GEO series

The loss of OPA1 accelerates intervertebral disc degeneration and osteoarthritis in aged mice

GSE270889 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/04/26 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: 6 × WT vs 6 × MUTGroups 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)

NP cells of the intervertebral disc and articular chondrocytes reside in avascular and hypoxic tissue niches. As a consequence of these environmental constraints the cells are primarily glycolytic in nature and were long thought to have a minimal reliance on mitochondrial function. Recent studies have challenged this long-held view and highlighted the increasingly important role of mitochondria in the physiology of these tissues.

Read the full summary ↓

However, the foundational understanding of mechanisms governing mitochondrial dynamics and function in these tissues is lacking. We investigated the role of mitochondrial fusion protein OPA1 in maintaining the spine and knee joint health in mice. OPA1 knockdown in NP cells altered mitochondrial size and cristae shape and increased the oxygen consumption rate without affecting ATP synthesis. OPA1 governed the morphology of multiple organelles, including peroxisomes, early endosomes and cis-Golgi and its loss resulted in the dysregulation of NP cell autophagy. Metabolic profiling and 13C-flux analyses revealed TCA cycle anaplerosis and altered metabolism in OPA1-deficient NP cells. Noteworthy, Opa1AcanCreERT2 mice with Opa1 deletion in disc and cartilage showed age-dependent disc degeneration, osteoarthritis, and vertebral osteopenia. Our findings underscore that OPA1 regulation of mitochondrial dynamics and multi-organelle interactions is critical in preserving metabolic homeostasis of disc and cartilage.

This dataset

Open GSE270889 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 GSE270889_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 PRJNA1128701 and SRA study SRP516301. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 × WT vs 6 × MUT

Supports a between-group comparison across 12 samples.

How we read this: 2 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

GSM8354234 WT_365 WT
GSM8354235 WT_366 WT
GSM8354236 WT_367 WT
GSM8354237 WT_369 WT
GSM8354238 WT_377 WT
GSM8354239 WT_384 WT
GSM8354240 MUT_370 MUT
GSM8354241 MUT_372 MUT
GSM8354242 MUT_373 MUT
GSM8354243 MUT_376 MUT
GSM8354244 MUT_380 MUT
GSM8354245 MUT_381 MUT

Datasets on a similar topic

GSE305927 Multi-omics Analysis and Evidence of IL1R1 as a Potential Biomarker for Diabetes-related Intervertebral Disc Degeneration 2 samples shares intervertebral, degeneration, disc
GSE320197 Epigenetic Activation of SIRT6 Protects the Aging Intervertebral Disc 20 samples shares intervertebral, disc
GSE280862 Loss of Sarm1 Mitigates Axonal Degeneration and Promotes Neuronal Regeneration After Ischemic Stroke 15 samples shares degeneration, loss
GSE298665 Loss of Prom1 triggers RPE Degeneration in Atrophic AMD 15 samples shares degeneration, loss
GSE288503 Secreted chemokines and transcriptomic analyses reveal diverse inflammatory and degenerative processes in the intervertebral disc of the STZ-HFD mouse model of Type 2 diabetes 14 samples shares intervertebral, disc
GSE322737 Loss of Neurofascin 186 and Ankyrin G in Purkinje Cells Causes Disruption of Axon Initial Segments, Neurodegeneration and Cerebellar Ataxia 11 samples shares degeneration, loss
GSE305276 Osteocyte-specific deletion of Gasdermin D drives osteoarthritis cartilage degeneration by promoting inflammation and remodeling in subchondral bone 9 samples shares osteoarthritis, degeneration
GSE289826 OPA1 mutations associated with dominant optic atrophy affect mitochondrial fusion and cell death in a domain-specific manner 15 samples shares opa1

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.