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Intracranial aneurysm associated single-nucleotide polymorphisms alter regulatory DNA in the human circle of Willis

ABSTRACT: Intracranial aneurysm associated single-nucleotide polymorphisms alter regulatory DNA in the human circle of Willis

PROVIDER: PRJNA419258 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6311280.fastq.gz	Fastqsanger.gz
	SRR6311271.fastq.gz	Fastqsanger.gz
	SRR6311281.fastq.gz	Fastqsanger.gz
	SRR6311272.fastq.gz	Fastqsanger.gz
	SRR6311282.fastq.gz	Fastqsanger.gz

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Similar Datasets

Intracranial aneurysm associated single-nucleotide polymorphisms alter regulatory DNA in the human circle of Willis

Project description:Background and Purpose: Genome-wide association studies significantly link intracranial aneurysm (IA) to single-nucleotide polymorphisms (SNPs) in six genomic loci. To gain insight into the relevance of these IA associated SNPs, we aimed to identify regulatory regions and analyze overall gene expression in the human circle of Willis (CoW), on which these aneurysms develop. Methods: We performed chromatin immunoprecipitation and sequencing for histone modifications H3K4me1 and H3K27ac to identify regulatory regions, including distal enhancers and active promoters, in post mortem specimens of the human CoW. These experiments were complemented with RNA sequencing on the same specimens. We determined whether these regulatory regions overlap with IA associated SNPs, using computational methods. By combining our results with publicly available data, we investigated the effect of IA associated SNPs on the newly identified regulatory regions and linked them to potential target genes. Results: We find that IA associated SNPs are significantly enriched in CoW regulatory regions. Some of the IA associated SNPs that overlap with a regulatory region are likely to alter transcription factor binding, and in proximity to these regulatory regions are 102 genes that are expressed in the CoW. In addition, gene expression in the CoW is enriched for genes related to cell adhesion and the extracellular matrix. Conclusions: CoW regulatory regions link IA associated SNPs to genes with a potential role in the development of IAs. Our data refine previous predictions on SNPs associated with IA and provide a substantial resource from which candidates for follow-up studies can be prioritized.

2018-01-04 | GSE107196 | GEO

RNA sequencing analysis of rupture-prone intracranial aneurysms and the remaining circle of Willis in rats

Project description:Comprehensive gene expression profile was obtained by RNA sequencing analysis using total RAN purified from intracranial aneurysm lesions and remaining circle of Willis in rats.

2020-11-09 | GSE161044 | GEO

Expression data of Intracranial aneurysm

Project description:Intracranial aneurysm is a cerebrovascular disorder in which degeneration of intima and internal elastic lamina of a cerebral artery or vein causes a localized dilation or ballooning of the blood vessel. Different molecular mechanisms are involved in sIA formation in patients. We used microarrays to detail the gene expression of intracranial aneurysm.

2016-12-01 | GSE75436 | GEO

Intracranial aneurysm sequencing data

Project description:Intracranial aneurysm sequencing data

| PRJNA665639 | ENA

Transcription profiling of peripheral blood from patients with intracranial aneurysm or intracranial aneurysm and subarachnoid haemorrhage

Project description:As the EU IP @neurIST Project aims at integrating biomedical informatics technologies in the assessment of rupture risks and treatments of cerebral aneurysms in humans. Genetic involvement in the disease is known, mRNA biomarkers will be searched as possible risk factors in easy to assess PBMCs (peripheral blood cells). The aim of this pilot study is specifically to check the clinical samples going from the patientï¾s bed side to the genomic analysis platform. Briefly, we hybridized biotin labelled cRNA from 2 controls (C1, C2), 1 patient bearing an intracranial aneurysm (I) and 1 patients bearing an intracranial aneurysm and subarachnoid haemorrhage (S). For each sample, one technical replicate was performed. Thus a total of 8 arrays was used.

2010-12-01 | E-TABM-421 | biostudies-arrayexpress

Proteomic analysis of intracranial aneurysm

Project description:Intracranial aneurysm (IA) is a pathological dilation of the cerebral artery which has a potential to rupture leading to sub arachnoid haemorrhage (SAH). One third of the patients with aneurysmal SAH (aSAH) develop symptomatic narrowing of the blood vessels called cerebral vasospasm. The outcomes in the above clinical scenarios are variable and devastating. The study was designed to decipher the molecular mechanisms underlying the pathophysiology of intracranial aneurysm formation, its rupture and subsequent development of vasospasm at the proteomic level. The study was done in two phases – discovery phase and validation phase. We performed iTRAQ-based quantitative proteomic analysis of brain vessel tissue and serum samples in three subgroups of patients with IA and compared them with those of control group (subjects with no cerebrovascular disorder) during the discovery phase. In validation phase, dysregulated proteins of biological significance i.e. ORM1 as a biomarker for unruptured aneurysm and MMP9 as a biomarker for cerebral vasospasm were validated in larger cohort of patients.

2022-09-07 | PXD013442 | Pride

Epigenome analysis of intracranial aneurysm and superficial temporal artery samples

Project description:Genomic DNA of intracranial aneurysm and matched superficial temporal artery from same patient (n=9) was extracted with QIAamp DNA Mini Kit (Qiagen, Valencia, CA). A total of 500 of genomic DNA was bisulfite conversion using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA) and then analyzed on an Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA) following the manufacturer’s instructions.

2016-12-01 | GSE75434 | GEO

Intracranial aneurysm sequencing data

Project description:Based on sequencing technology to evaluate the differential lncRNA and mRNA expression of intracranial aneurysms. Provide ideas for the study of epigenetic regulation of intracranial aneurysms

2020-09-26 | GSE158558 | GEO

Comparison of circular RNA microarray analysis between human unruptured and ruptured intracranial aneurysms

Project description:Arraystar Human circRNA Microarray is designed for the profiling of human circRNAs. In this study, we applied a circRNA microarray to screen the potential biomarker for intracranial aneurysm. A total of 10 samples were used to perform microarray analysis. Our study contained 2 groups, un-ruptured intracranial aneurysm group(B1-B5) and ruptured intracranial aneurysm group(C1-C5). Each group contained five samples.

2021-07-15 | E-MTAB-10683 | biostudies-arrayexpress

Chromatin conformation links enhancers in intracranial aneurysm associated regions to potential candidate genes

Project description:Background and Purpose: We previously showed that intracranial aneurysm (IA)-associated single nucleotide polymorphisms (SNPs) are enriched in promoters and putative enhancers of the human circle of Willis (CoW), on which IAs develop, suggesting a role for such regulatory regions in IA. In this study we further investigated the role of these putative enhancers in the pathogenesis of IA by identifying the target genes of these enhancers and validating their regulatory activity. Methods: We selected putative enhancers in IA-associated regions from genome wide association studies, using our previously published CoW chromatin immunoprecipitation and sequencing data. Next, we used a chromatin conformation capture technique (4C) to identify physical interactions between these putative enhancers and the promoters of their target genes. Subsequently, we assessed the activity of the identified enhancers in vivo in zebrafish embryos and we analyzed gene expression of the target genes identified with 4C in CoW RNA-sequencing data and by in situ hybridization on CoW paraffin sections. Results: We identified fifteen enhancers that interact with the promoters of six target genes: SOX17, CDKN2B, MTAP, CNNM2, RPEL1 and GATA6. For eight out of eleven enhancers that could be tested, we confirmed in vivo activity in the zebrafish embryos. These eight enhancers reside in four out of six IA-associated GWAS regions. All six target genes are expressed in the CoW and in situ hybrdization showed that these genes are expressed in multiple cell types in the CoW. Conclusions: In four out of six IA-associated GWAS regions we identified eight enhancers that are active in vivo and interact with six nearby genes, suggesting that these genes are regulated by the identified enhancers. These genes, SOX17, CDKN2B, MTAP, CNNM2, RPEL1 and GATA6, are potential candidate genes involved in IA pathogenesis and should be studied using animal models in the future.

2019-04-27 | GSE115304 | GEO

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