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The new cohort of EMT genes are activated by benzo(a)pyrene and/or SATB1 during the malignant transformation of breast epithelial cells

GSE285433 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2025/02/28 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 48 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
48 samples: 48 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
Genome Organizer SATB1 selectively activates a defined subset of EMT genes driving metastatic breast cancerbioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
Tumor metastasis, the migration of tumor cells from a primary site to distant organs, is the leading cause of death among cancer patients. Despite significant advancements in cancer research, much remains to be learned about how tumor cells acquire invasive properties at the molecular level. Here, we investigated the transcriptional program that enables breast epithelial cells to develop highly invasive malignant phenotypes.
Read the full summary ↓
We focused on genes that promote epithelial-to mesenchymal transition (EMT), a process critical for both embryogenesis and cancer cell invasion, and we compiled a cohort of 339 genes associated with EMT functions with many identified in recent literature. Using an immortalized, non-malignant breast epithelial cell line, MCF10A, we analyzed changes in the transcriptional activity of these genes through Global Run-On Sequencing (GRO-seq) and RNA-seq following stable SATB1 transduction. SATB1 is a nuclear protein with genome-organizing functions that promotes metastatic cancer, including breast cancer. SATB1-expressing MCF10A cells acquire both tumorigenic and metastatic properties. We identified a total of 98 EMT promoting genes that were upregulated in SATB1-expressing MCF10A cells compared to control cells. Additionally, we investigated the effects of the chemical carcinogen benzo[a]pyrene (B[a]P), known to induce malignancy in MCF10A cells. Our findings revealed that B[a]P significantly upregulated 54 EMT genes after 3 hours. By day 3, this number increased to 72 genes, with 36 genes being common between those elevated by SATB1. Notably, the significant effects of B[a]P on EMT gene expression observed in MCF10A cells were largely diminished in SATB1 expressing MCF10A cells, suggesting that the pre-existing SATB1-regulated transcriptional program is dominant. Our results indicate that, despite the distinct causes of breast cancer, both the chemical carcinogen B[a]P and SATB1 activate many common EMT genes during the malignant transformation of breast epithelial cells. This suggests a key network of gene expression that drives the malignant phenotypes of these cells.
Published in
Genome Organizer SATB1 selectively activates a defined subset of EMT genes driving metastatic breast cancer
Kohwi Y, Vayn Y, Grange M et al. · bioRxiv : the preprint server for biology 2026 · PMID 42282767 · doi:10.64898/2026.05.29.728584
This dataset
Open GSE285433 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 GSE285433_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 PRJNA1203628 and SRA study SRP554091. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42282767) ↗
Study design
48 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 48 sample titles: 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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