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Probiotic Bacteria-Released Extracellular Vesicles Enhance Macrophage Phagocytosis in Polymicrobial Sepsis Through Activating the FPR1/2 Pathway

GSE274800 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/11/20 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 12 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
12 samples: 3 × BMDM-Ctrl vs 3 × BMDM-BEVpH5 vs 3 × BMDM-BEVpH6.5 vs 3 × BMDM-BEVpH8Groups 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
Probiotic bacteria-released extracellular vesicles enhance macrophage phagocytosis in polymicrobial sepsis by activating the FPR1/2 pathwayMolecular medicine (Cambridge, Mass.) · 2024
Summary (written by the submitters)
Background: Sepsis-induced organ failure and high mortality are largely ascribed to the failure of bacterial clearance from the infected tissues. Recently, probiotic bacteria-released extracellular vesicles (BEVs) have been implicated as critical mediators of intercellular communication which are widely involved in the regulation inflammatory response.
Read the full summary ↓
However, their functional role in macrophage phagocytosis during sepsis has never been explored. Methods: BEVs were collected from three different strains of probiotics including Lactobacillus plantarum WCFS1 (LP WCFS1), Lactobacillus rhamnosus Gorbach-Goldin (LGG), and Escherichia coli Nissle 1917 (EcN), or from LGG cultured under three pH conditions (pH5-acid, pH6.5-standard, pH8-akaline) through differential centrifugation, filtering, and ultracentrifugation of their culture supernatants. In vitro phagocytosis was measured in Raw264.7 and bone marrow-derived macrophages using pHrodo red E. coli BioParticles. The in vivo therapeutic effects of BEVs were tested using a feces-intraperitoneal-injection (FIP) model of polymicrobial sepsis. Results: LGG-derived EVs (BEVLGG) were the best among these three probiotics BEVs in stimulating macrophages to take up bacteria. Furthermore, BEVLGG collected from pH8 culture condition (BEVpH8) exhibited the strongest capacity of phagocytosis, compared with BEVpH5 and BEVpH6.5. Treatment of septic mice with BEVpH8 significantly prolonged animal survival, increased bacterial clearance from the blood, peritoneal lavage, and multiple organs, decreased serum levels of pro-inflammatory cytokines, alanine aminotransferase (ALT, marker of liver injury) and creatinine (Cr, marker of kidney injury), in comparison with control-treated septic mice. Mechanistically, RNA-seq and bioinformatic analysis identified that the FPR1/2 signaling was remarkably activated, along with its downstream pathways (PI3K-Akt-MARCO and NADPH-ROS) in BEVpH8-treated macrophages, compared with control cells. Accordingly, pre-addition of Boc2, a specific antagonist of FPR1/FPR2, to macrophages significantly attenuated BEVpH8-mediated phagocytosis, compared to controls. Conclusions: This study demonstrates that LGG-derived BEVs may have therapeutic effects against sepsis-induced organ injury and mortality through enhancing FPR1/2-mediated macrophage phagocytosis.
Published in
Probiotic bacteria-released extracellular vesicles enhance macrophage phagocytosis in polymicrobial sepsis by activating the FPR1/2 pathway
Zhu R, Zhang Y, Wang X et al. · Molecular medicine (Cambridge, Mass.) 2024 · PMID 39543493 · doi:10.1186/s10020-024-00959-9
This dataset
Open GSE274800 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 GSE274800_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1148074 and SRA study SRP526318. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39543493) ↗
Study design
3 × BMDM-Ctrl vs 3 × BMDM-BEVpH5 vs 3 × BMDM-BEVpH6.5 vs 3 × BMDM-BEVpH8

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

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