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Neutrophils physically interact with tumor cells to form a signaling niche promoting breast cancer aggressiveness

GSE278570 Mus musculus (mouse) Single-cell RNA-seq 309 samples Submitted 2024/12/22 Platform GPL24247Platform GPL19057
At a glance

Single-cell RNA-seq · mouse · 309 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
309 samples: 94 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
Neutrophils physically interact with tumor cells to form a signaling niche promoting breast cancer aggressivenessNature cancer · 2025
Summary (written by the submitters)
Tissue remodeling and cell plasticity in the mammary gland are activated by multi-lineage communications. However, the dynamic signaling promoting breast cancer remains unclear. Here, by RNA-sequencing of single cells and physically interacting cells (PIC-seq) along mammary gland development and carcinogenesis, we uncovered that neutrophils appear transiently during early development and re-emerge in physical interaction with tumor cells in advanced carcinoma.
Read the full summary ↓
Neutrophil heterogeneity analysis characterized transcriptional states linked to age and cancer stage. Integrating ligand-receptor and PIC-seq analyses with various functional experiments unveiled a physical and secreted pro-tumorigenic signaling niche. This approach revealed that neutrophils are recruited by ductal macrophages and physically interact with tumor cells, increasing tumor cell proliferative and invasive properties, as well as endothelial proliferation and angiogenesis. The molecular program upregulated in neutrophil-PICs correlates with lower survival in advanced breast cancer patients. Our interaction-driven perspective highlights potential molecular targets and biomarkers for breast cancer treatment.
Published in
Neutrophils physically interact with tumor cells to form a signaling niche promoting breast cancer aggressiveness
Camargo S, Moskowitz O, Giladi A et al. · Nature cancer 2025 · PMID 40055573 · doi:10.1038/s43018-025-00924-3
This dataset
Open GSE278570 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 GSE278570_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 PRJNA1088451 and SRA study SRP495445. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40055573) ↗
Study design
94 conditions, mostly in duplicate
Depletion daily-12w_tumor_Rep4_AB ×10 Depletion-12w_tumor_Rep1_AB ×9 Isotype daily-12w_tumor_Rep3_AB ×9 12w_tumor_Rep6_AB ×8 Depletion-6w_tumor_Rep1_AB ×8 Isotype-6w_tumor_Rep1_AB ×8 Depletion daily-12w_tumor_Rep3_AB ×7 12w_tumor_Rep5_AB ×6 +137 more

Supports a case/control comparison: 220 samples read as cases, 89 as controls.

How we read this: 94 replicated groups read from 309 sample titles; they account for 258 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

+ 269 more — browse all 309 samples with per-sample file links →

Datasets on a similar topic

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