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Epigenomic disorder and partial EMT impair luminal progenitor integrity in Brca1-associated breast tumorigenesis

GSE198337 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2025/04/23 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 11 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
11 samples: 9 distinct titles, 1 of them repeatedGroups 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
Epigenomic disorder and partial EMT impair luminal progenitor integrity in Brca1-associated breast tumorigenesisMolecular cancer · 2025
Summary (written by the submitters)
Defects in double-strand repair mechanisms - both through germline or somatic inactivation of repair genes - is a hallmark of basal-like breast cancers. In this genetically-unstable context, a recurrent major shift in cell identity occurs within the mammary epithelium. Basal-like BRCA1 tumors have indeed been proposed to originate from luminal progenitor cells yet tumor-initiating events remain poorly understood.
Read the full summary ↓
Here, we map the state transitions leading luminal progenitors to tumor formation, using a mouse model launching tumorigenesis in multiple LP cells. We identify a population of cycling p16-expressing cells, emerging from the luminal progenitor compartment, undergoing partial epithelial-to-mesenchymal transition and losing luminal identity. Pseudo-temporal analyses position these cells as a transitory state between aberrant Brca1-deficient luminal progenitors and growing tumor cells. Concomitant to p16 activation, we show that LP cells undergo an epigenomic crisis attested by the general re-organization of their heterochromatin. They accumulate multiple H3K27me3 micro-foci - reminiscent of the formation of senescence-associated heterochromatin foci (SAHFs) - and lose their inactive X (Xi). Both p16 activation and heterochromatin reorganization are hallmarks of human basal-like breast tumors, we propose that these events occur during initial LP transformation and are scars of an initial transitory senescent-like state.
Published in
Epigenomic disorder and partial EMT impair luminal progenitor integrity in Brca1-associated breast tumorigenesis
Landragin C, Saichi M, Laisné M et al. · Molecular cancer 2025 · PMID 40289099 · doi:10.1186/s12943-025-02331-9
This dataset
Open GSE198337 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 GSE198337_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 PRJNA814651 and SRA study SRP363419. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40289099) ↗
Study design
9 distinct titles, 1 of them repeated
T ×3

How we read this: Read from 11 sample titles: 9 distinct titles with little repetition. 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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