GEO series

Epigenetic silencing of interleukin-10 by host-derived oxidized phospholipids supports a lethal inflammatory response to infections supports a lethal inflammatory response to infections

GSE297479 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/08/06 Platform GPL24247

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, LPS, 3h, vs 3 × BMDM, LPS+oxPAPC, 3h, vs 3 × BMDM, LPS, 24h, vs 3 × BMDM, LPS+oxPAPC, 24h,Groups 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: Epigenetic silencing of interleukin-10 by host-derived oxidized phospholipids supports a lethal inflammatory response to infectionsImmunity · 2025

Summary (written by the submitters)

Phagocytes initiate immunity to invading microorganisms by detecting pathogen-associated molecular patterns via pattern recognition receptors. Pathogen encounter and consequent activation of the immune system cause tissue damage and release of host-derived damage-associated molecular patterns, contributing to shape immunity. How self-derived factors are sensed by phagocytes and impact the immune response remains poorly understood.

Read the full summary ↓

Here we demonstrate that, in mice and humans, host-derived oxidized phospholipids (oxPLs) are formed after microbial encounter. We show that oxPLs exacerbate inflammation without affecting pathogen burden. Mechanistically, oxPLs bind and inhibit AKT, potentiating the methionine cycle and the activity of the epigenetic writer enhancer of zeste homolog 2 (EZH2). EZH2 epigenetically dampens the pluripotent anti-inflammatory cytokine interleukin-10, contributing to death of the host. Overall, we found that host-derived oxPLs set the balance between protective and detrimental anti-microbial responses and that they can be prophylactically or therapeutically targeted to protect the host against deranged inflammation and immunopathology.

Published in

Epigenetic silencing of interleukin-10 by host-derived oxidized phospholipids supports a lethal inflammatory response to infections

Di Gioia M, Poli V, Tan PJ et al. · Immunity 2025 · PMID 40680750 · doi:10.1016/j.immuni.2025.06.017

This dataset

Open GSE297479 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 GSE297479_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 PRJNA1264981 and SRA study SRP586220. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40680750) ↗

Study design

3 × BMDM, LPS, 3h, vs 3 × BMDM, LPS+oxPAPC, 3h, vs 3 × BMDM, LPS, 24h, vs 3 × BMDM, LPS+oxPAPC, 24h,

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

GSM8992920 BMDM, LPS, 3h, rep 1 BMDM, LPS, 3h,
GSM8992921 BMDM, LPS, 3h, rep 2 BMDM, LPS, 3h,
GSM8992922 BMDM, LPS, 3h, rep 3 BMDM, LPS, 3h,
GSM8992923 BMDM, LPS+oxPAPC, 3h, rep 1 BMDM, LPS+oxPAPC, 3h,
GSM8992924 BMDM, LPS+oxPAPC, 3h, rep 2 BMDM, LPS+oxPAPC, 3h,
GSM8992925 BMDM, LPS+oxPAPC, 3h, rep 3 BMDM, LPS+oxPAPC, 3h,
GSM8992926 BMDM, LPS, 24h, rep 1 BMDM, LPS, 24h,
GSM8992927 BMDM, LPS, 24h, rep 2 BMDM, LPS, 24h,
GSM8992928 BMDM, LPS, 24h, rep 3 BMDM, LPS, 24h,
GSM8992929 BMDM, LPS+oxPAPC, 24h, rep 1 BMDM, LPS+oxPAPC, 24h,
GSM8992930 BMDM, LPS+oxPAPC, 24h, rep 2 BMDM, LPS+oxPAPC, 24h,
GSM8992931 BMDM, LPS+oxPAPC, 24h, rep 3 BMDM, LPS+oxPAPC, 24h,

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