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Quorum sensing by Streptococcus pyogenes induces global inflammatory suppression in host macrophages

GSE289076 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2025/02/08 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples: 10 conditions, mostly in triplicateGroups 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
The Streptococcus pyogenes Rgg2/Rgg3 quorum sensing system causes global suppression of macrophage inflammatory programs via an intranuclear mechanismmBio · 2025
Summary (written by the submitters)
Streptococcus pyogenes or Group A Streptococcus (GAS), a significant human pathogen, employs quorum sensing (QS) systems to coordinate its behavior and genetic regulation to enhance survival. Our previous research established that one such QS system, the Rgg2/3 system, can suppress macrophage NFκB activity and production of pro-inflammatory cytokines.
Read the full summary ↓
Yet, the scope of suppression and the mechanism by which it occurs remain unknown. In this study, transcriptomic and phosphoproteomic approaches were used to address these unanswered questions. It was found that QS-ON GAS broadly suppressed most inflammatory transcriptional pathways, including those of NFκB, type I and type II interferon responses, and intracellular stress responses. Yet, we found that no alternative transcriptional programs were activated after QS-ON GAS infection. Additionally, phosphoproteomics showed no disruption in typical inflammatory pathways such as those related to NFκB and MAPK activation, which was confirmed by western blotting and translocation assays. Instead, the proteomic data highlighted a potential role for epigenetic mechanisms of inflammatory regulation. A role for epigenetic regulation in QS-mediated immunomodulation was validated using pharmacological inhibitors of histone and chromatin modifiers. These findings expand our understanding of QS-mediated suppression and of GAS virulence strategies that appear to employ atypical methods of restricting inflammation. Uncovering this mechanism will offer invaluable insight into GAS itself, as well as into understudied immunological pathways.
Published in
The Streptococcus pyogenes Rgg2/Rgg3 quorum sensing system causes global suppression of macrophage inflammatory programs via an intranuclear mechanism
Feldstein SF, Rahbari KM, Leonardo TR et al. · mBio 2025 · PMID 40996031 · doi:10.1128/mbio.00373-25
This dataset
Open GSE289076 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 GSE289076_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 PRJNA1221266 and SRA study SRP562368. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40996031) ↗
Study design
10 conditions, mostly in triplicate
Uninfected 2h ×3 Mix_2h ×3 Mix_4h ×3 Mix_8h ×3 Off_2h ×3 Off_4h ×3 Off_8h ×3 On_2h ×3 +2 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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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