GEO series

OCT-2 is associated with pro-metastatic epigenomic properties of triple-negative breast cancer cells

GSE292004 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/05/14 Platform GPL17303

At a glance

RNA-seq (gene expression) · human · 12 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)
Samples: 12 samples: 6 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: OCT-2 Is Associated With Pro-Metastatic Epigenomic Properties of Triple-Negative Breast Cancer CellsCancer science · 2025

Summary (written by the submitters)

Triple-negative breast cancer (TNBC) is a malignant type of breast cancer. Owing to the lack of expression of receptors that serve as molecular targets for standard therapy for breast cancer, conventional cytotoxic chemotherapy is the primary treatment option for TNBC. However, TNBC exhibits a high degree of genomic heterogeneity, rendering it resistant to chemotherapy.

Read the full summary ↓

Therefore, there is an urgent need to identify novel therapeutic targets for the treatment of TNBC. Advances in massively parallel sequencing technology have enabled the identification of cancer cell-specific gene expression patterns and epigenetic alterations that regulate their expression. Cancer cell-specific super-enhancers (SEs) have been identified as effective therapeutic targets for cancer. In this study, we identified the functional roles of epigenetic changes and their regulatory mechanisms in TNBC cells. TNBC cell-specific SEs were formed near several genes that contribute to malignant cancer cell acquisition. We found that the transcription factor OCT-2 (encoded by POU2F2) was responsible for the formation of SEs and the expression of genes encoded in the vicinity of the SE regions. Overexpression of POU2F2 enhances the metastasis of TNBC cells in mice and their expression is highly correlated to poor prognosis of TNBC patients. Our findings provide a new insight into cancer cell-specific epigenetic changes induced by OCT-2, which trigger the progression of TNBC, and suggest possible candidates that could be targeted for the treatment of TNBC.

Published in

OCT-2 Is Associated With Pro-Metastatic Epigenomic Properties of Triple-Negative Breast Cancer Cells

Ogikubo K, Nishida J, Takahashi-Yamashiro K et al. · Cancer science 2025 · PMID 40364745 · doi:10.1111/cas.70093

This dataset

Open GSE292004 in finder → Find more human 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 GSE292004_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 PRJNA1236320 and SRA study SRP570486. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40364745) ↗

Study design

6 conditions, mostly in duplicate

parental MDA-MB-231 cell line, TGF-beta treat… ×2 parental MDA-MB-231 cell line, no TGF-beta, ×2 highly metastatic clone of MDA-MB-231 cell li… ×2 highly metastatic clone of MDA-MB-231 cell li… ×2 parental MDA-MB-231 cell line expressing OCT-… ×2 parental MDA-MB-231 cell line expressing GFP, ×2

Supports a case/control comparison: 4 samples read as cases, 6 as controls.

How we read this: 6 replicated groups read from 12 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

GSM8846400 parental MDA-MB-231 cell line, TGF-beta treated, replicate 1 parental MDA-MB-231 cel…
GSM8846401 parental MDA-MB-231 cell line, TGF-beta treated, replicate 2 parental MDA-MB-231 cel…
GSM8846402 parental MDA-MB-231 cell line, no TGF-beta, replicate 1 parental MDA-MB-231 cel…
GSM8846403 parental MDA-MB-231 cell line, no TGF-beta, replicate 2 parental MDA-MB-231 cel…
GSM8846404 highly metastatic clone of MDA-MB-231 cell line, TGF-beta treated, replicate 1 highly metastatic clone…
GSM8846405 highly metastatic clone of MDA-MB-231 cell line, TGF-beta treated, replicate 2 highly metastatic clone…
GSM8846406 highly metastatic clone of MDA-MB-231 cell line, no TGF-beta, replicate 1 highly metastatic clone…
GSM8846407 highly metastatic clone of MDA-MB-231 cell line, no TGF-beta, replicate 2 highly metastatic clone…
GSM8846408 parental MDA-MB-231 cell line expressing OCT-2, replicate 1 parental MDA-MB-231 cel…
GSM8846409 parental MDA-MB-231 cell line expressing OCT-2, replicate 2 parental MDA-MB-231 cel…
GSM8846410 parental MDA-MB-231 cell line expressing GFP, replicate 1 parental MDA-MB-231 cel…
GSM8846411 parental MDA-MB-231 cell line expressing GFP, replicate 2 parental MDA-MB-231 cel…

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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.