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RNA sequencing of zbtb46+ conventional dendritic cells in the mediastinal lymph nodes of naïve and previously influenza infected memory mice

ABSTRACT: Purpose: The goal of this study was to compare the transcriptome of conventional dendritic cells (cDC) isolated from the mediastinal lymph nodes (medLN) of mice that were uninfected (naïve) or had been infected 25 days previously with X31 (memory) Methods: medLN cDC were isolated from naïve and memory mice in biological triplicates and RNA was sequenced using Illumina Novaseq 6000. Reads were mapped to mouse genome using Kallisto and differential gene expression determined by DESeq2 Results: 61 differentially expressed genes were found between naive and memory medLN cDC after a workflow that filtered out the bottom third of genes by number of reads and had a padj ≤0.05 and fold change ≥2.

ORGANISM(S): Mus musculus

PROVIDER: GSE144755 | GEO | 2020/09/23

REPOSITORIES: GEO

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Project description:The biological functions of epicardial adipose tissue (EAT) remain largely elusive. However, the proximity of EAT to the coronary arteries suggests a role in the pathogenesis of coronary artery disease (CAD). Objectives of this study were to identify genes that are up- or down-regulated among three adipose tissues (AT), namely EAT, mediastinal (MAT) and subcutaneous (SAT) and to study their possible relationships with the development of cardiovascular diseases. Samples were collected from patients undergoing coronary artery bypass grafting surgeries. Gene expression was evaluated in all three AT depots of six men using the lllumina® HumanWG-6 v3.0 expression BeadChips. Twenty-two and 73 genes were up-regulated in EAT compared to mediastinal and subcutaneous AT, respectively. Ninety-four genes were down-regulated in EAT compared to subcutaneous adipose depot. However, none were significantly down-regulated in EAT compared to mediastinal fat. More specifically, the expression of the adenosine A1 receptor (ADORA1), involved in myocardial ischemia, was significantly up-regulated in EAT. Levels of the prostaglandin D2 synthase (PTGDS) gene, recently associated with the progression of atherosclerosis, were significantly different in the three pairwise comparisons (epicardial > mediastinal > subcutaneous). The results of ADORA1 and PTGDS were confirmed by qPCR in 25 biological replicates. Overall, the transcriptional profiles of EAT and MAT were similar compared to the subcutaneous compartment. Despite this similarity, two genes involved in cardiovascular diseases, ADORA1 and PTGDS, were up-regulated in EAT. These results provide insights about the biology of EAT and its potential implication in CAD. Samples of epicardial, mediastinal and subscutaneous adipose tissue were collected from the chest of 6 male patients undergoing coronary artery bypass grafting surgeries. The RNA was labeled and hybridized using a standard Illumina protocol (https://icom.illumina.com/Login?ReturnUrl=%2ficom%2fsoftware.ilmn%3fid%3d214&id=214). Three pairwise comparison among the three adipose tissue were made using significance analysis of microarrays.

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RNA sequencing of zbtb46+ conventional dendritic cells in the mediastinal lymph nodes of naïve and previously influenza infected memory mice

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