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Methionine cycle dysregulation mediates REDD1 overexpression-induced muscle atrophy in cancer cachexia

GSE275001 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2024/10/11 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
12 samples: 3 × C2C12_myotubes_ATACseq_Ctrl_N vs 3 × C2C12_myotubes_ATACseq_C26_CC vs 3 × LLC_cachexia_muscle_RNAseq_N vs 3 × LLC_cachexia_muscle_RNAseq_CCGroups 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
Disrupted methionine cycle triggers muscle atrophy in cancer cachexia through epigenetic regulation of REDD1Cell metabolism · 2025
Summary (written by the submitters)
The essential amino acid methionine plays a pivotal role in one-carbon metabolism, facilitating the production of S-adenosylmethionine (SAMe), a critical supplier for DNA methylation. Here we find the disruption of methionine metabolism by rapid SAMe depletion in skeletal muscle in cancer cachexia, leading to endoplasmic reticulum (ER) stress and the overexpression of regulated in development and DNA damage responses (REDD1).
Read the full summary ↓
Targeting the DNA methylation process via DNA methyltransferases (DNMTs) and REDD1 knockout can alleviate cancer cachexia-induced skeletal muscle atrophy. Methionine supplementation maintains the DNA methylation of DNA damage-inducible transcript 4 (Ddit4) by DNMT3A, thereby inhibiting activating transcription factor 4 (ATF4)-mediated Ddit4 transcription. Our study suggests that methionine or SAMe supplementation can effectively reverse muscle atrophy in cancer cachexia, providing valuable mechanistic insights and a promising therapeutic strategy for clinical application.
Published in
Disrupted methionine cycle triggers muscle atrophy in cancer cachexia through epigenetic regulation of REDD1
Lin K, Wei L, Wang R et al. · Cell metabolism 2025 · PMID 39729999 · doi:10.1016/j.cmet.2024.10.017
This dataset
Open GSE275001 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE275001_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1148933 and SRA study SRP526827. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39729999) ↗
Study design
3 × C2C12_myotubes_ATACseq_Ctrl_N vs 3 × C2C12_myotubes_ATACseq_C26_CC vs 3 × LLC_cachexia_muscle_RNAseq_N vs 3 × LLC_cachexia_muscle_RNAseq_CC

Supports a between-group comparison across 12 samples.

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
Datasets on a similar topic

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