GEO series

The CXCL10/CXCR3 axis is essential for sustaining immunological dormancy in triple-negative breast cancer

GSE304626 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/02/02 Platform GPL34475

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 3 × D2A1 wildtype vs 3 × D2.0R wildtype vs 3 × D2.0R sh Control vs 3 × D2.0R shCXCL10Groups 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: The CXCL10/CXCR3 axis is essential for sustaining immunological dormancy in triple-negative breast cancerNPJ breast cancer · 2026

Summary (written by the submitters)

Immune surveillance plays a pivotal role in controlling tumor emergence, dormancy and progression, including in breast cancer. Despite its potential clinical relevance, the mechanisms governing dormancy initiation, maintenance and escape, as well as the molecular mediators involved, remain poorly understood. Here, we identify the interferon-inducible chemokine CXCL10 and its receptor CXCR3 as key regulators of immunological dormancy in triple-negative breast cancer (TNBC).

Read the full summary ↓

By transcriptomic profiling, we observed high expression of Cxcl10 in dormant cells in two different orthotopic, syngeneic models of breast cancer dormancy (D2.0R and 4T1-MR20). Genetic silencing of Cxcl10 in dormant cells or pharmacological blockade of CXCR3 in vivo led to early tumor onset and rapid growth in immunocompetent mice. In contrast, dormant cells effectively formed tumors in immune-deficient mice independently of Cxcl10 status, demonstrating that the CXCL10/CXCR3 axis-mediated dormancy requires a functional immune system. Further analysis confirmed that Cxcl10 silencing altered the local immune microenvironment, reducing CD4+ and CD8+ T cell infiltration while increasing the presence of granulocytic Myeloid Derived Suppressor Cells and Natural Killer cells. Moreover, Cxcl10 silencing significantly increased the burden of tumor cells disseminated to the lung. Leveraging these findings, we identified a CXCL10-mediated dormancy signature that predicts improved overall survival in TNBC patients. Our findings have identified a new mechanism modulating breast cancer dormancy with two important clinical implications: the CXCL10/CXCR3 axis as a potential therapeutic target for improving survival of patients with TNBC, and the CXCL10-dependent dormancy signature as a tool for identifying these patients.

Published in

The CXCL10/CXCR3 axis is essential for sustaining immunological dormancy in triple-negative breast cancer

Yilmaz A, Haerri L, Granda ME et al. · NPJ breast cancer 2026 · PMID 41617729 · doi:10.1038/s41523-026-00903-6

This dataset

Open GSE304626 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 GSE304626_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 PRJNA1301942 and SRA study SRP606673. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41617729) ↗

Study design

3 × D2A1 wildtype vs 3 × D2.0R wildtype vs 3 × D2.0R sh Control vs 3 × D2.0R shCXCL10

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM9154254 D2A1 wildtype rep1 D2A1 wildtype
GSM9154255 D2A1 wildtype rep2 D2A1 wildtype
GSM9154256 D2A1 wildtype rep3 D2A1 wildtype
GSM9154257 D2.0R wildtype rep2 D2.0R wildtype
GSM9154258 D2.0R wildtype rep3 D2.0R wildtype
GSM9154259 D2.0R wildtype rep4 D2.0R wildtype
GSM9154260 D2.0R sh Control rep2 D2.0R sh Control
GSM9154261 D2.0R sh Control rep3 D2.0R sh Control
GSM9154262 D2.0R sh Control rep4 D2.0R sh Control
GSM9154263 D2.0R shCXCL10 rep1 D2.0R shCXCL10
GSM9154264 D2.0R shCXCL10 rep2 D2.0R shCXCL10
GSM9154265 D2.0R shCXCL10 rep3 D2.0R shCXCL10

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GSE276098 Immunosuppressive microenvironment restrains chemotherapy efficacy in liver metastases of triple-negative breast cancer 16 samples shares triple-negative, breast
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