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CXCL12-CXCR4 signaling mediates the formation of a macrophageal niche for mammary gland stem cells

GSE262432 Mus musculus (mouse) RNA-seq (gene expression) 17 samples Submitted 2025/04/15 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 17 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
17 samples: 5 conditions, mostly in duplicateGroups 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
CXCR4(+) mammary gland macrophageal niche promotes tumor initiating cell activity and immune suppression during tumorigenesisNature communications · 2025
Summary (written by the submitters)
Niche-associated signals, essential for stem cell maintenance, are spatially confined and exert their influence locally among adjacent cells. Here, we demonstrate that CXCR4+ macrophages are enriched in the mammary ducts and enhance MaSC activity in basal cells in response to the CXCL12 secreted by luminal cells. Conditional knockout of CXCR4 in macrophages or CXCL12 in luminal cells results in similar phenotypes, including impaired branching morphogenesis, decreased stem cell functionality in basal cells, and diminished ductal association of macrophages.
Read the full summary ↓
CXCL12 stimulation of macrophages triggers an AKT-mediated stabilization of β-catenin, increasing the expression of pro-migratory genes and multiple Wnt ligands. This process enhances the infiltration of macrophages into intraepithelial regions and their ability to support MaSC functions. Our findings elucidate a crucial role of the CXCL12-CXCR4 axis in facilitating a complex interaction among ductal macrophages and two mammary epithelial cell lineages in establishing a supportive environment for MaSCs during mammary gland development.
Published in
CXCR4(+) mammary gland macrophageal niche promotes tumor initiating cell activity and immune suppression during tumorigenesis
Lee E, Hong JJ, Samcam Vargas G et al. · Nature communications 2025 · PMID 40413176 · doi:10.1038/s41467-025-59972-z
This dataset
Open GSE262432 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 GSE262432_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 PRJNA1091707 and SRA study SRP497754. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40413176) ↗
Study design
5 conditions, mostly in duplicate
Mammary gland residential macrophage from Lys… ×2 Mammary gland residential macrophage with Cxc… ×2 Mammary gland residential macrophage subpopul… ×2 Mammary gland residential macrophage from K8-… ×2 Mammary gland residential macrophage from mic… ×2 Mammary gland residential macrophage subpopul… ×1 MaSC enriched subpopulation P4 (Lin-CD24+CD29… ×1 MaSC enriched subpopulation P4 (Lin-CD24+CD29… ×1 +4 more

Supports a case/control comparison: 3 samples read as cases, 5 as controls.

How we read this: 5 replicated groups read from 17 sample titles; they account for 10 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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