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Identification of Targets of Clinical FOXA1 Mutants Involved in EMT and Immune Suppression in Prostate Cancer

GSE306036 Homo sapiens (human) RNA-seq (gene expression) 9 samples Submitted 2026/06/17 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 9 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
Homo sapiens (human)
Topic
Prostate cancerThis series is part of our curated briefing on it.
Samples
9 samples: 5 × 22Rv1_M253K_xeno vs 4 × 22Rv1_WT_xenoGroups 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.
Summary (written by the submitters)
FOXA1 is a critical transcription factor in prostate cancer (PCa) progression, functioning as a pioneer factor for the androgen receptor (AR). Its expression is elevated in advanced stages of PCa and plays a central role in oncogenic reprogramming. Recurrent coding mutations in the forkhead DNA-binding domain (FKHD) of FOXA1 become increasingly prevalent in drug-resistant metastatic PCa, particularly clustering in the Wing2 region of FKHD.
Read the full summary ↓
While recent studies demonstrated that these mutations promote PCa progression, the downstream targets of FKHD mutants remain poorly understood. In this study, we employed three analytical approaches to elucidate these targets: (i) traditional transcriptomic analyses, (ii) chromatin structure–based super-enhancer (SE) profiling, and (iii) immune deconvolution. We identified HPSE, an enzyme that degrades heparan sulfate, as a druggable target activated by FKHD mutants both in vitro and in vivo. SE profiling further revealed that FKHD mutants can reprogram the SE landscape, with FOXP1 emerging as a consistently SE-driven and upregulated gene across multiple FOXA1 mutants. Additionally, FOXA1 mutations were associated with immune suppression in PCa patient samples, and B2M, a key gene in antigen processing and presentation, was notably downregulated in FKHD-mutant tumors. Together, our findings provide new insights into how FOXA1 FKHD mutations drive PCa progression and highlight potential therapeutic targets in tumors harboring these mutations.
This dataset
Open GSE306036 in finder → Find more human RNA-seq datasets → Prostate cancer landscape →
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 GSE306036_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 PRJNA1309000 and SRA study SRP610487. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × 22Rv1_M253K_xeno vs 4 × 22Rv1_WT_xeno

Supports a between-group comparison across 9 samples.

How we read this: 2 replicated groups read from 9 sample titles; they account for 9 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
More Prostate cancer datasets

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.