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Targeting inflammation with chimeric antigen receptor macrophages using a signal switch

GSE250551 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2025/04/23 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 32 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
32 samples: 8 conditions, mostly with about 4 replicates eachGroups 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
Targeting inflammation with chimeric antigen receptor macrophages using a signal switchNature biomedical engineering · 2025
Summary (written by the submitters)
Chimeric antigen receptor-T (CAR-T) cell immunotherapy has shown great success in clinical cancer, bringing hope that applying CAR strategies to other immune cell lineages may be beneficial in other clinical settings. We developed a CAR-macrophage (CAR-M) that recognizes the major inflammatory molecule TNF-α and activates an intracellular IL-4 signaling pathway, thereby programming engineered macrophages for an anti-inflammatory function.
Read the full summary ↓
Infused CAR-Ms switched to an anti-inflammatory phenotype in inflamed kidney and attenuated kidney ischemia reperfusion injury (IRI). The anti-inflammatory phenotype of infused CAR-Ms switched off during the recovery phase of kidney IRI, coinciding with the disappearance of TNF-α. In Adriamycin-induced nephropathy, a model of chronic kidney disease, infused CAR-Ms maintained an anti-inflammatory phenotype for several weeks in response to sustained high levels of TNF-α, resulting in an anti-inflammatory milieu that improved kidney function and structure. CAR-Ms also effectively reduced tissue injury in another organ, liver. The CAR-M design, utilizing signal switching, holds promise for the treatment of a broad range of acute and chronic inflammatory diseases.
Published in
Targeting inflammation with chimeric antigen receptor macrophages using a signal switch
Cao Q, Wang Y, Chen J et al. · Nature biomedical engineering 2025 · PMID 40335685 · doi:10.1038/s41551-025-01387-8
This dataset
Open GSE250551 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 GSE250551_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 PRJNA1050807 and SRA study SRP479019. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40335685) ↗
Study design
8 conditions, mostly with about 4 replicates each
macrophage, control, ×4 macrophage, M1, ×4 macrophage, M2, ×4 macrophage, CAR.M, ×4 macrophage, CAR.M.TNF-a, ×4 macrophage, CARΔ-M, ×4 macrophage, CARΔ-M.TNF-a, ×4 macrophage, TNF-a , ×4

Supports a between-group comparison across 32 samples.

How we read this: 8 replicated groups read from 32 sample titles; they account for 32 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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