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Opposing Regulation of TNF Responses and IL-1b+ Macrophages by PGE2-cAMP Signaling and IFN-g [RNA-seq]

GSE272019 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2025/03/27 Platform GPL24676Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 48 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
Homo sapiens (human)
Samples
48 samples: 16 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
Opposing regulation of TNF responses by IFN-γ and a PGE2-cAMP axis that is apparent in rheumatoid and immune checkpoint inhibitor-induced arthritis human IL-1β+ macrophageseLife · 2025
Summary (written by the submitters)
IL-1b-expressing macrophages elicited by cooperation between PGE2 and TNF signaling have been identified and proposed to be pathogenic in rheumatoid arthritis (RA) and pancreatic cancer, but mechanisms that induce these cells and the extent to which they contribute to arthritic phenotypes are not known. In this study we used an integrated transcriptomic and epigenomic analysis in primary human monocytes to study PGE2-TNF crosstalk, and how it is regulated by IFN-g, as occurs in RA synovial macrophages.
Read the full summary ↓
We identified a (TNF + PGE2)-induced gene expression signature that is enriched in RA and post-immune checkpoint blockade arthritis macrophage subsets and includes genes in pathogenic IL-1, Notch and neutrophil chemokine pathways. This gene expression signature, which is distinct from canonical inflammatory NF-kB target genes such as TNF, IL6 and IL12B, was driven by cooperation of PGE2-induced AP-1, CEBP and NR4A family transcription factors with TNF-induced NF-kB activity. Unexpectedly, IFN-g suppressed induction AP-1, CEBP and NR4A activity to ablate induction of IL-1, Notch and neutrophil chemokine genes, while promoting expression of distinct inflammatory genes such as TNF and T cell chemokines like CXCL10. These results reveal the basis for synergistic induction of inflammatory genes by PGE2 and TNF, and a novel regulatory axis whereby IFN-g and PGE2 oppose each other to determine the balance between two distinct TNF-induced inflammatory gene expression programs.
Published in
Opposing regulation of TNF responses by IFN-γ and a PGE2-cAMP axis that is apparent in rheumatoid and immune checkpoint inhibitor-induced arthritis human IL-1β+ macrophages
Sokhi UK, Yuan R, Mishra B et al. · eLife 2025 · PMID 40662950 · doi:10.7554/eLife.104367
This dataset
Open GSE272019 in finder → Find more human 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 GSE272019_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 PRJNA1134654 and SRA study SRP519312. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40662950) ↗
Study design
16 conditions, mostly in triplicate
CTRL_3h ×3 CTRL_24h ×3 PGE_3h ×3 PGE_24h ×3 TNF_3h ×3 TNF_24h ×3 TNF-PGE_3h ×3 TNF-PGE_24h ×3 +8 more

Supports a between-group comparison across 48 samples.

How we read this: 16 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.