GEO series

Tractable mouse TNBC models capture the heterogeneous tumor immune microenvironment and adaptation to PD-L1 blockade

GSE292146 Mus musculus (mouse) RNA-seq (gene expression) 38 samples Submitted 2025/12/22 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 38 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: 38 samples: 12 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: Tractable mouse TNBC models capture the heterogeneous tumor immune microenvironment and adaptation to PD-L1 blockadeNPJ breast cancer · 2025

Summary (written by the submitters)

Triple-negative breast cancer (TNBC) patients exhibit variable responses to programmed death (PD)-ligand (L)1 blockade, largely determined by the ‘hot’ versus ‘cold’ state of the tumor immune microenvironment (TIME). We here characterized 9 mouse TNBC models, relying on intraductal mammary gland inoculation of established mouse TNBC cell lines, with a heterogeneous TIME to study anti-PD-L1 resistance mechanisms.

Read the full summary ↓

Complementary in vitro and in vivo screening classified the 4T1-hot-based model, a highly inflamed control through its immunogenic luciferase tag expression compared to the untagged 4T1-cold-based model, as displaying the ‘hottest’ TIME. However, both 4T1-based counterparts did not respond to anti-PD-L1, which was attributed to their immunosuppressive myeloid cell content as well as upregulation of cancer-associated fibroblasts in the 4T1-hot and high PD-L1-expressing CXCL10+ tumor-associated macrophages in 4T1-cold primary tumors. These anti-PD-L1 adaptation mechanisms across TIME states as captured by mouse TNBC models highlight specific cellular targets for future studies.

Published in

Tractable mouse TNBC models capture the heterogeneous tumor immune microenvironment and adaptation to PD-L1 blockade

Salembier R, De Haes C, Demeyere K et al. · NPJ breast cancer 2025 · PMID 41453911 · doi:10.1038/s41523-025-00880-2

This dataset

Open GSE292146 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 GSE292146_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 PRJNA1237281 and SRA study SRP570903. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41453911) ↗

Study design

12 conditions, mostly in triplicate

Py230 primary tumo ×4 AT3 primary tumo ×4 4T1-hot primary tumo ×3 D2A1 primary tumo ×3 66cl4 primary tumo ×3 MET1 primary tumo ×3 FVBN mammary gland ×3 C57BL6 mammary gland ×3 +7 more

Supports a between-group comparison across 35 samples.

How we read this: 12 replicated groups read from 38 sample titles; they account for 35 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

GSM8851117 4T1-hot primary tumor 1 4T1-hot primary tumo
GSM8851118 4T1-hot primary tumor 2 4T1-hot primary tumo
GSM8851119 4T1-hot primary tumor 3 4T1-hot primary tumo
GSM8851120 EMT6 priamry tumor 1
GSM8851121 EMT6 primary tumor 2 EMT6 primary tumo
GSM8851122 EMT6 primary tumor 3 EMT6 primary tumo
GSM8851123 D2A1 primary tumor 1 D2A1 primary tumo
GSM8851124 D2A1 primary tumor 2 D2A1 primary tumo
GSM8851125 D2A1 primary tumor 3 D2A1 primary tumo
GSM8851126 4T1-cold primary tumor 1 4T1-cold primary tumo
GSM8851127 4T1-cold primary tumor 2 4T1-cold primary tumo
GSM8851128 4T1-cold primarty tumor 3
GSM8851129 66cl4 primary tumor 1 66cl4 primary tumo
GSM8851130 66cl4 primary tumor 2 66cl4 primary tumo
GSM8851131 66cl4 primary tumor 3 66cl4 primary tumo
GSM8851132 Py230 primary tumor 1 Py230 primary tumo
GSM8851133 Py230 primary tumor 2 Py230 primary tumo
GSM8851134 Py230 primary tumor 3 Py230 primary tumo
GSM8851135 Py230 primary tumor 4 Py230 primary tumo
GSM8851136 AT3 primary tumor 1 AT3 primary tumo
GSM8851137 AT3 primary tumor 2 AT3 primary tumo
GSM8851138 AT3 primary tumor 3 AT3 primary tumo
GSM8851139 AT3 primary tumor 4 AT3 primary tumo
GSM8851140 MET1 primary tumor 1 MET1 primary tumo
GSM8851141 MET1 primary tumor 2 MET1 primary tumo
GSM8851142 MET1 primary tumor 3 MET1 primary tumo
GSM8851143 MVT1 primary tumor 1 MVT1 primary tumo
GSM8851144 MVT1 primary tumor 2 MVT1 primary tumo
GSM8851145 MVT1 priamry tumor 3
GSM8851146 FVBN mammary gland 1 FVBN mammary gland
GSM8851147 FVBN mammary gland 2 FVBN mammary gland
GSM8851148 FVBN mammary gland 3 FVBN mammary gland
GSM8851149 C57BL6 mammary gland 1 C57BL6 mammary gland
GSM8851150 C57BL6 mammary gland 2 C57BL6 mammary gland
GSM8851151 C57BL6 mammary gland 3 C57BL6 mammary gland
GSM8851152 BALBC mammary gland 1 BALBC mammary gland
GSM8851153 BALBC mammary gland 2 BALBC mammary gland
GSM8851154 BALBC mammary gland 3 BALBC mammary gland

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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.