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Inhibition of Histone Methyltransferase EZH2 for Immune-Interception of Colorectal Cancer in Lynch Syndrome

GSE277544 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2025/02/14 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 11 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
11 samples: 3 × VCMsh2THu organoid lines (polyp), GSK, vs 3 × VCMsh2THu organoid lines (normal), Control, vs 3 × VCMsh2THu organoid lines (normal), GSK, vs 2 × VCMsh2THu organoid lines (polyp), Control,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.
Paper
Inhibition of histone methyltransferase EZH2 for immune interception of colorectal cancer in Lynch syndromeJCI insight · 2025
Summary (written by the submitters)
This study investigates the potential of EZH2 inhibition as a preventive strategy for colorectal cancer in Lynch Syndrome (LS) by modulating the immune system. Using a mouse model of LS and colonic organoids, researchers treated the mice with the EZH2 inhibitor GSK503 and observed increased CD4+ and CD8+ T cells in both spleen and colon tissue.
Read the full summary ↓
Over a 9-week period, the inhibitor reduced adenoma formation, indicating its preventive efficacy. RNA sequencing and ChIPseq analyses revealed that EZH2 inhibition activated immune and apoptotic markers and decreased H3K27 methylation, leading to changes in gene regulation. These findings suggest that EZH2 inhibitors hold promise for cancer prevention in LS by reprogramming immune responses and gene expression patterns.
Published in
Inhibition of histone methyltransferase EZH2 for immune interception of colorectal cancer in Lynch syndrome
Bowen CM, Duzagac F, Martel-Martel A et al. · JCI insight 2025 · PMID 39946195 · doi:10.1172/jci.insight.177545
This dataset
Open GSE277544 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 GSE277544_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 PRJNA1162779 and SRA study SRP533585. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39946195) ↗
Study design
3 × VCMsh2THu organoid lines (polyp), GSK, vs 3 × VCMsh2THu organoid lines (normal), Control, vs 3 × VCMsh2THu organoid lines (normal), GSK, vs 2 × VCMsh2THu organoid lines (polyp), Control,

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 11 sample titles; they account for 11 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
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