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Ablation of VEGFA following a lumbar intervertebral disc injury attenuates intradiscal neurovascular features and prevents chronic low back pain symptoms

GSE294577 Homo sapiens (human) RNA-seq (gene expression) 28 samples Submitted 2026/01/07 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 28 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
Homo sapiens (human)
Samples
28 samples: 11 conditions, mostly in duplicateGroups 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
Ablation of VEGFA following a lumbar intervertebral disc injury attenuates intradiscal neurovascular features and prevents chronic low back pain symptomsbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
There are currently no therapies for the staggering disability and public health costs of chronic low back pain (LBP). Innervation of the degenerating intervertebral disc (IVD) is suspected to cause discogenic LBP, but the mechanisms that orchestrate the IVD’s neo-innervation and subsequent symptoms of LBP remain unknown. We hypothesize that Vascular Growth Endothelial Factor-A (VEGFA) critically mediates the neurite invasion in the IVD and contributes to prolonged LBP.
Read the full summary ↓
Initiating IVD degeneration through a mechanical injury, we evaluated the progression of neurovascular features into the IVD, as well as resultant LBP symptoms and locomotive performance at acute (3-weeks) and prolonged (12-weeks) time points following IVD injury. To determine the role of VEGFA, we used a mouse model with ubiquitous inducible recombination of the floxed VEGFA allele (UBC-CreERT2; VEGFAfl/fl). The ablation of VEGFA attenuated the neurite and vessel infiltration into the degenerating IVD, and the VEGFA-null animals exhibited alleviated mechanical allodynia and improved locomotive performance. To determine the effects of IVD-derived VEGFA on endothelial cells and neurons, we cultured HMEC-1 endothelial cells and SH-SY5Y neurons using conditioned media from VEGFA-silenced (siRNA) human primary IVD cells stimulated by IL1b. The endothelial cells and neurons exposed to the secretome of the VEGFA-silenced IVD cells exhibited reduced growth, suggesting that the inhibition of IVD-derived VEGFA may be sufficient to attenuate intradiscal neurovascular features. Together, we show that VEGFA orchestrates the growth of intradiscal vessels and neurites that cause low back pain and impaired function, and the inhibition of VEGFA can prevent prolonged low back pain.
Published in
Ablation of VEGFA following a lumbar intervertebral disc injury attenuates intradiscal neurovascular features and prevents chronic low back pain symptoms
Potter RS, Moon HJ, Clayton SW et al. · bioRxiv : the preprint server for biology 2025 · PMID 40501758 · doi:10.1101/2025.06.03.657641
This dataset
Open GSE294577 in finder → Find more human 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 GSE294577_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 PRJNA1250530 and SRA study SRP578503. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40501758) ↗
Study design
11 conditions, mostly in duplicate
Nerve cells co-cultured with IL-1ϐ stimulated… ×3 Naive nerve cells (not co-cultured), sample ×3 Nerve cells co-cultured with Scrambled siRNA … ×3 Nerve cells co-cultured with Vegf siRNA trans… ×3 Naive endothelial cells (not co-cultured), sa… ×2 Endothelial cells co-cultured with Scrambled … ×2 Endothelial cells co-cultured with Scrambled … ×2 Endothelial cells co-cultured with Scrambled … ×2 +5 more

Supports a case/control comparison: 3 samples read as cases, 15 as controls.

How we read this: 11 replicated groups read from 28 sample titles; they account for 26 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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