GEO series

Decoding the Multiple Functions of ZBP1 in the Mechanism of Sepsis-Induced Acute Lung Injury

GSE278767 Mus musculus (mouse) Single-cell RNA-seq 14 samples Submitted 2024/10/10 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 14 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 14 samples: 4 × WT CLP24h vs 4 × ZBP1ko Sham vs 3 × WT Sham vs 3 × ZBP1ko CLPGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Decoding the multiple functions of ZBP1 in the mechanism of sepsis-induced acute lung injuryCommunications biology · 2024

Summary (written by the submitters)

Sepsis-induced acute lung injury (ALI), characterized by severe hypoxemia and pulmonary leakage, remains a leading cause of mortality in intensive care units. The exacerbation of ALI during sepsis is largely attributed to uncontrolled inflammatory responses and endothelial dysfunction. Emerging evidences suggest an important role of Z-DNA binding protein 1 (ZBP1) as a sensor in innate immune to drive inflammatory signaling and cell death during infections.

Read the full summary ↓

However, the role of ZBP1 in sepsis-induced ALI has yet to be defined. We utilized ZBP1 knockout mice and combined single-cell RNA sequencing with experimental validation to investigate ZBP1's roles in the regulation of macrophages and lung endothelial cells during sepsis. We demonstrate that in sepsis, ZBP1 deficiency in macrophages reduces mitochondrial damage and inhibits glycolysis, thereby altering the metabolic status of macrophages. Consequently, this metabolic shift leads to a reduction in the differentiation of macrophages into pro-inflammatory states and decreases macrophage pyroptosis triggered by activation of the NLRP3 inflammasome. These changes significantly weaken the inflammatory signaling pathways between macrophages and endothelial cells, and alleviate endothelial dysfunction and cellular damage. These findings reveal important roles for ZBP1 in mediating multiple pathological processes involved in sepsis-induced ALI by modulating the functional states of macrophages and endothelial cells, thereby highlighting its potential as a promising therapeutic target.

Published in

Decoding the multiple functions of ZBP1 in the mechanism of sepsis-induced acute lung injury

Gong T, Fu Y, Wang Q et al. · Communications biology 2024 · PMID 39433574 · doi:10.1038/s42003-024-07072-x

This dataset

Open GSE278767 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE278767_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1168866 and SRA study SRP536571. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39433574) ↗

Study design

4 × WT CLP24h vs 4 × ZBP1ko Sham vs 3 × WT Sham vs 3 × ZBP1ko CLP

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8554645 WT Sham_1 WT Sham
GSM8554646 WT Sham_2 WT Sham
GSM8554647 WT Sham_3 WT Sham
GSM8554648 WT CLP24h_1 WT CLP24h
GSM8554649 WT CLP24h_2 WT CLP24h
GSM8554650 WT CLP24h_3 WT CLP24h
GSM8554651 WT CLP24h_4 WT CLP24h
GSM8554652 ZBP1ko Sham_1 ZBP1ko Sham
GSM8554653 ZBP1ko Sham_2 ZBP1ko Sham
GSM8554654 ZBP1ko Sham_3 ZBP1ko Sham
GSM8554655 ZBP1ko Sham_4 ZBP1ko Sham
GSM8554656 ZBP1ko CLP_1 ZBP1ko CLP
GSM8554657 ZBP1ko CLP_2 ZBP1ko CLP
GSM8554658 ZBP1ko CLP_3 ZBP1ko CLP

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