Single-Cell Analysis Reveals the Range of Transcriptional States of Circulating Human Neutrophils
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ABSTRACT:
PROVIDER: PRJNA778206 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16816712.fastq.gz | Fastqsanger.gz | |||
| SRR16816713.fastq.gz | Fastqsanger.gz | |||
| SRR16816714.fastq.gz | Fastqsanger.gz | |||
| SRR16816715.fastq.gz | Fastqsanger.gz | |||
| SRR16816716.fastq.gz | Fastqsanger.gz |
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Project description:Neutrophils are the most abundant leukocytesin human peripheral blood and are essential components of the innate immune system. Until recently, neutrophils were thought to be homogeneous and transcriptionally inactive, but both concepts are being challenged by a growing body of data. To date, neutrophils have been characterized based on discrete parameters like cell-surface markers, buoyancy, maturity, or tissue localization.Single-cell RNA sequencing (scRNA-seq) has been an important addition to the set of analytical tools, as itoffers an unbiased view of cells along a continuum of transcriptional states, including those that fall between theoretically more stable endpoints. However, the use of scRNA-seqto characterize transcriptional variation in neutrophils has proven technically difficult, explaining in part the paucity of published single-cell data on neutrophils compared to other celltypes. We report a modified analysis pipeline that substantially increases the detection of human neutrophils in scRNA-seq. We applied this pipeline to the study of > 185,000 human neutrophils. Our findings indicate that circulating human neutrophils are transcriptionally heterogeneous cells, which can be classified based on their transcriptional state into one of four clusters that are highly reproducible among healthy human subjects. We demonstrate that neutrophils shiftfrom relatively immature (Nh0) cells, through a transitional phenotype (Nh1), into one of two endpoints defined by either relative transcriptional inactivity (Nh2) or high expression oftype I interferon-induciblegenes (Nh3).Transitions among states are characterized by the expression of specific transcription factors. By simultaneouslymeasuring surface proteinand intracellular transcriptabundance at the single-cell level, we show that these four transcriptional subsets are independent of the canonical surface proteins that are commonly used to define and characterize human neutrophils.These findings provide a new view of human neutrophil heterogeneity, along a continuum of transcriptional states, with potential implications for the characterization of neutrophils in health and disease.
2022-05-24 | GSE188288 | GEO
Project description:Neutrophils are the most abundant leukocytes in human blood and are essential components of innate immunity. Until recently, neutrophils were considered homogeneous and transcriptionally inactive cells, but both concepts are being challenged. Single-cell RNA sequencing (scRNA-seq) offers an unbiased view of cells along a continuum of transcriptional states. However, the use of scRNA-seq to characterize neutrophils has proven technically difficult, explaining in part the paucity of published single-cell data on neutrophils. We have found that modifications to the data analysis pipeline, rather than to the existing scRNA-seq chemistries, can significantly increase the detection of human neutrophils in scRNA-seq. We have then applied a modified pipeline to the study of human peripheral blood neutrophils. Our findings indicate that circulating human neutrophils are transcriptionally heterogeneous cells, which can be classified into one of four transcriptional clusters that are reproducible among healthy human subjects. We demonstrate that peripheral blood neutrophils shift from relatively immature (Nh0) cells, through a transitional phenotype (Nh1), into one of two end points defined by either relative transcriptional inactivity (Nh2) or high expression of type I IFN-inducible genes (Nh3). Transitions among states are characterized by the expression of specific transcription factors. By simultaneously measuring surface proteins and intracellular transcripts at the single-cell level, we show that these transcriptional subsets are independent of the canonical surface proteins that are commonly used to define and characterize human neutrophils. These findings provide a new view of human neutrophil heterogeneity, with potential implications for the characterization of neutrophils in health and disease.
| S-EPMC9712146 | biostudies-literature
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: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:Neutrophils exhibited remarkable plasticity and heterogenicity in both homeostasis and pathology conditions. Here, we conducted a “multi-states” proteomics methodology to explore how neutrophils respond upon infection and inflammation stress including bacterial analog LPS, virus analog Poly(I:C), pro-inflammatory cytokine TNF-α, and PKC activator PMA challenge.
2024-12-23 | PXD059138 |
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: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: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.
2025-05-28 | GSE278206 | GEO
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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Project description:Profile in circulating neutrophils from COPD patients
| PRJNA1167183 | ENA