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Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases

ABSTRACT: Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases

PROVIDER: PRJNA766030 | ENA |

REPOSITORIES: ENA

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Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases

Project description:Purpose: Using single-cell RNA sequencing to explore the common and unique pathways between progressive (SarcP) and remitting (SarcR) sarcoidosis as well as chronic beryllium disease (CBD) and sarcoidosis, focusing on macrophages and macrophages subpopulations (recruited vs. resident). Methods: We used scRNA-seq to analyze BAL cells from SarcP (N=2), SarcR (N=2), and CBD (N=3) compared to beryllium sensitized non-diseased subjects (BeS; N=2) or healthy control (Con; N=4). The controls were from Mould KJ, et al. Airspace Macrophages and Monocytes Exist in Transcriptionally Distinct Subsets in Healthy Adults. Am J Respir Crit Care Med 2020. We used the R package Seurat to project cells unto Uniform Manifold Approximation and Projection (UMAP) 2D space, identify cell clusters, and detect differentially expressed (DE) genes. Results: We focused our analysis on macrophages (excluding cell clusters going through the cell cycle). We first compared disease groups to healthy control Using False Discovery Rate (FDR) adjusted p<0.05 and absolute log fold change (log FC)>0.25. We identified 191, 242, and 234 DE genes within all macrophages for the comparisons of SarcP vs. Con, SarcR vs. Con, and CBD vs. Con, respectively, with 82 genes common to all three comparisons; 47 out of the 82 genes were common to all comparisons in regards to recruited macrophages. Conclusions: We focused this first single-cell transcriptome study in granulomatous lung disease on macrophages. This study offers investigators cell-specific transcriptional changes (genes and networks/pathways) to consider mechanisms of granulomatous disease and as potential drug targets.

2021-09-27 | GSE184735 | GEO

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Project description:Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization

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Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization [RNA-Seq]

Project description:Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization [RNA-Seq]

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Transcriptional Profiling of Pediatric Cholestatic Livers Identifies Three Distinct Macrophage Populations

Project description:Transcriptional Profiling of Pediatric Cholestatic Livers Identifies Three Distinct Macrophage Populations

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Genome wide gene expression analysis of chronic granulomatous disease patients

Project description:Whole blood was collected from chronic granulomatous patients, carriers and healthy controls.

2014-11-01 | GSE44969 | GEO

DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease [sarcexp]

Project description:The goal of this study was to investigate and correlate differential methylation and expression in cells from the target organ in non-infectious granulomatous lung diseases, specifically sarcoidosis and chronic beryllium disease (CBD). To that end, cells were collected from patients via bronchoalveolar lavage (BAL), and extracted nucleic acids were hybridized to genome-wide arrays. We conclude that there are many genes that are both differentially methylated and expressed in the BAL fluid of patients with granulomatous lung disease. We identified 2,726 differentially methylated CpGs mapping to 1,944 unique genes when comparing CBD patients to beryllium-sensitized (BeS) individuals without disease. 69% of these genes were also differentially expressed in CBD. Sarcoidosis patients exhibited directional consistency at many loci, but genome-wide significance was not achieved, likely due to heterogeneity in the patient population.

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