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Inflammation awakens dormant cancer cells by modulating epithelial-mesenchymal phenotypic state

GSE280817 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2025/08/19 Platform GPL22245Platform GPL24676Platform GPL16791
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 5 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
Inflammation awakens dormant cancer cells by modulating the epithelial-mesenchymal phenotypic stateProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
The awakening of dormant disseminated cancer cells appears to be responsible for the clinical relapses of patients whose primary tumors have been successfully cured months and even years earlier. In the present study, we demonstrate that dormant breast cancer cells lodged in the lungs reside in a highly mesenchymal, non-proliferative phenotypic state.
Read the full summary ↓
The awakening of these cells is not triggered by a cancer cell-autonomous process. Instead, lung inflammation induced by the chemotherapeutic agent bleomycin effectively awakens dormant cancer cells, providing useful models for studying metastatic awakening. Mechanistically, the awakened cells shift from a highly mesenchymal to a quasi-mesenchymal phenotypic state in which they acquire tumorigenicity and proliferative ability. Once awakened, these cells can stably reside in this quasi-mesenchymal state and maintain their tumor-initiating ability, doing so without ongoing heterotypic signaling from the lung microenvironment. EGFR ligands released by the cells of the injured tissue microenvironment, including notably M2 type macrophages, promote dormant cancer cells to move toward this quasi-mesenchymal state, a transition that is critical for the awakening process. An understanding of the mechanisms of metastatic awakening may lead in the future to treatment strategies designed to prevent such awakening and resulting metastatic relapse.
Published in
Inflammation awakens dormant cancer cells by modulating the epithelial-mesenchymal phenotypic state
Zhang J, Zhang J, Han L et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40901881 · doi:10.1073/pnas.2515009122
This dataset
Open GSE280817 in finder → Find more 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 GSE280817_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 PRJNA1180601 and SRA study SRP506264. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40901881) ↗
Study design
5 conditions, mostly in duplicate
Sum159 ITGB4 low clone 1 biol ×3 Sum159 ITGB4 low clone 1 bleomycin treated bi… ×3 Day3 control ×2 Day3 Bleomycin ×2 Sum159 ITGB4 high cells biol ×2 Day7 control ×1 Day7 Bleomycin ×1 Sum159 ITGB4 high cells ×1 +5 more

Supports a case/control comparison: 6 samples read as cases, 5 as controls.

How we read this: 5 replicated groups read from 20 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
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