Characterization of H3K4me3 profile in circulating neutrophils from COPD patients [ChIP-Seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1167187 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR30835777.fastq.gz | Fastqsanger.gz | |||
| SRR30835778.fastq.gz | Fastqsanger.gz | |||
| SRR30835779.fastq.gz | Fastqsanger.gz | |||
| SRR30835780.fastq.gz | Fastqsanger.gz |
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Project description:The aim of this study is to comprehensively charatcterizethe transcriptional and epigenetic profile of circulating neutrophils from COPD patients and to explore correlations with neutrophils’ functional dysregulation and clinical disease parameters.
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Project description:Profile in circulating neutrophils from COPD patients
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Project description:Compared to circulating neutrophils (NC cells), splenic neutrophils (NBH cells) have an activated phenotype and enhanced B cell-helper activity. The transcriptome analysis of splenic and circulating neutrophils was performed to verify whether the enhanced B cell-helper activity of splenic neutrophils correlated with a specific gene signature. Unstimulated neutrophils were FACS sorted from the peripheral blood and spleen of six adult healthy subjects for RNA isolation and Agilent analysis.
2015-11-12 | E-GEOD-63298 | biostudies-arrayexpress
Project description:Compared to circulating neutrophils (NC cells), splenic neutrophils (NBH cells) have an activated phenotype and enhanced B cell-helper activity. The transcriptome analysis of splenic and circulating neutrophils was performed to verify whether the enhanced B cell-helper activity of splenic neutrophils correlated with a specific gene signature.
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Project description:Although the accumulation of neutrophils in the lungs and airways is common to many inflammatory lung diseases, including acute lung injury, the alterations that neutrophils undergo as they leave the peripheral circulation and migrate into the lungs have not been well characterized. Human volunteers were exposed to endotoxin by bronchoscopic instillation. The resulting air space neutrophil accumulation and peripheral blood neutrophils were isolated 16 h later, compared with circulating neutrophils isolated before or after to the pulmonary endotoxin exposure, and compared with circulating neutrophils exposed to endotoxin in vitro. Microarray analysis was performed on air space, circulatory, and in vitro endotoxin-stimulated neutrophils. Functional analysis included the determination of neutrophil apoptosis, chemotaxis, release of cytokines and growth factors, and superoxide anion release. Dramatic gene expression differences were apparent between air space and circulating neutrophils: approximately 15% of expressed genes have altered expression levels, including broad increases in inflammatory- and chemotaxis-related genes, as well as antiapoptotic and IKK-activating pathways. Functional analysis of air space compared with circulating neutrophils showed increased superoxide release, diminished apoptosis, decreased IL-8-induced chemotaxis, and a pattern of IL-8, macrophage inflammatory protein-1beta, monocyte chemoattractant protein-1, and tumor necrosis factor-alpha release different from either unstimulated or LPS-stimulated circulating neutrophils. Many of these changes are not elicited by in vitro treatment with endotoxin. Limited differences were detected between circulating neutrophils isolated before and 16 h after pulmonary endotoxin instillation. These results suggest that neutrophils sequestered in the lung become fundamentally different from those resident in the circulation, and this difference is distinct from in vitro activation with endotoxin.
2007-10-02 | E-GEOD-2322 | biostudies-arrayexpress
Project description:Polymorphonuclear cells (neutrophils) play an important role in the systemic inflammatory response syndrome and the development of sepsis. These cells are essential for the defense against microorganisms, but may also cause tissue damage. Therefore, neutrophil numbers and activity are considered to be tightly regulated. Previous studies have investigated gene transcription during experimental endotoxemia in whole blood and peripheral blood mononuclear cells. However, the gene transcription response of the circulating pool of neutrophils to systemic inflammatory stimulation in vivo is currently unclear. We examined neutrophil gene transcription kinetics in healthy human subjects (n=4) administered a single dose of endotoxin (LPS, 2 ng/kg iv). In addition, freshly isolated neutrophils were stimulated ex vivo with LPS, TNFM-NM-1, G-CSF and GM-CSF to identify stimulus-specific gene transcription responses. Whole transcriptome microarray analysis of circulating neutrophils at 2, 4 and 6 hours after LPS infusion revealed activation of inflammatory networks which are involved in signaling of TNFM-NM-1 and IL-1M-NM-1 and IL-1M-NM-2. The transcriptome profile of inflammatory activated neutrophils in vivo reflects extended survival and regulation of inflammatory responses. We show that these changes in neutrophil transcriptome are most likely due to a combination of early activation of circulating neutrophils by TNFM-NM-1 and G-CSF and a mobilization of young neutrophils from the bone marrow. After LPS infusion blood was taken at t=0, t=2, t=4 and t=6 hours. Neutrophils were isolated and gene expression of these cells was assessed. T=2, t=4 and t=6 were related to t=0 as control condition
2012-06-04 | E-GEOD-35590 | biostudies-arrayexpress
Project description:Background: CD8 cells seem to play an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, relatively little is known about their phenotype and function. Aims: To define the transcriptome of pulmonary CD8 cells in COPD and compare to paired circulating CD8 cells and smoker control pulmonary CD8 cells. COPD was defined according to the Global initiative for chronic Obstructive Lung Disease guidelines. Severity of disease was defined according to the patients lung function. In particular the forced evpiratroy volume in 1 second (FEV1).
2013-08-01 | E-MTAB-1688 | biostudies-arrayexpress
Project description:Colorectal cancer represents a major public health problem in France because of its high incidence and severe prognosis. Early stages of the disease are well know and have justified the establishment of a mass screening strategy. Unfortunately, the factors determining the progression to metastatic disease about them much harder to grasp. Various prognostic factors and predictors of treatment response have been identified and are being used but most of them are In practice, they are sometimes coarse and relatively little discriminant for patients.
It is now possible to directly quantify the amount of circulating tumor cells in peripheral blood. Quantification of circulating tumor cells beyond a threshold of 3 cells/7,5 ml has been established as a major prognostic factor, and the rapid decrease in the number of these cells under treatment is also a predictor of response for patients suffering from metastatic colorectal cancer . Furthermore, it has also been shown that the quality and importance of the systemic and peritumoral inflammatory response in carcinomas, including colorectal, played a key role in the prognosis of patients. In particular, the presence of high levels of blood neutrophils has been raised by many studies as being followed by a poorer prognosis.
However, the correlation between the presence of circulating tumor cells and high levels of neutrophils has never been studied. There is a rational to assume that this association exists, and secondly that the presence of circulating tumor cells in a proinflammatory environment represented by a high levels of blood neutrophils promotes metastasis by exerting a negative synergistic effect on the prognosis of patients.
The main objective of this pilot study is to find a correlation between the amount of circulating neutrophils and the presence of circulating tumor cells in patients with colon cancer metastatic unresectable non-pretreated. The secondary objective is to investigate whether this association results in a negative synergistic effect in terms of progression-free survival and survival to one year. This is a non-interventional study. The investigators expect the inclusion in one year of thirty patients in two centers (University Hospital Centre Antoine Lacassagne Nice) to achieve these goals.
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