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Improved health by combining dietary restriction and promoting muscle growth in DNA repair-deficient progeroid mice

GSE268971 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2024/12/19 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples
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
Improved health by combining dietary restriction and promoting muscle growth in DNA repair-deficient progeroid miceJournal of cachexia, sarcopenia and muscle · 2024
Summary (written by the submitters)
Ageing is a complex multifactorial process, impacting all organs and tissues, with DNA damage accumulation serving as a common underlying cause. To decelerate ageing, various strategies have been applied to model organisms and evaluated for health and lifespan benefits. Dietary restriction (DR, also known as caloric restriction) is a well-established long-term intervention recognised for its universal anti-ageing effects.
Read the full summary ↓
DR temporarily suppresses growth, and when applied to progeroid DNA repair-deficient mice doubles lifespan with systemic health benefits. Counterintuitively, attenuation of myostatin/activin signalling by soluble activin receptor (sActRIIB), boosts the growth of muscle, and in these animals prevents muscle wasting, improves kidney functioning, and compresses morbidity. Here we investigated a combined approach, applying an anabolic regime (sActRIIB) at the same time as DR to Ercc1d/- progeroid mice. Following both single treatments and combined, we monitored global effects on body weight, lifespan and behaviour, and local effects on muscle and tissue weight, muscle morphology and function, and ultrastructural and transcriptomic changes in muscle and kidney. Lifespan was mostly influenced by DR (extended from approx. 20 to 40-weeks; p<0.001), with sActRIIB clearly increasing muscle mass (35-65%) and tetanic force (p<0.001). The combined regime yielded a stable uniform body weight, but increased compared to DR alone, synergistically improved motor coordination and further delayed the onset and development of balance problems. sActRIIB significantly increased muscle fibre size (p<0.05) in mice subjected to DR and lowered all signs of muscle damage. In the neuromuscular junction of Ercc1d/- mice the junctional folding of the basement membrane at the postsynaptic side was either rudimentary or completely missing. Single interventions by sActRIIB treatment or DR only partially rescued this phenotype, while in the double intervention group the regularly shaped junctional foldings were maintained. In kidney of Ercc1d/- mice we observed a mild but significant foot process effacement, which was restored by either intervention. Transcriptome analysis also pointed towards reduced levels of DNA damage in muscle and kidney by DR, but not sActRIIB, while these levels retained lower in the double intervention. In muscle we found synergistic effects of combining sActRIIB with DR, but not in kidney, with an overall better health in the double intervention group. Crucially, the benefits of each single intervention are not lost when administered in combination, but rather strengthened, even when sActRIIB was applied late in life, opening opportunities for translation to human.
Published in
Improved health by combining dietary restriction and promoting muscle growth in DNA repair-deficient progeroid mice
Vermeij WP, Alyodawi K, van Galen I et al. · Journal of cachexia, sarcopenia and muscle 2024 · PMID 39245994 · doi:10.1002/jcsm.13570
This dataset
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.

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 GSE268971_RAW.tar (it can run to tens of gigabytes).

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.

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 PRJNA1119525 and SRA study SRP511462. Searching any of these in the dataset finder brings you back here.

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