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Tumor-Initiating Stem Cells Fine-tune the Cell States of Neutrophils to Drive Cancer Relapse from Immunotherapy [neutrophil bulk RNAseq]

GSE278430 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2025/10/07 Platform GPL34328
At a glance

Single-cell RNA-seq · mouse · 10 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
10 samples: 3 × Sox2low control tumor neutrophil, naïve, vs 3 × Sox2Hi SCC tumor neutrophil, naïve, vs 2 × Sox2low control tumor neutrophil, treated, vs 2 × Sox2Hi SCC tumor neutrophil, treated,Groups 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
Tumor-initiating stem cells fine-tune the plasticity of neutrophils to sculpt a protective nicheCancer cell · 2026
Summary (written by the submitters)
The highly heterogeneous and plastic nature of tumor-associated neutrophils (TANs) has been recognized, but how different cell states of TANs emerge, evolve, distribute, and impact cancer immunotherapy efficacy remains elusive. Using single-cell RNA sequencing, spatial transcriptomic analysis, and genetic manipulations, we show that, while anti-PDL1/CD40 agonist immunotherapy can reprogram TANs to gain strong anti-tumor activities in squamous cell carcinomas (SCCs), a subset of neutrophils residing at the tumor-stroma interface can preserve their immune-suppressive state.
Read the full summary ↓
Importantly, we identified a group of Sox2Hi tumor-initiating stem cells (tSCs) at the tumor-stroma interface that can activate Fatty Acid Desaturase 1 (Fads1) and produce arachidonic acid (AA) to induce autocrine prostaglandin E2 signaling which can disrupt the interferon responses in neutrophils. Thus, through this interaction, tSCs fine-tunes the cell states of neutrophils, shapes neutrophil heterogeneity, and sculpts a protective micro-niche to drive cancer relapse following immunotherapy.
Published in
Tumor-initiating stem cells fine-tune the plasticity of neutrophils to sculpt a protective niche
Guo W, Luan J, Huang X et al. · Cancer cell 2026 · PMID 41349542 · doi:10.1016/j.ccell.2025.11.001
This dataset
Open GSE278430 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 GSE278430_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 PRJNA1167245 and SRA study SRP535727. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41349542) ↗
Study design
3 × Sox2low control tumor neutrophil, naïve, vs 3 × Sox2Hi SCC tumor neutrophil, naïve, vs 2 × Sox2low control tumor neutrophil, treated, vs 2 × Sox2Hi SCC tumor neutrophil, treated,

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 10 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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