Ansari et al. 2022 (PRJNA858047)

General Details

Title Ribosome profiling (Ribo-Seq) and mRNA sequencing (RNA-Seq) of Human leukemia monocytic cell line (THP-1) cells upon treatment with LPS and LPS+dexamethasone (Dex).
Organism
Number of Samples 15
Release Date 2022/07/12 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP386079
ENA SRP386079
GEO GSE208041
BioProject PRJNA858047

Publication

Title
Authors Ansari SA, Dantoft W, Ruiz-Orera J, Syed AP, Blachut S, van Heesch S, Hübner N, Uhlenhaut NH
Journal Computational and structural biotechnology journal
Publication Date 2022
Abstract Glucocorticoids such as dexamethasone (Dex) are widely used to treat both acute and chronic inflammatory conditions. They regulate immune responses by dampening cell-mediated immunity in a glucocorticoid receptor (GR)-dependent manner, by suppressing the expression of pro-inflammatory cytokines and chemokines and by stimulating the expression of anti-inflammatory mediators. Despite its evident clinical benefit, the mechanistic underpinnings of the gene regulatory networks transcriptionally controlled by GR in a context-specific manner remain mysterious. Next generation sequencing methods such mRNA sequencing (RNA-seq) and Ribosome profiling (ribo-seq) provide tools to investigate the transcriptional and post-transcriptional mechanisms that govern gene expression. Here, we integrate matched RNA-seq data with ribo-seq data from human acute monocytic leukemia (THP-1) cells treated with the TLR4 ligand lipopolysaccharide (LPS) and with Dex, to investigate the global transcriptional and translational regulation (translational efficiency, ΔTE) of Dex-responsive genes. We find that the expression of most of the Dex-responsive genes are regulated at both the transcriptional and the post-transcriptional level, with the transcriptional changes intensified on the translational level. Overrepresentation pathway analysis combined with STRING protein network analysis and manual functional exploration, identified these genes to encode immune effectors and immunomodulators that contribute to macrophage-mediated immunity and to the maintenance of macrophage-mediated immune homeostasis. Further research into the translational regulatory network underlying the GR anti-inflammatory response could pave the way for the development of novel immunomodulatory therapeutic regimens with fewer undesirable side effects. © 2022 The Authors.
PMC PMC9582734
PMID 36284713
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR20106168 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106167 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106166 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106165 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106164 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106163 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106162 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106161 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106160 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106159 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106158 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106157 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106156 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106155 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
SRR20106154 PRJNA858047 Homo sapiens THP1 Ribo-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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