Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Transcriptional and Phenotypic Characteristics that Define Alveolar Macrophage Subsets in Acute Hypoxemic Respiratory Failure

ABSTRACT: The Transcriptional and Phenotypic Characteristics that Define Alveolar Macrophage Subsets in Acute Hypoxemic Respiratory Failure

PROVIDER: PRJNA983740 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

The Transcriptional and Phenotypic Characteristics that Define Alveolar Macrophage Subsets in Acute Hypoxemic Respiratory Failure

Project description:The transcriptional and phenotypic characteristics that define alveolar monocyte and macrophage subsets in acute hypoxemic respiratory failure (AHRF) are poorly understood. We applied CITE-seq (single-cell RNA-sequencing + cell-surface protein quantification) to bronchoalveolar lavage fluid and peripheral blood cells longitudinally collected from subjects with AHRF to identify novel alveolar monocyte/macrophage subsets, and then validated their identity in an external cohort using flow cytometry. We identified 2 monocyte and 6 macrophage subsets in alveolar samples using CITE-seq data. Some of the subsets had similar transcriptional profiles as those reported in healthy subjects (metallothionein genes) or patients with COVID-19 (LGMN-expressing). We also identified novel subsets with transcriptional signatures that straddled previously reported monocyte and macrophage subsets. We used information from CITE-seq to determine cell-surface proteins that distinguish transcriptional subsets (CD14, CD163, CD123, CD71, CD48, CD86, and CD44). In the external cohort, we found a higher proportion of CD163/LGMN alveolar macrophages was associated with mortality. We report a parsimonious set of cell-surface proteins that can distinguish alveolar monocyte/macrophage subsets using scalable approaches that can be applied to clinical cohorts.

2023-10-10 | GSE234918 | GEO

Characterization of Alveolar macrophage subsets infected by Cryptococcus neoformans

Project description:We examined four subsets of alveolar macrophages differentiated by CXCL2 expression and FLT3 fate mapping induced by Cryptococcus neoformans infection. These four subpopulations have distinct mRNA expression pattern indicating the heterogenity within alveolar macrophages.

2020-06-08 | GSE133026 | GEO

Characterization of Alveolar macrophage subsets infected by Cryptococcus neoformans

Project description:Characterization of Alveolar macrophage subsets infected by Cryptococcus neoformans

| PRJNA549708 | ENA

Characterization of Alveolar macrophage subsets infected by Cryptococcus neoformans [ATAC-seq]

Project description:Characterization of Alveolar macrophage subsets infected by Cryptococcus neoformans [ATAC-seq]

| PRJNA609745 | ENA

B cell characteristics define HCV reinfection outcome

Project description:B cell characteristics define HCV reinfection outcome

| PRJNA1123702 | ENA

Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets.

Project description:The recognized diversity of innate lymphoid cells (ILCs) is rapidly expanding. Three ILC classes have emerged, ILC1, ILC2 and ILC3, with ILC1 and ILC3 including several subsets. The classification of some subsets is unclear, and it remains controversial whether natural killer (NK) cells and ILC1 cells are distinct cell types. To address these issues, we analyzed gene expression in ILCs and NK cells from mouse small intestine, spleen and liver, as part of the Immunological Genome Project. The results showed unique gene-expression patterns for some ILCs and overlapping patterns for ILC1 cells and NK cells, whereas other ILC subsets remained indistinguishable. We identified a transcriptional program shared by small intestine ILCs and a core ILC signature. We revealed and discuss transcripts that suggest previously unknown functions and developmental paths for ILCs.

| S-EPMC4372143 | biostudies-literature

Characterization of Alveolar macrophage subsets infected by Cryptococcus neoformans [ATAC-seq]

Project description:We examined two subpopulations of alveolar macrophages differentiated by CXCL2 expression stimulated by Cryptococcus neoformans. The two subpopulations have distinct mRNA expression pattern indicating the heterogenity within alveolar macrophages.

2020-06-08 | GSE146234 | GEO

Epithelial Yap/Taz are required for functional alveolar regeneration following acute lung injury

Project description:A hallmark of idiopathic pulmonary fibrosis (IPF) and other interstitial lung diseases is dysregulated repair of the alveolar epithelium. The Hippo pathway effector transcription factors YAP and TAZ are implicated as essential for type 1 and type 2 alveolar epithelial cell (AT1 and AT2) differentiation in the developing lung, yet aberrant activation of YAP/TAZ is a prominent feature of the dysregulated alveolar epithelium in IPF. In these studies, we sought to define the functional role of YAP/TAZ activity during alveolar regeneration. We demonstrated that Yap and Taz are normally activated in AT2 cells shortly after injury, and deletion of Yap/Taz in AT2 cells led to pathologic alveolar remodeling, failure of AT2 to AT1 cell differentiation, increased collagen deposition, exaggerated neutrophilic inflammation, and increased mortality following injury induced by a single dose of bleomycin. Loss of Yap/Taz activity prior to a LPS injury prevented AT1 cell regeneration, led to intra-alveolar collagen deposition, and resulted in persistent innate inflammation. Together these findings established that AT2 cell Yap/Taz activity is essential for functional alveolar epithelial repair and prevention of fibrotic remodeling.

2023-11-15 | GSE243135 | GEO

Global gene expression profiling of cardiac dendritic cells subsets

Project description:Innate and adaptive immune cells modulate heart failure pathogenesis during viral myocarditis, yet their identity and functions remain poorly defined. In this study we characterized the phenotype, life-cycle and function of different conventional dendritic cells (cDC) populations in the heart, with focus on the 2 major subsets (CD103+ and CD11b+), which differentially rely on local proliferation and precursor recruitment to maintain tissue residency. Following viral infection of the myocardium, cDCs accumulate in the heart coincident with monocyte infiltration and loss of resident reparative embryonic-derived cardiac macrophages. cDC depletion abrogates antigen-specific CD8+ T cell proliferative expansion, transforming subclinical cardiac injury to overt heart failure. Importantly, these effects are mediated by BATF3-dependent CD103+ cDCs. Collectively, our findings definitively identify resident cardiac cDC subsets, define their origins, and implicate an essential role for CD103+ cDCs in antigen-specific T cell responses during viral myocarditis.

2018-01-01 | GSE102828 | GEO

Alveolar Injury and Regeneration Following Deletion of ABCA3

Project description:Surfactant deficiency, diffuse alveolar damage and respiratory failure caused by loss of Abca3 in AT2 cells was followed by remarkable proliferation of alveolar cells and selective survival of ABCA3 sufficient cells resulting in regeneration of alveolar structure and function, providing the conceptual framework for the development of therapies to ameliorate lung diseases caused by mutations in ABCA3 and other genes critical for AT2 cell function or surfactant homeostasis.

2018-02-15 | GSE103506 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data