GEO series

CXCL12-CXCR4 signaling mediates the formation of a macrophageal niche for mammary tumorigenesis [tumor]

GSE275906 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2025/04/15 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 10 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: 10 samples
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 the maintenance of normal stem cells and tumor-initiating cells, are spatially confined and exert their influence locally among adjacent cells. Here, we demonstrate that CXCR4+ macrophages are enriched in the normal mammary ducts and enhance regenerative activity in basal cells in response to the CXCL12 secreted by luminal cells.

Read the full summary ↓

Conditional knockout of CXCR4 in macrophages or CXCL12 in luminal cells results in similar phenotypes, including impaired branching morphogenesis, decreased regenerative functionality in basal cells, and diminished ductal association of macrophages. CXCL12 stimulation of macrophages triggers an AKT-mediated stabilization of β-catenin, increasing the expression of pro-migratory genes and multiple Wnt ligands, which enhances the infiltration of macrophages and their ability to support stem-like regenerative functions of basal cells. Importantly, the identical CXCR4+ niche macrophages also govern the tumor-initiating activity of breast tumors by promoting the survival and tumor-forming capacity of tumor-initiating cells and inducing early immune evasion through the accumulation of regulatory T cells. Our findings elucidate a crucial role of the CXCL12-CXCR4 axis in facilitating a complex interaction among niche macrophages, two mammary epithelial cell lineages, and other stromal components, thereby establishing a supportive environment for both normal tissue regeneration and mammary tumor initiation.

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 GSE275906 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 GSE275906_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 PRJNA1153577 and SRA study SRP529194. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40413176) ↗

Samples in this study

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+ 10 more — browse all 10 samples with per-sample file links →

Datasets on a similar topic

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GSE277228 Changing dynamics of the fibroblast differentiation hierarchy during mammary gland morphogenesis and tumorigenesis [scRNA-Seq I] 13 samples shares tumorigenesis, mammary
GSE280084 A Multipotent PROX1+ Tumor Cell Population Emerges During Intestinal Tumorigenesis and Mediates Radioresistance in Colorectal Cancer 13 samples shares tumorigenesis, mediates
GSE299463 Stem cell specification and niche formation in developing incisor depend on actomyosin forces 10 samples shares formation, niche
GSE315243 Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis 69 samples shares tumorigenesis, niche
GSE269928 Arid1a mediates cell recovery upon gastric injury to prevent tumorigenesis [Multiome] 9 samples shares tumorigenesis, mediates
GSE233979 Wnt signaling dosage controlled by a Ctnnb1 enhancer balances homeostasis and tumorigenesis of intestinal epithelia 20 samples shares tumorigenesis

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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.