Isolation and culture of carotid atherosclerotic plaque inner mass cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA477848 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7425050.fastq.gz | Fastqsanger.gz | |||
| SRR7425051.fastq.gz | Fastqsanger.gz | |||
| SRR7425052.fastq.gz | Fastqsanger.gz | |||
| SRR7425045.fastq.gz | Fastqsanger.gz | |||
| SRR7425046.fastq.gz | Fastqsanger.gz |
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Project description:To characterize atherosclerotic plaque cells we isolated cells from the body of vulnerable and stable human atherosclerotic plaques and performed RNA-Seq gene expression profiling of obtained samples.
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Project description:In order to identify potential new biomarkers of atherosclerotic plaque composition we performed a large scale analysis of gene expression patterns in human atherosclerotic lesions. Whole genome expression analysis of 101 peripheral plaques identified a robust gene signature (1514 genes) dominated by inflammatory processes, and cholesterol metabolism and storage genes. Specific pathways enriched in this signature included activation of the Toll-like receptor signaling pathway, T-cell activation, cholesterol efflux, oxidative stress response, inflammatory cytokine production, vasoconstriction and lysosomal activity. Analysis of gene expression in plaque micro-dissected material revealed that the signature is strongly up-regulated in macrophage-rich regions and down-regulated in regions with high smooth muscle cell content. A smaller qPCR biomarker panel and inflammatory composite score (ICS) were developed to facilitate clinical translation of discoveries from gene expression profiling. We found that ICS correlates with histological features related to plaque vulnerability. In addition, ICS is able to separate groups of plaques obtained from symptomatic and asymptomatic patients undergoing carotid endarerectomy. In summary, we identified a robust mRNA biomarker panel associated with histo-pathological as well as clinical hallmarks of vulnerable atherosclerotic plaque. This panel may be used as a diagnostic and prognostic tool in clinical setting to evaluate novel anti-atherosclerotic therapies. 6 human carotid plaques were sectioned in 1 mm thick slices. Alternative slices were used for gene expression profiling in Affymetrix/Merck custom 1.0 arrays (GPL10687), or for immunohistochemistry studies (CD68, Actin)
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Project description:In order to identify potential new biomarkers of atherosclerotic plaque composition we performed a large scale analysis of gene expression patterns in human atherosclerotic lesions. Whole genome expression analysis of 101 peripheral plaques identified a robust gene signature (1514 genes) dominated by inflammatory processes, and cholesterol metabolism and storage genes. Specific pathways enriched in this signature included activation of the Toll-like receptor signaling pathway, T-cell activation, cholesterol efflux, oxidative stress response, inflammatory cytokine production, vasoconstriction and lysosomal activity. Analysis of gene expression in plaque micro-dissected material revealed that the signature is strongly up-regulated in macrophage-rich regions and down-regulated in regions with high smooth muscle cell content. A smaller qPCR biomarker panel and inflammatory composite score (ICS) were developed to facilitate clinical translation of discoveries from gene expression profiling. We found that ICS correlates with histological features related to plaque vulnerability. In addition, ICS is able to separate groups of plaques obtained from symptomatic and asymptomatic patients undergoing carotid endarerectomy. In summary, we identified a robust mRNA biomarker panel associated with histo-pathological as well as clinical hallmarks of vulnerable atherosclerotic plaque. This panel may be used as a diagnostic and prognostic tool in clinical setting to evaluate novel anti-atherosclerotic therapies.
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Project description:The objective of this study is to identify genes and pathways involved in the progression of atherosclerotic plaques from early to advanced stage in humans. Samples from atherosclerotic carotid artery segments, from early ((pathological) intimal thickening and intimal xanthoma) and from advanced (thin or thick fibrous cap atheroma) lesions, have been retrieved from the Maastricht Pathology Tissue Collection (MPTC). Tissue was obtained during autopsy (Dept of Pathology, Maastricht University Medical Centre). Collection, storage in the Maastricht Pathology Tissue Collection (MPTC) and use of tissue and patient data were performed in agreement with the "Code for Proper Secondary Use of Human Tissue"
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Project description:Atherosclerotic plaque rupture is the etiology of ischemic stroke and myocardial infarction. Ribosome-depleted total RNA was sequenced from carotid plaques obtained from patients undergoing carotid endarterectomy with high-grade stenosis and either 1) a carotid-related ischemic cerebrovascular event within the previous 5 days ('recently ruptured,' n=6) or 2) an absence of a cerebrovascular event ('asymptomatic,' n=5). Examination of the differentially expressed genes supported the importance of inflammation and inhibition of proliferation and migration coupled with an increase in apoptosis. Thus, the transcriptome of recently ruptured plaques is enriched with transcripts associated with inflammation and fibrous cap thinning and support further examination of the role of B lymphocytes and interferons in atherosclerotic plaque rupture.
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Project description:Protein profiles were determined from different distinct regions of human atherosclerotic plaques, including: internal control, fatty streak, plaque shoulder, plaque centre, and fibrous cap. Protein extracts from all 5 regions, from 3 men and 3 women, were separated by two-dimensional gel electrophoresis (in total 30 2-DE gels). Stained gels were matched by protein spot distribution, and a protein mapping was performed to identify as many protein spots as possible, by MALDI-TOF MS / peptide mass fingerprinting (Voyager DE Pro; Applied Biosystems). This resulted in the identification of 97 protein spots, corresponding to 52 unique protein by accession number. To expand on this nLC-MS/MS (Easy-nLC / LTQ Orbitrap Velos Pro; Thermo Fisher Scientific) experiments were run on additional carotid plaque samples from 10 men and 10 women, using three of the predefined regions; internal control, fatty streak, plaque core. MS/MS analysis resulted in the identification of over 1000 proteins. Human carotid atherosclerotic plaques (n = 26) were obtained from the Linköping Carotid Study, and all methods/protocols described herein have been approved by the local ethics committee (Linköping University Hospital, Linköping, Sweden). Written informed consent was also obtained from all patients.
2016-05-24 | PXD003930 | Pride
Project description:In order to identify potential new biomarkers of atherosclerotic plaque composition we performed a large scale analysis of gene expression patterns in human atherosclerotic lesions. Whole genome expression analysis of 101 peripheral plaques identified a robust gene signature (1514 genes) dominated by inflammatory processes, and cholesterol metabolism and storage genes. Specific pathways enriched in this signature included activation of the Toll-like receptor signaling pathway, T-cell activation, cholesterol efflux, oxidative stress response, inflammatory cytokine production, vasoconstriction and lysosomal activity. Analysis of gene expression in plaque micro-dissected material revealed that the signature is strongly up-regulated in macrophage-rich regions and down-regulated in regions with high smooth muscle cell content. A smaller qPCR biomarker panel and inflammatory composite score (ICS) were developed to facilitate clinical translation of discoveries from gene expression profiling. We found that ICS correlates with histological features related to plaque vulnerability. In addition, ICS is able to separate groups of plaques obtained from symptomatic and asymptomatic patients undergoing carotid endarerectomy. In summary, we identified a robust mRNA biomarker panel associated with histo-pathological as well as clinical hallmarks of vulnerable atherosclerotic plaque. This panel may be used as a diagnostic and prognostic tool in clinical setting to evaluate novel anti-atherosclerotic therapies. Total RNA from peripheral plaque (n=101) profiled in the Merck/Agilent 44k v1.1 against a reference pool of total RNA from 7 carotid plaques.
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