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EPAS1 induction drives myocardial degeneration in Desmoplakin-cardiomyopathy [RNA-seq]

GSE289628 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2025/02/15 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 16 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
16 samples: 4 × WT Cardiomyocytes - AAV-Control vs 4 × WT Cardiomyocytes - AAV-EPAS1 vs 4 × DSP Mutant Cardiomyocytes - siScramble vs 4 × DSP Mutant Cardiomyocytes - siEPAS1Groups 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
EPAS1 induction drives myocardial degeneration in desmoplakin-cardiomyopathyiScience · 2025
Summary (written by the submitters)
Arrhythmogenic cardiomyopathy (ACM) is frequently attributed to desmosomal mutations, such as those in the desmoplakin (DSP) gene. Patients with DSP- cardiomyopathy are predisposed to myocardial degeneration and arrhythmias. Despite advancements, the underlying molecular mechanisms remain incompletely understood, thus limiting therapeutic options.
Read the full summary ↓
Here, we employed spatial transcriptomics on an explanted heart from a patient with a pathogenic DSP variant. Our transcriptional analysis revealed endothelial PAS domain-containing protein 1 (EPAS1) as a potential regulator of mitochondrial homeostasis in stressed cardiomyocytes. Elevated EPAS1 levels were associated with mitochondrial dysfunction and hypoxic stress in both human-relevant in vitro ACM models and additional explanted hearts with genetic cardiomyopathy. Collectively, cardiomyocytes bearing pathogenic DSP variants exhibit mitochondrial dysfunction, increased apoptosis, and impaired contractility, which are linked to the increased EPAS1 levels. These findings implicate EPAS1 as a key regulator of myocardial degeneration in DSP-cardiomyopathy, which expand to other forms of ACM.
Published in
EPAS1 induction drives myocardial degeneration in desmoplakin-cardiomyopathy
Kyriakopoulou E, van Kampen SJ, Wehrens M et al. · iScience 2025 · PMID 40034852 · doi:10.1016/j.isci.2025.111895
This dataset
Open GSE289628 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 GSE289628_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 PRJNA1223854 and SRA study SRP563978. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40034852) ↗
Study design
4 × WT Cardiomyocytes - AAV-Control vs 4 × WT Cardiomyocytes - AAV-EPAS1 vs 4 × DSP Mutant Cardiomyocytes - siScramble vs 4 × DSP Mutant Cardiomyocytes - siEPAS1

Supports a case/control comparison: 4 samples read as cases, 8 as controls.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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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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.