Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential DNA methylation profiles of HS ILAE type 1 in human temporal lobe epilepsy

ABSTRACT: Purpose:To provide new perspectives for molecular diagnosis of HS subtypes and find new therapeutic targets for the TLE patients with HS ILAE type 1. Methods:DNA methylation was detected by Whole Genome Bisulfite Sequencing (WGBS). The distribution of differentially methylated regions (DMRs) in the whole genome and different functional regions of genes was comprehensively analyzed. Results:A total of 3708 DMRs, including 1171 highly methylated DMRs and 2537 low methylated DMRs. Distinctions were found in the distributions of DMRs in different regions of genes as well. Six hundred and thirty-two DMGs were found in the promoter region. The results of functional enrichment analysis showed that DMR-related genes were mainly enriched in some signal pathways related to axonal growth, neuronal cytoskeleton, neurotransmitter release, synapse reorganization, epileptogenesis, excess synchronization, and hyperexcitability of neurons. Conclusions:This study preliminarily identified the differential DNA methylation profiles of HS ILAE type 1 in patients with TLE, which provides a theoretical basis for further understanding the molecular mechanism and novel biomarkers for subtypes of HS.

ORGANISM(S): Homo sapiens

PROVIDER: GSE140658 | GEO | 2021/09/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

chronic temporal lobe epilepsy: biopsy hippocampus

Project description:Analysis of biopsy hippocampal tissue of patients with pharmacoresistant temporal lobe epilepsy (TLE) undergoing neurosurgical removal of the epileptogenic focus for seizure control. Chronic TLE goes along with focal hyperexcitability. Results provide insight into molecular mechanisms that may play a role in seizure propensity 150 human hippocampus samples

2014-12-04 | E-GEOD-63808 | biostudies-arrayexpress

Altered RNAs in patients of temporal lobe epilepsy

Project description:Over the past decades, the immune responses have been suspected of participating in the mechanisms for epilepsy. To assess the immune related pathway in temporal lobe epilepsy (TLE), we explored the altered immune pathways in TLE patients with and without hippocampal sclerosis (HS).We analyzed RNA-seq data from 3 TLE-HS and 3 TLE-nonHS patients, including identification of differentially expressed RNA, function pathway enrichment, the protein-protein interaction network and construction of ceRNA regulatory. network. We illustrated the immune related landscape of molecules and pathways on human TLE-HS. Also, we identified several differential immune related genes like HSP90AA1 and SOD1 in TLE-HS patients. Further ceRNA regulatory network analysis found SOX2-OT connected to miR-671-5p and upregulated the target gene SPP1 in TLE-HS patients. Also, we identified both SOX2-OT and SPP1 were significantly upregulated in five different databases including TLE-HS patients and animal models

2024-02-13 | GSE255223 | GEO

The mircoRNA expression profiles of human temporal lobe epilepsy in HS ILAE type 1

Project description:Temporal lobe epilepsy (TLE) is associated with neurodegeneration, often leading to hippocampal sclerosis (HS). The type 1 HS, which is characterized by severe neuronal cell loss and gliosis predominantly in regions CA1 and CA4, is the most common subtype and is associated with best prognosis according to ILAE classification system. MiRNAs are participate in the biological processes underlying many nervous system diseases including epilepsy. However, the miRNA expression profile of HS ILAE type 1 is not completely understood. A total of 14 patients were identified as having the ILAE subtype, as determined by NeuN immunohistochemistry (ILAE type 1=7; no-HS=7). Next-generation sequencing and reverse transcription polymerase chain reaction technology was used to validate the dysregulated miRNAs. Bioinformatics analysis of the predicted target gene was conducted using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. In total, 1643 mature miRNAs were detected in this study, along with 5 miRNAs were upregulated and 2 miRNAs were downregulated expression in the type 1 group. Bioinformatics analysis showed that 1545 target genes were predicted using miRDB and Targetscan databases, and these predicted genes showed enrichment in the pathway associated with nucleic acid binding, intracellular and cellular macromolecule metabolic processes, and the PI3K-Akt signaling pathway. This study is the first to report the miRNA expression profile of HS ILAE type 1 compared with no-HS. These results provide new insights into the neuron loss pathology and offer fundamental evidence as to why there is a good prognosis among patients with type 1 HS.

2019-01-01 | GSE124507 | GEO

iTRAQ-based proteomic analysis of dentate gyrus in temporal lobe epilepsy with hippocampal sclerosis

Project description:Temporal lobe epilepsy (TLE) is the most frequent type of focal epilepsy in adults, typically resistant to pharmacological treatment and mostly present with cognitive impairment and psychiatric comorbidities. The most common neuropathological hallmark in TLE patients is hippocampal sclerosis(HS). However, the underlying molecular mechanisms involved remain poorly characterized. Dentate gyrus(DG), one specific hippocampal subarea, structural and functional changes imply a key involvement of the DG in the development of TLE. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) -based quantitative proteomic technique was performed to analysis of hippocampal DG obtained from patients with TLE-HS compared to control samples obtained from the autopsy. Our proteomic data identified 5583 proteins, of which 82 proteins were up-regulated and 90 proteins were down-regulated. Bioinformatics analysis indicated that differential expressed proteins enriched in “synaptic vesicle”, “mitochondrion”, “cell-cell adhesion”, “regulation of synaptic plasticity”, “ATP binding” and “Oxidative phosphorylation”. Protein-protein interaction network analysis found a pivotal module of 10 proteins that relate to “Oxidative phosphorylation”. This study is the first to investigate proteomic alterations in DG region of TLE-HS patients, and pave the way to better understanding of epileptogenesis mechanisms and future therapeutic intervention.

2021-01-18 | PXD023048 | Pride

chronic temporal lobe epilepsy: biopsy hippocampus

2014-12-04 | GSE63808 | GEO

Whole genome methylation profiliing between the IMU and KRT subtypes of HPV-associated head and neck cell carcinoma (HNSCC)

Project description:We compared the whole-genome methylation profiles between IMU and KRT samples in a 36 HNSCC cohort and identified 270,326 differentially methylated regions (DMRs; FDR < 0.05 and absolute methylation difference >= 20%) between IMU and KRT HPV(+) subtypes.

2022-11-02 | GSE180260 | GEO

Purified human leukocyte subtype DNA methylation profiles

Project description:The objective of the study was to identify differentially methylated regions of DNA (DMRs) that distinguish human leukocyte subtypes, and hence serve as biomarkers for those immune cell types. This file contains Illumina Infinium HumanMethylation27 BeadChip data for human leukocyte subtypes that were purified from whole blood samples via magnetic activated cell sorting (MACS) and purity confirmed by flourescence activated cell sorting (FACS). Bisulphite converted DNA from the 73 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2012-11-05 | E-GEOD-39981 | biostudies-arrayexpress

Purified human leukocyte subtype DNA methylation profiles

2012-11-05 | GSE39981 | GEO

Transcription profiling of human hippocampi from epilepsy patients with and without hippocampal sclerosis and autopsy controls

Project description:Genome wide gene expression was compared between nonHS, HS temporal lobe epilepsy patients (TLE) and autopsy control hippocampi in a 3-way analysis. In many TLE patients the hippocampus is subject to massive neuronal damage, gliosis and hippocampal sclerosis (HS), while in others there is no apparent hippocampal damage (nonHS). This three way analysis enabled us to differentiate between pathology and epilepsy related processes.

2008-01-01 | E-MEXP-744 | biostudies-arrayexpress

Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome

Project description:The impact of healthy aging on molecular programming of immune cells is poorly understood. Here, we report comprehensive characterization of healthy aging in human classical monocytes, with a focus on epigenomic, transcriptomic, and proteomic alterations, as well as the corresponding proteomic and metabolomic data for plasma, using healthy cohorts of 20 young and 20 older males (~27 and ~64 years old on average). For each individual, we performed eRRBS-based DNA methylation profiling, which allowed us to identify a set of age-associated differentially methylated regions (DMRs) – a novel, cell-type specific signature of aging in DNA methylome. Hypermethylation events were associated with H3K27me3 in the CpG islands near promoters of lowly-expressed genes, while hypomethylated DMRs were enriched in H3K4me1 marked regions and associated with age-related increase of expression of the corresponding genes, providing a link between DNA methylation and age-associated transcriptional changes in primary human cells.

2022-02-16 | PXD021821 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data