GEO series

FOXA1 loss drives basal/squamous de-differentiation of prostate cancer and induces an immunosuppressive tumor microenvironment

GSE313915 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2026/02/21 Platform GPL34290

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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: FOXA1 loss drives basal/squamous de-differentiation of prostate cancer and induces an immunosuppressive tumor microenvironmentNature communications · 2026

Summary (written by the submitters)

FOXA1 is an epithelial transcription factor that is often found dysregulated in prostate cancer. Previous studies have reported both tumor-promoting and -inhibitory functions of FOXA1. However, a comprehensive analysis of FOXA1 in a physiological, immune-competent setting is still lacking. We here report a novel genetically engineered mouse model with Foxa1 KO in the Pten-null prostate epithelium for the study of FOXA1 loss within an immune-competent prostate tumor context.

Read the full summary ↓

Here, we report Foxa1 loss induces prostate cancer lineage switch from a luminal-like to a more aggressive basal/squamous-like phenotype, which is accompanied by inflammatory and immunosuppressive cytokine signaling. Mechanistically, in addition to inducing luminal genes, we found FOXA1 directly inhibits several basal/squamous, inflammatory, and cytokine genes, such that its loss unleashes their expression. Moreover, Foxa1 loss induces a striking remodeling of the prostate tumor immune microenvironment, leading to increased immunosuppressive myeloid accumulation and dysfunctional and spatially confined T cells. Altogether, we report critical roles for FOXA1 loss in inducing basal/squamous de-differentiation and an immunosuppressive microenvironment.

Published in

FOXA1 loss drives basal/squamous de-differentiation of prostate cancer and induces an immunosuppressive tumor microenvironment

Brea L, Shi H, Keo V et al. · Nature communications 2026 · PMID 41904157 · doi:10.1038/s41467-026-71121-8

This dataset

Open GSE313915 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE313915_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1387237 and SRA study SRP656839. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41904157) ↗

Study design

12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 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

GSM9377752 Mice-1751, prostate tissue, Pten/Foxa1 Double Knock Out, FOXA1(ChIP)
GSM9377753 Mice-1751, prostate tissue, Pten/Foxa1 Double Knock Out, H3K27ac(ChIP)
GSM9377754 Mice-2378, prostate tissue, Pten/Foxa1 Double Knock Out, ,FOXA1(ChIP)
GSM9377755 Mice-2378, prostate tissue, Pten/Foxa1 Double Knock Out, H3K27ac(ChIP)
GSM9377756 Mice-2033, prostate tissue, Pten Single Knock Out, ,FOXA1(ChIP)
GSM9377757 Mice-2033, prostate tissue, Pten Single Knock Out, H3K27ac(ChIP)
GSM9377758 Mice-2717, prostate tissue, Pten Single Knock Out, ,FOXA1(ChIP)
GSM9377759 Mice-2717, prostate tissue Pten Single Knock Out, H3K27ac(ChIP)
GSM9377760 Mice-2573, prostate tissue, Pten Single Knock Out, ,FOXA1(ChIP)
GSM9377761 Mice-2573, prostate tissue, Pten Single Knock Out, H3K27ac(ChIP)
GSM9377762 Mice-1943, prostate tissue, Pten/Foxa1 Double Knock Out, ,FOXA1(ChIP)
GSM9377763 Mice-1943, prostate tissue, Pten/Foxa1 Double Knock Out, H3K27ac(ChIP)

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