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High-throughput sequencing and analysis of gene modification regulated by epigenetics modification in adult and old intracerebral hemorrhage rats. [RNA-Seq]

ABSTRACT: Here we performed in depth epigenome sequencing and analysis to study the mechanism of high mortality rate of ICH in rat brain. It reveals a systematical transcription activation of mRNA genes enriched in inflammation and immune responses. These genes are clustered to specific genomic loci and regulated by repressive and activation chromatin markers. We show that epigenetic reprogramming responding to ICH in old rat brains differs greatly from that in the adult.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE106924 | GEO | 2023/04/01

REPOSITORIES: GEO

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High-throughput sequencing and analysis of gene modification regulated by epigenetics modification in adult and old intracerebral hemorrhage rats. [ChIP-Seq]

Project description:Here we performed in depth epigenome sequencing and analysis to study the mechanism of high mortality rate of ICH in rat brain. It reveals a systematical transcription activation of mRNA genes enriched in inflammation and immune responses. These genes are clustered to specific genomic loci and regulated by repressive and activation chromatin markers. We show that epigenetic reprogramming responding to ICH in old rat brains differs greatly from that in the adult.

2020-11-30 | GSE106951 | GEO

Identification of inflammation-related microRNAs deregulated in the plasma from intracerebral hemorrhage patients

Project description:We tested the hypothesis that circulating microRNAs (miRNAs) present in plasma might display a specific signature in patients with intracerebral hemorrhage (ICH). Global miRNA profiles were determined with the Agilent Human miRNA Microarray platform, 027233. ICH patients display a characteristic inflammation-related miRNA profile as compared to healthy controls. Plasma samples were collected from the following 6 subject groups: male ICH patients (n=8), female ICH patients (n=7), male healthy control (n=4), female healthy control (n=4), male ischemic stroke patients (n=8) and female ischemic stroke patients (n=8). Total RNAs isolated from 1 ml plasma were pooled for each group. A fixed volume of RNA sample was withdrawn from each pool and used for microarray detection.

2013-01-19 | E-GEOD-43618 | biostudies-arrayexpress

Transcriptome profiling of rat brain samples in two age groups in responding to intracerebral hemorrhage

Project description:Aging-induced decline of endogenous neuroprotection has been shown to aggravate intracerebral hemorrhage (ICH)-induced acute brain injury, however, the underlying mechanisms in brain are still little known. In this study, we applied a rat ICH model to study the transcriptional responses in the early and late aging (13-month and 22-month old) rats that show substantial differences in brain damage and recovery. Transcriptome analysis (RNA-seq) reveals that brain expression of neuroinflammation genes is similarly and selectively upregulated in ICH, which includes genes in the cellular response to interferon gamma function. We show that the anti-IFN-γ treatment effectively reduces ICH-induced acute brain injury.

2020-04-27 | GSE149317 | GEO

Intracerebral Hemorrhage Induces Inflammatory Gene Expression in Peripheral Blood: Global Transcriptional Profiling in ICH Patients

Project description:Intracerebral hemorrhage (ICH) is a severe neurological disorder with no proven treatment. While there is substantial interest in post-ICH neuroinflammation and associated pathophysiological mechanisms, these processes remain poorly understood. To further advance our understanding, we performed RNA-seq in the peripheral blood of ICH patients to test the hypothesis that ICH would induce inflammatory biological pathways. 16,640 genes were identified and 216 were significant DEGs after ICH (FDR<0.1). IPA identified three canonical pathways as the most statistically significantly activated by ICH: colorectal cancer metastasis signaling (Z-score 3.00, P=1.71E-5), interleukin-8 (IL-8) signaling (3.00, 8.44E-5), and nuclear factor-kappa B (NF-kB) activation by viruses (2.55, 1.78E-4). Inflammatory mediators of particular relevance included IL-8, NF-kB, ERK 1/2, and the integrins β3, α2b, and β5. Conclusion: ICH induced peripheral blood gene expression at 72 to 96 hours compared with 0 to 24 hours from symptom onset. DEGs that were highly expressed in the significant biological pathways included those related to inflammation and activation of the immune response. Further research is needed to determine if these changes affect outcomes and may represent new therapeutic targets.

2019-04-21 | GSE125512 | GEO

Development of gene expression signatures in experimental intracerebral hemorrhage

Project description:To identify the potential lncRNA and mRNA post intracerebral hemorrhage (ICH), we have employed lncRNA microarray expression profiling. 570 mRNAs and 313 lncRNAs were identified in the ICH vs sham group .Expression of six mRNA (Saa3, Col10a1, Mmp13, Oxt, Pcdhb6 and Resp18) and lncRNA (ENSMUT00000141700, AK143011, ENSMUT00000128306, AK030988, ENSMUST00000187076 and ENSMUST00000134129) from this signature was quantified by qPCR.

2023-05-17 | GSE227683 | GEO

Succinylation profiles of brain injury after intracerebral hemorrhage

Project description:Protein posttranslational modifications (PTMs) has been shown to regulate biological processes of human diseases via expanding the genetic code and for regulating cellular pathophysiology, however, the system-wide changes at the PTMs levels in ICH brain remains little known. Given that succinylation is one of the important PTMs in regulating many biological processes. Therefore, in this study, we used a high-resolution mass spectrometry-based, quantitative succinyllysine proteomics approach to firstly investigated the ICH-associated brain protein succinyllysine modifications. We totally identified the concentration of approximately 6000 succinylation events and quantified approximately 3500 sites. Among them, 25 succinyllysine sites on 23 proteins were increased, while 13 succinyllysine sites on 12 proteins were downregulated after ICH. Additionally, the subcellular localization analysis of these significantly changed succinylproteins showed that 58.3% hyposuccinylated proteins were located in the mitochondria, while the percentage of succinylproteins located in mitochondria was decreased to about 35% in ICH brains with concomitant increasing in the percentage of cytoplasm to 30.4%. Further bioinformatic analysis showed that the succinylated proteins were mostly located in mitochondria and synapse-related subcellular spaces, and participate in many pathophysiological processes, such as metabolism, cytoskeleton organization, synapse working and ferroptosis, etc.. Moreover, we performed a combination analysis of our succinylproteomics data with previously published transcriptome data and found that most of the differentially succinylated proteins were distributed into neurons, endothelial cells and astrocytes. In conclusion, our analyses uncover a number of succinylation-affected processes and pathways in ICH brains and provide new insights for understanding ICH pathophysiological processes.

2021-10-29 | PXD025621 | Pride

Development of gene expression signatures for Buyang Huanwu decoction in treating intracerebral hemorrhage

Project description:To identify the potential lncRNA and mRNA asscociated with Buyang Huanwu decoction (BYHWD) in treating intracerebral hemorrhage (ICH), we have employed lncRNA microarray expression profiling. 1596 and 1114 mRNAs were identified in the ICH vs sham group and the BYHWD vs ICH group, respectively. Specifically, 180 DEmRNAs were intersected among the three groups. 2287 and 2245 lncRNAs were identified in the ICH vs sham group and the BYHWD vs ICH group, respectively. Specifically, 342 DElncRNAs were intersected among the three groups. Expression of four mRNA (Spata2, Nkiras, Mef2c, Sh2b3) and lncRNA (Gm16045, Gm14005, Gm41118, 493304012Rik) from this signature was quantified by qPCR.

2023-07-01 | GSE220886 | GEO

Effect of Pterostilbene (PTE) treatment on gene expression after intracerebral hemorrhage injury

Project description:To investigate the effect of Pterostilbene(PTE) on gene expression after intracerebral hemorrhage injury, we employed RNA sequencing (RNA-seq) to profile the mRNA expression ensuing PTE treatment after ICH. Different gene distribution could be clearly seen on the volcano plot between diferent comparisions among Sham, ICH, and ICH+PTE group. Finally, we showed that 1021 shared genes overlapping between those differentially expressed genes, which was reversed by PTE treatment

2024-03-01 | GSE228222 | GEO

Genome-wide DNA methylation pattern in whole blood associated with primary intracerebral hemorrhage

Project description:To reveal the role of DNA methylation in peripheral blood from primary intracerebral hemorrhage(ICH) ,DNAs from 30 ICH patients and 34 matched controls were analyzed by methylation microarray. In total, we identified 1377 hypomethylated and 153 hypermethylated differentially methylated positions (DMPs) in peripheral blood from ICH patients compared to healthy controls.

2021-07-10 | GSE179759 | GEO

Effect of P7C3-A20 treatment on gene expression after intracerebral hemorrhage injury

Project description:To investigate the effect of P7C3-A20 on gene expression after intracerebral hemorrhage injury, we employed RNA sequencing (RNA-seq) to profile the mRNA expression ensuing P7C3-A20 treatment after ICH. Different gene distribution could be clearly seen on the volcano plot between diferent comparisions among Sham, ICH, and ICH+P7C3-A20 group. Finally, we showed that 1047 shared genes overlapping between those differentially expressed genes, which was reversed by P7C3-A20 treatment

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