blood, demonstrates that the aDMR signature is a multi-tissue phenomenon. Moreover, we demonstrate that aging-associated DNA hypermethylation occurs predominantly at bivalent chromatin domain promoters. This same category of promoters, associated with key developmental genes, is frequently hypermethylated in cancers and in vitro cell culture, pointing to a novel mechanistic link between aberrant hypermethylation in cancer, aging, and cell culture. We measured the methylation state of 27,578 CpG sites (Illumina HumanMethylation27 array) in whole blood samples from 93 heathy human females aged between 49 and 74, to discover sites which change methylation state with age.
2010-06-24 | E-GEOD-20236 | biostudies-arrayexpress
Project description:In summary, our study demonstrated the methylation sites of SFRP1 gene promoter in patients with colorectal cancer and adenoma and found SFRP1_16_17_18 CpG site was good performance as a diagnostic marker of colorectal cancer.
| 2401959 | ecrin-mdr-crc
Project description:Epigenetic alternations in addition to genetic factors are important contributors to the pathogenesis of Systemic Lupus Erythematosus (SLE). Recent studies revealed that aberrant changes in DNA methylation occur in SLE patients, and potentially contributes to the pathogenesis. Using genome-wide DNA methylation microarray, the Illumina Infinium HumanMethylation450 BeadChip, we compared the DNA methylation level of white blood cells between Chinese female SLE patients with that of healthy controls. There was no difference in global levels of DNA methylation between SLE patients and controls. However, we identified 36 CpG sites with differential loss of DNA methylation and 8 CpG sites with differential gain of DNA methylation, representing 26 genes and 7 genes respectively. Surprisingly, nearly half of the hypomethylated CpG sites were located in the CpG shores, which implicated the functional importance of loss of DNA methylation in the CpG shores in SLE.
2016-12-21 | GSE76056 | GEO