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CX3CR1+ Synovial Macrophages for Barrier Restore in Rheumatoid Arthritis: A New Target for Mesenchymal Stem Cell-Based Therapy?

GSE273883 Mus musculus (mouse) Single-cell RNA-seq 35 samples Submitted 2025/03/12 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 35 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
35 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
Adipose-derived stem cells attenuate rheumatoid arthritis by restoring CX(3)CR1(+) synovial lining macrophage barrierStem cell research & therapy · 2025
Summary (written by the submitters)
Objective: In this study, we explored the interaction between Mesenchymal stem cells (MSCs) and synovial CX3CR1+ macrophages with rheumatoid arthritis (RA) model mice during the process of barrier reconstruction, deeply analyzed the therapeutic mechanism of MSCs and the underlying mechanisms of the dynamic state changes of the macrophage barrier.
Read the full summary ↓
Design: ScRNA-seq analysis was conducted 4 days after MSCs/PBS injection in serum transfer-induced arthritis model mice. The role of mitochondria transfer and transplantation of MSCs were also explored. Bulk RNA-seq analysis was performed after the co-culture of MSCs and synovial CX3CR1+ macrophages in vitro. MSCs were retrieved 0/2/4/7 days after injection for Bulk RNA-seq analysis to explore their fate in vivo. Results: Intra-articular injection of MSCs could help restore CX3CR1+ macrophage barrier and attenuate the pathological process of RA mice. ScRNA-seq analysis revealed that an Atf3high Ccl3high subset of CX3CR1+ macrophages with poor oxidative phosphorylation increased in abundance during RA progression. MSCs reduced this subset's abundance through mitochondria transfer. Mitochondria transplantation by MSCs was also effective in treating RA. Bulk RNA-seq and scRNA- seq analyses revealed multiple interaction mechanisms between MSCs and CX3CR1+ macrophages such as Cd74/Mif axis and GAS6/MERTK axis to restore CX3CR1+ macrophage barrier. Bulk RNA-seq analysis showed that MSCs primarily contribute to tissue repair and immune regulation subsequently. Conclusions: Our results suggest that MSCs enhanced the oxidative phosphorylation capacity of CX3CR1+ lining macrophages through mitochondria transfer and promote barrier restoration. In addition, we elucidated the fate of MSCs and the therapeutic potential of mitochondria in RA treatment.
Published in
Adipose-derived stem cells attenuate rheumatoid arthritis by restoring CX(3)CR1(+) synovial lining macrophage barrier
Wang L, Hao M, Xu Y et al. · Stem cell research & therapy 2025 · PMID 40038808 · doi:10.1186/s13287-025-04144-5
This dataset
Open GSE273883 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 GSE273883_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 PRJNA1143545 and SRA study SRP523969. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40038808) ↗
Study design
8 conditions, mostly with about 4 replicates each
ADSCs, recovered from mice knee, 48h, repeat ×6 ADSCs, recovered from mice knee, 96h, repeat ×6 ADSCs, co-cultured with MFs, repeat ×4 MFs, cultured alone, repeat ×4 MFs, co-cultured with ADSCs, repeat ×4 ADSCs, cultured alone, repeat ×3 ADSCs, recovered from mice knee, 0h, repeat ×3 ADSCs, recovered from mice knee, 168h, repeat ×3 +2 more

Supports a between-group comparison across 33 samples.

How we read this: 8 replicated groups read from 35 sample titles; they account for 33 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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