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The immune landscape of the “deregulated host response” in sepsis: newly emerging MDSCs with high expression of CD47 leads to B cell suppression via App-CD74 signaling [RNA-seq]

GSE222996 Mus musculus (mouse) Single-cell RNA-seq 61 samples Submitted 2025/03/12 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 61 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
61 samples: 21 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
CD47-amyloid-β-CD74 signaling triggers adaptive immunosuppression in sepsisEMBO reports · 2025
Summary (written by the submitters)
Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. However, how this dysregulation occurs remains unclear. Herein, we used scRNA-seq to define the immune landscape of infection and found that when sepsis occurred, adaptive immunity was acutely and strongly suppressed, which manifested as a striking increase in the number of myeloidderived suppressor cells (MDSCs), a decrease in the number of lymphocytes and drastic downregulation of the expression levels of B-cell-related genes and MHC class II molecules.
Read the full summary ↓
Transcriptomic analysis showed that systemic immunosuppression occurred not only in the peripheral blood but also in all other immune compartments, including the spleen, lymph nodes, and bone marrow. Patients diagnosed with infection in the emergency department with extremely low expression levels of adaptive immunity related genes had a high risk for developing sepsis. CD47 was identified as the key molecule that triggered this immunosuppression by inducing the production of amyloid-b precursor protein (App), which caused adaptive immunosuppression via B-cell suppression. Our study outlines a framework for how the dysregulated host response occurs and provides translational opportunities for sepsis immunotherapies
Published in
CD47-amyloid-β-CD74 signaling triggers adaptive immunosuppression in sepsis
Feng Z, Wang L, Li Y et al. · EMBO reports 2025 · PMID 40185975 · doi:10.1038/s44319-025-00442-4
This dataset
Open GSE222996 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 GSE222996_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA924677 and SRA study SRP417818. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40185975) ↗
Study design
21 conditions, mostly in triplicate
C_Kidney ×3 C_Live ×3 M_Kidney ×3 Sham_Kidney ×3 Sham_Live ×3 Sham_Lung ×3 M_PBMC ×3 M_LN ×3 +15 more

Supports a between-group comparison across 59 samples.

How we read this: 21 replicated groups read from 61 sample titles; they account for 59 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

+ 21 more — browse all 61 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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