GEO series

Small molecule MBD2 pathway inhibitor KCC-07 suppresses breast cancer cell fitness

GSE317591 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/04/24 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 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: Mus musculus (mouse)
Samples: 12 samples: 3 × RNA-seq of Control PYMT-R221A replicate # vs 3 × RNA-seq of KCC-treated PYMT-R221A replicate # vs 3 × RNA-seq of siMBD2-transfected PYMT-R221A replicate # vs 3 × RNA-seq of scramble siRNA PYMT-R221A replicate #Groups 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)

Elevated expression of the DNA methylation reader methyl-CpG-binding domain protein 2 (MBD2) reprograms the transcriptional landscape of cancer cells to promote proliferation and invasion. Despite its emerging importance in cancer biology, pharmacological targeting of MBD2 to treat cancer is underexplored because of the presence of intrinsically disordered regions, which confound drug discovery.

Read the full summary ↓

Here, we pharmacologically target MBD2 using KCC-07, a small-molecule inhibitor that blocks its DNA-binding ability, to evaluate its therapeutic potential in well-established in vitro and in vivo models of breast cancer. We found that KCC-07 administration caused a dose-dependent decrease in proliferative and clonogenic survival capabilities of mouse PyMT-R221A and E0771 breast cancer cells and substantially reduced their invasiveness in vitro. The anti-cancer effects of KCC-07 were further validated in vivo, where it markedly reduced the growth of orthotopic PyMT-R221A primary breast tumors in immunocompetent mice compared to the controls. In contrast, KCC-07 treatment neither prevented nor reduced lung colonization by PyMT-R221A cells in an experimental lung colonization model. Biochemical analyses of blood from KCC-07-treated mice showed no hepatotoxicity or nephrotoxicity. Transcriptomic analyses revealed that KCC-07 treatment upregulated the p53-associated gene expression program, which likely mediates its anti-cancer effects. Overall, our findings suggest that KCC-07, with its high selectivity, could be a promising therapeutic modality for treating primary tumors with elevated MBD2 expression.

This dataset

Open GSE317591 in finder → Find more mouse 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 GSE317591_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 PRJNA1412533. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × RNA-seq of Control PYMT-R221A replicate # vs 3 × RNA-seq of KCC-treated PYMT-R221A replicate # vs 3 × RNA-seq of siMBD2-transfected PYMT-R221A replicate # vs 3 × RNA-seq of scramble siRNA PYMT-R221A replicate #

Supports a case/control comparison: 3 samples read as cases, 6 as controls.

How we read this: 4 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

GSM9474770 RNA-seq of Control PYMT-R221A replicate #1 RNA-seq of Control PYMT…
GSM9474771 RNA-seq of Control PYMT-R221A replicate #2 RNA-seq of Control PYMT…
GSM9474772 RNA-seq of Control PYMT-R221A replicate #3 RNA-seq of Control PYMT…
GSM9474773 RNA-seq of KCC-treated PYMT-R221A replicate #1 RNA-seq of KCC-treated …
GSM9474774 RNA-seq of KCC-treated PYMT-R221A replicate #2 RNA-seq of KCC-treated …
GSM9474775 RNA-seq of KCC-treated PYMT-R221A replicate #3 RNA-seq of KCC-treated …
GSM9474776 RNA-seq of siMBD2-transfected PYMT-R221A replicate #1 RNA-seq of siMBD2-trans…
GSM9474777 RNA-seq of siMBD2-transfected PYMT-R221A replicate #2 RNA-seq of siMBD2-trans…
GSM9474778 RNA-seq of siMBD2-transfected PYMT-R221A replicate #3 RNA-seq of siMBD2-trans…
GSM9474779 RNA-seq of scramble siRNA PYMT-R221A replicate #1 RNA-seq of scramble siR…
GSM9474780 RNA-seq of scramble siRNA PYMT-R221A replicate #2 RNA-seq of scramble siR…
GSM9474781 RNA-seq of scramble siRNA PYMT-R221A replicate #3 RNA-seq of scramble siR…

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