Differential glia activation in early epileptogenesis - insights from cell-specific analysis of DNA methylation and gene expression in the contralateral hippocampus
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ABSTRACT:
PROVIDER: PRJNA644632 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12168755.fastq.gz | Fastqsanger.gz | |||
| SRR12168756.fastq.gz | Fastqsanger.gz | |||
| SRR12168757.fastq.gz | Fastqsanger.gz | |||
| SRR12168758.fastq.gz | Fastqsanger.gz | |||
| SRR12168759.fastq.gz | Fastqsanger.gz |
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Project description:Morphological changes in mesial Temporal Lobe Epilepsy with Hippocampal Sclerosis (mTLE-HS) are well characterized. Yet it remains elusive whether these are a consequence of seizures or originate from a hitherto unknown underlying pathology. We recently published data on changes in gene expression (GE) and DNA methylation (DNAm) in the ipsilateral hippocampus (ILH), using the intracortical kainate mouse model of mTLE-HS. In order to explore the effects of epileptic activity alone and also to further disentangle what triggers morphological alterations, we investigated glial and neuronal changes in GE and DNAm in the contralateral hippocampus (CLH). The intracortical kainic acid mouse model of mTLE-HS was used to elicit status epilepticus. Hippocampi contralateral to injection site from 8 kainate injected (KA) and 8 sham (SH) mice were extracted, and shock frozen at 24 hours post injection. Glial- and neuronal nuclei were sorted by flow cytometry. Alterations in GE and DNAm were assessed using reduced representation bisulfite sequencing (RRBS) and RNA sequencing (RNAseq). The R package edgeR was used for statistical analysis. The CLH featured substantial, mostly cell-specific changes in both GE and DNAm in glia and neurons. While changes in GE overlapped to a great degree between CLH and ILH, alterations in DNAm did not. In the CLH we found a significantly lower number of glial genes up- and downregulated compared to previous results from the ILH. Furthermore, several genes and pathways potentially involved in anti-epileptogenic effects were upregulated in the CLH. By comparing GE data from the CLH to previous results from the ILH (featuring hippocampal sclerosis), we derive potential upstream targets for epileptogenesis, including glial Cox2 and Cxcl10. Despite the absence of morphological changes, the CLH displays substantial changes in GE and DNAm. We find that GE changes related to potential anti-epileptogenic effects seem to dominate compared to pro-epileptogenic effects in the CLH and speculate whether this imbalance contributes to prevent morphological alterations like neuronal death and reactive gliosis.
2020-11-12 | GSE153976 | GEO
Project description:Purpose: to evaluate changes in the transcriptome of hippocampal cells during the course of epileptogenesis, from the early events post status epilepticus (SE) to the onset of recurrent spontaneous seizures. Experimental Design: Gene expression profiling was analyzed in hippocampi of rats subjected to the pilocarpine model of epilepsy at different times during the course of epileptogenesis: 3 days post-SE (3D), 7 days post-SE (7D), and immediately (up to 12h) after the first spontaneous seizure (Chronic). All three pilocarpine subgroups had a corresponding age-matched control group (saline-treated rats), from which normal hippocampi samples were obtained at the same experimental time points. Independent microarray hybridizations were carried out for each sample (n = 5, per experimental group) with oligonucleotide microarrays covering 34,000 transcripts representing most of the known and predictive genes of the rat genome (CodeLink⢠Rat Whole Genome Bioarrays, GE Healthcare), following the manufacturerâs protocol. Results: differential expression of almost 1,400 genes was detected during the course of epileptogenesis, from the early events post status epilepticus (SE) to the onset of recurrent spontaneous seizures. Most of these genes are novel and displayed an up-regulation after SE. Noteworthy, a group of 128 genes functioning in neurogenesis, apoptosis, immune response, and intracellular signal transduction was found consistently hyper-expressed throughout epileptogenesis, indicating stable molecular alterations within the hippocampus. Those include modulation of the MAPK, Jak-STAT, PI3K, TGF-beta, and mTOR signaling pathways. Differential expression of genes from the p38 MAPK pathway, mediating inflammation and neurogenesis, was also confirmed by real-time PCR. These findings reveal dynamic molecular changes occurring in the hippocampus that may serve as a starting point for the generation of new hypothesis regarding the underlying mechanisms of epilepsy and for the designing of alternative therapeutic strategies. Keywords: gene expression changes during epileptogenesis. We performed a genome wide analysis of genes differentially expressed during epileptogenesis. Virtually, all possible changes in the rat transcriptome were monitored at distinct time points corresponding to the latent to chronic phase transition of the pilocarpine model of epilepsy, which is probably the most extensively studied chemically inductive model of TLE. Genes identified as being differentially expressed were classified based on their respective biological functions to envisage processes and pathways likely implicated in epileptogenesis, as well as their possible value as targets for therapy. Results were expressed as fold variation, and genes displaying greater than 2-fold changes in transcript abundance and p<0.01 were selected.
2010-02-09 | E-GEOD-14763 | biostudies-arrayexpress
Project description:Purpose: to evaluate changes in the transcriptome of hippocampal cells during the course of epileptogenesis, from the early events post status epilepticus (SE) to the onset of recurrent spontaneous seizures. Experimental Design: Gene expression profiling was analyzed in hippocampi of rats subjected to the pilocarpine model of epilepsy at different times during the course of epileptogenesis: 3 days post-SE (3D), 7 days post-SE (7D), and immediately (up to 12h) after the first spontaneous seizure (Chronic). All three pilocarpine subgroups had a corresponding age-matched control group (saline-treated rats), from which normal hippocampi samples were obtained at the same experimental time points. Independent microarray hybridizations were carried out for each sample (n = 5, per experimental group) with oligonucleotide microarrays covering 34,000 transcripts representing most of the known and predictive genes of the rat genome (CodeLink™ Rat Whole Genome Bioarrays, GE Healthcare), following the manufacturer’s protocol. Results: differential expression of almost 1,400 genes was detected during the course of epileptogenesis, from the early events post status epilepticus (SE) to the onset of recurrent spontaneous seizures. Most of these genes are novel and displayed an up-regulation after SE. Noteworthy, a group of 128 genes functioning in neurogenesis, apoptosis, immune response, and intracellular signal transduction was found consistently hyper-expressed throughout epileptogenesis, indicating stable molecular alterations within the hippocampus. Those include modulation of the MAPK, Jak-STAT, PI3K, TGF-beta, and mTOR signaling pathways. Differential expression of genes from the p38 MAPK pathway, mediating inflammation and neurogenesis, was also confirmed by real-time PCR. These findings reveal dynamic molecular changes occurring in the hippocampus that may serve as a starting point for the generation of new hypothesis regarding the underlying mechanisms of epilepsy and for the designing of alternative therapeutic strategies. Keywords: gene expression changes during epileptogenesis.
2010-02-09 | GSE14763 | GEO
Project description:Mesial Temporal Lobe Epilepsy is characterized by progressive changes of both neurons and glia, also referred to as epileptogenesis. No curative treatment options, apart from surgery, are available. DNA methylation (DNAm) is a potential upstream mechanism in epileptogenesis and may serve as a novel therapeutic target. To our knowledge, this is the first study to investigate epilepsy-related DNAm, gene expression (GE) and their relationship, in neurons and glia. We used the intracortical kainic acid injection model to elicit status epilepticus. At 24 hours post injection, hippocampi from eight kainic acid- (KA) and eight saline-injected (SH) mice were extracted and shock frozen. Separation into neurons and glial nuclei was performed by flow cytometry. Changes in DNAm and gene expression were measured with reduced representation bisulfite sequencing (RRBS) and mRNA-sequencing (mRNAseq). Statistical analyses were performed in R with the edgeR package. We observed fulminant DNAm- and GE changes in both neurons and glia at 24 hours after initiation of status epilepticus. The vast majority of these changes were specific for either neurons or glia. At several epilepsy-related genes, like HDAC11, SPP1, GAL, DRD1 and SV2C, significant differential methylation and differential gene expression coincided. We found neuron- and glia-specific changes in DNAm and gene expression in early epileptogenesis. We detected single genetic loci in several epilepsy-related genes, where DNAm and GE changes coincide, worth further investigation. Further, our results may serve as an information source for neuronal and glial alterations in both DNAm and GE in early epileptogenesis.
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Project description:Background and Aims: Morphological changes in mesial temporal lobe epilepsy with hippocampal sclerosis (mTLE-HS) are well-characterized. Yet, it remains elusive whether these are a consequence of seizures or originate from a hitherto unknown underlying pathology. We recently published data on changes in gene expression and DNA methylation in the ipsilateral hippocampus (ILH) using the intracortical kainate mouse model of mTLE-HS. In order to explore the effects of epileptic activity alone and also to further disentangle what triggers morphological alterations, we investigated glial and neuronal changes in gene expression and DNA methylation in the contralateral hippocampus (CLH). Methods: The intracortical kainic acid mouse model of mTLE-HS was used to elicit status epilepticus. Hippocampi contralateral to the injection site from eight kainate-injected and eight sham mice were extracted and shock frozen at 24 h post-injection. Glial and neuronal nuclei were sorted by flow cytometry. Alterations in gene expression and DNA methylation were assessed using reduced representation bisulfite sequencing and RNA sequencing. The R package edgeR was used for statistical analysis. Results: The CLH featured substantial, mostly cell-specific changes in both gene expression and DNA methylation in glia and neurons. While changes in gene expression overlapped to a great degree between CLH and ILH, alterations in DNA methylation did not. In the CLH, we found a significantly lower number of glial genes up- and downregulated compared to previous results from the ILH. Furthermore, several genes and pathways potentially involved in anti-epileptogenic effects were upregulated in the CLH. By comparing gene expression data from the CLH to previous results from the ILH (featuring hippocampal sclerosis), we derive potential upstream targets for epileptogenesis, including glial Cox2 and Cxcl10. Conclusion: Despite the absence of morphological changes, the CLH displays substantial changes in gene expression and DNA methylation. We find that gene expression changes related to potential anti-epileptogenic effects seem to dominate compared to the pro-epileptogenic effects in the CLH and speculate whether this imbalance contributes to prevent morphological alterations like neuronal death and reactive gliosis.
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