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Single cell RNA sequencing of distal thrombus tissue from CTEPH patients

ABSTRACT: Single cell RNA sequencing of distal thrombus tissue from CTEPH patients

PROVIDER: PRJNA929967 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23290213_1.fastq.gz	Fastqsanger.gz
	SRR23290213_2.fastq.gz	Fastqsanger.gz
	SRR23290214_1.fastq.gz	Fastqsanger.gz
	SRR23290214_2.fastq.gz	Fastqsanger.gz
	SRR23290215_1.fastq.gz	Fastqsanger.gz

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Single cell RNA sequencing of distal thrombus tissue from CTEPH patients

Project description:Our current understanding of CTEPH pathobiology is primarily derived from cell-based studies limited by the use of specific cell markers or phenotypic modulation in cell culture. Therefore, our main objective is to identify the multiple cell types that comprise the CTEPH thrombus and to study their dysfunction. Here we used single cell RNA sequencing (scRNAseq) of tissue removed at the time of pulmonary endarterectomy (PEA) surgery from five patients to identify the multiple cell types. Our scRNAseq identify the multiple cell types including macrophages, T cells, and smooth muscle cells, that comprise CTEPH thrombus. Notably, multiple macrophage subclusters were identified but broadly split into two categories, with the larger group characterized by an upregulation of inflammatory signaling predicted to promote pulmonary vascular remodeling. Both CD4+ and CD8+ T cells were identified and likely contribute to chronic inflammation in CTEPH. Smooth muscle cells were a heterogeneous population, with a cluster of myofibroblasts that express markers of fibrosis and are predicted to arise from other smooth muscle cell clusters based on pseudotime analysis. Lastly, our analysis identified protease-activated receptor 1 (PAR1) as a potential therapeutic target that links thrombosis to chronic PE in CTEPH

2023-02-07 | GSE224143 | GEO

Gene expression profile at single cell level of pulmonary endarterectomy surgical specimens from chronic thromboembolic pulmonary hypertension (CTEPH)

Project description:Endothelial cells are implicated in delayed thrombus resolution. We use single cell RNA sequencing of CTEPH surgical specimens to assess endothelial cell phenotypes that contribute to delayed thrombus resolution.

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Transcriptome profile of fibroblasts in chronic thromboembolic pulmonary hypertension

Project description:The hallmark of chronic thromboembolic pulmonary hypertension (CTEPH) is fibrotic transformation of pulmonary arterial thrombus, leading to mechanical obstruction of pulmonary arteries. We report the transcriptome profile of fibroblasts isolated from pairs of CTEPH thrombus and pulmonary artery adventitia of the same patient. Fibroblasts isolated from CTEPH thrombus demonstrated upregulation of genes associated with the TGF-β pathway indicating that TGF-β upregulation is associated with the intravascular remodeling process.

2020-12-31 | GSE149413 | GEO

RNA sequencing for cancer tissues and adjacent tissues of third-stage rectal cancer patients with and without blood vascular thrombus

Project description:The Agilent Human Gene Expression(8*60K，Design ID：039494) was used in this experiment of sequencing of the 12 samples. A total of 12 tissues were sequenced from adjacent and cancerous tissues of 6 patients with TNM stage 3 colon cancer. Three patients had cancer thrombus and three patients had no cancer thrombus.

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Comparing CTEPH to Control and IPAH pulmonary arteries

Project description:Samples surgically extracted from CTEPH pulmonary arteries were compared to post-transplant pulmonary arteries from IPAH and failed donor pulmonary arteries from controls The goal was to determine if altered gene expression in CTEPH associated with development of chronic thrombi

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Differential expression of lncRNAs enriched in coronary thrombus-derived exosomes from AMI patients relative to serum patients with AMI and their functional differences

Project description:Purpose: to detect the expression differences of Long chain non coding RNA(Lnc RNA) in exosomes derived from Thrombus-derived exosomes in AMI patients, healthy human serum-source exosomes and AMI patients serum-source exosomes. Methods: Total RNA containing Long chain non coding RNA was extracted from Thrombus-derived exosomes in AMI patients. Use Agilent lncRNA array for lncRNA analysis. Each lncRNA was repeatedly detected by the probe 30 times. The array also contains 2164 Agilent control probes. Agilent Feature Extraction (Agilent) was used to analyze the lncRNA array data for data aggregation, standardization and quality control. Perform the default 90th percentile normalization method for date preprocessing. To select differentially expressed genes, we used thresholds of ≥2 and ≤−2 fold change, and the Benjamini-Hochberg corrected p vlaue was 0.05. Results: Compared with the Normal group, there were 2148 lncRNAs up-regulated and 2415 lncRNAs down-regulated in the serum group, and 2615 lncRNAs up-regulated and 452 lncRNAs down-regulated in the thrombus group. Compared with the serum group, there were 1374 lncRNAs up-regulated and 1218 lncRNAs down-regulated in the thrombus group. Conclusion: The 2615 lncRNAs upregulated relative to the Noormal group are candidates for regulatory targets of thrombosis-related regulatory pathways.

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Non-invasive approach for evaluation of CTEPH using extracellular vesicle-associated small non-coding RNA

Project description:The aim of this study was to determine whether extracellular vesicle (EV)-associated small non-coding RNAs (sncRNAs) have potential as biomarkers for chronic thromboembolic pulmonary hypertension (CTEPH). EVs were isolated using different methods from serum of 23 CTEPH patients and 23 controls. EV-associated RNAs were analysed by next-generation sequencing using the TrueQuant method for molecular barcoding, and differentially expressed sncRNAs were validated by qRT-PCR. We identified 18 miRNAs and 21 piRNAs or piRNA clusters that were differentially expressed in CTEPH patients compared with the control group. Bioinformatic analysis predicted a contribution of these piRNAs to the progression of cardiac and vascular remodelling. Furthermore, the expression levels of DQ593039 correlated with clinically meaningful parameters such as mean pulmonary arterial pressure, pulmonary vascular resistance, right ventricular systolic pressure, and levels of N-terminal pro-brain natriuretic peptide. In summary, EV-associated piRNA DQ593039 shows promise as biomarker and may be a potential therapeutic target for CTEPH.

2019-12-31 | GSE138107 | GEO

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Project description:To better understand the molecular mechanisms of right ventriuclar dysfunction in CTEPH pig model, a RNA sequencing analysis was performed in RV tissues collected from 5 CTEPH pigs and 5 sham opereted pigs.

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Proteomic analysis of ccRCC thrombus.

Project description:Proteomic analysis of ccRCC thrombus and tumors derived from patients.

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Differential gene expression in thrombus-derived white blood cells of patients with acute coronary syndrome

Project description:Inflammatory mechanisms and immune cells are involved in acute coronary syndromes (ACS) and may lead to acute plaque rupture. However, the local expression of the different genes potentially involved is largely unknown. We therefore performed an Affymetrix analysis of genes expressed in white blood cells obtained from an occluding coronary thrombus or peripheral blood of patients with ST-elevation myocardial infarction.

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