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Single-nuclei transcriptional and chromatin accessibility profile of Beckwith-Wiedemann Syndrome liver suggests metabolic dysregulation driven by PPARA signaling

GSE269947 Homo sapiens (human) Single-nucleus RNA-seq 18 samples Submitted 2025/03/07 Platform GPL24676
At a glance

Single-nucleus RNA-seq · human · 18 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
18 samples: 9 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
Single-nucleus multiomic analysis of Beckwith-Wiedemann syndrome liver reveals PPARA signaling enrichment and metabolic dysfunctionCommunications biology · 2025
Summary (written by the submitters)
Beckwith-Wiedemann Syndrome (BWS) is an epigenetic overgrowth syndrome caused by methylation changes in the human 11p15 chromosomal locus. Patients with BWS exhibit tissue overgrowth, as well as an increased risk of childhood neoplasms in the liver and kidney.
Read the full summary ↓
To understand the new impact of these 11p15 changes, specifically in the liver, we performed single nucleus RNA sequencing (snRNA-seq) and single nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) to generate paired, cell-type-specific transcriptional and chromatin accessibility profiles of both BWS-liver and nonBWS-liver nontumorous tissue. The integrated RNA+ATACseq multi-omic approach showed cell-type-specific enrichment and activation of the peroxisome proliferator-activated receptor ? (PPARA) – a liver metabolic regulator. To confirm our findings, we utilized a BWS-induced pluripotent stem cell (iPSC) model, where cells were differentiated into hepatocytes. Our data demonstrates the dysregulation of lipid metabolism in BWS-liver, which coincided with observed upregulation of PPARA during hepatocyte differentiation. BWS liver cells exhibited decreased neutral lipids, increased fatty acid beta oxidation, and increased lipid peroxidation, relative to controls. Excess reactive oxygen species (ROS) induces lipid peroxidation and cellular DNA damage. This study proposes a potential mechanism for overgrowth and cancer predisposition in BWS liver due to perturbed metabolism.
Published in
Single-nucleus multiomic analysis of Beckwith-Wiedemann syndrome liver reveals PPARA signaling enrichment and metabolic dysfunction
Nirgude S, Tichy ED, Liu Z et al. · Communications biology 2025 · PMID 40133415 · doi:10.1038/s42003-025-07961-9
This dataset
Open GSE269947 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 GSE269947_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1124156 and SRA study SRP514057. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40133415) ↗
Study design
9 conditions, mostly in duplicate
iPSC, IC2del-3D1, Day0, biol ×2 iPSC, IC2del-3D1, Day15, biol ×2 iPSC, IC2del-3D1, Day20, biol ×2 iPSC, IC2del-3H5, Day0, biol ×2 iPSC, IC2del-3H5, Day15, biol ×2 iPSC, IC2del-3H5, Day20, biol ×2 iPSC, WT, Day0, biol ×2 iPSC, WT, Day15, biol ×2 +1 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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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