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A FOXA1/SPDEF Co-regulatory Axis Maintains Luminal Identity in HER2-Positive Breast Cancer by Driving ERBB2 Expression and Suppressing a TEAD/YAP-Driven EMT Program [RNA-Seq]

GSE312017 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2026/03/01 Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 16 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
Breast cancerThis series is part of our curated briefing on it.
Samples
16 samples: 4 × MCF7 cells, Control WT vs 4 × MCF7 cells, SPDEF knockdown vs 4 × SKBR3 cells, Control WT vs 4 × SKBR3 cells, SPDEF knockdownGroups 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)
The function of the pioneer factor forkhead box A1 (FOXA1) in estrogen receptor (ER)-negative, human epidermal growth factor receptor 2 (HER2, encoded by the ERBB2 gene)-positive breast cancer represents a critical gap in our understanding of lineage identity in tumorigenesis. Here, we solve this enigma by addressing this question through the identification of an indispensable, co-dependent regulatory circuit formed between FOXA1 and the SAM pointed domain containing ETS-family transcription factor (SPDEF).
Read the full summary ↓
Using integrative multi-omics analyses of patient tumors and experimental models, we demonstrate that this circuit functions as the master guardian of the HER2-positive luminal state. It executes this role via two distinct, essential mechanisms: it directly binds regulatory elements to drive high-level expression of the ERBB2 oncogene, and it simultaneously preserves epithelial identity by suppressing a latent program of epithelial-to-mesenchymal transition (EMT). Mechanistically, the FOXA1/SPDEF circuit promotes the expression of the transcriptional repressor TRPS1, which in turn antagonizes the pro-mesenchymal activity of the TEAD/YAP complex. Our findings define a central regulatory node that couples lineage fidelity to oncogenic output in HER2-positive cancer, revealing the FOXA1/SPDEF–TRPS1 axis as a critical determinant of tumor plasticity and a potential therapeutic target for overcoming resistance in HER2-positive breast cancer.
This dataset
Open GSE312017 in finder → Find more human RNA-seq datasets → Breast 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 GSE312017_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 PRJNA1372059 and SRA study SRP650406. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × MCF7 cells, Control WT vs 4 × MCF7 cells, SPDEF knockdown vs 4 × SKBR3 cells, Control WT vs 4 × SKBR3 cells, SPDEF knockdown

Supports a case/control comparison: 8 samples read as cases, 8 as controls.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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 Breast 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.