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Duodenal-derived organoids from MASH patients exhibit altered digestive homeostasis.

GSE268518 Homo sapiens (human) RNA-seq (gene expression) 39 samples Submitted 2024/12/13 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 39 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
39 samples: 14 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
Duodenal Organoids From Metabolic Dysfunction-Associated Steatohepatitis Patients Exhibit Absorptive and Barrier AlterationsGastro hep advances · 2025
Summary (written by the submitters)
Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive disease linked to conditions like fibrosis, cirrhosis, and liver cancer, often resulting in higher mortality rates, primarily due to cardiovascular events. While MASH is closely tied to metabolic syndrome, recent research underscores the importance of the gut-liver axis in its pathogenesis, an aspect less explored in human studies.
Read the full summary ↓
To address this gap, duodenal epithelial organoids were generated from both MASH and healthy (controls) subjects. Organoid formation efficiency was similar between controls derived epithelial organoids (CDEOs) and MASH derived epithelial organoids (MDEOs) groups. Variability in growth patterns was observed, with MDEOs frequently exhibiting cystic spheroid morphology. MASH-derived organoids displayed altered homeostasis and digestive potential in the duodenal epithelium. Despite potential lineage bias, MDEOs retained their lipid metabolic capacity, possibly mediated by lipid oxidation in stem/progenitor cells. Notably, cell adhesion components were misexpressed in MASH-derived organoids, indicating significant intrinsic alterations in cell-cell adhesion potential compared to controls. However, MDEOs maintained transepithelial electric resistance and leak pathway integrity, indicating that the intestinal epithelial barrier remained functionally intact in MDEOs under tested conditions. This study sheds light on the intricate dynamics of duodenal epithelial alterations in MASH, highlighting potential therapeutic avenues for restoring intestinal homeostasis.
Published in
Duodenal Organoids From Metabolic Dysfunction-Associated Steatohepatitis Patients Exhibit Absorptive and Barrier Alterations
Hadefi A, Leprovots M, Dinsart G et al. · Gastro hep advances 2025 · PMID 39996241 · doi:10.1016/j.gastha.2024.100599
This dataset
Open GSE268518 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 GSE268518_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 PRJNA1117492 and SRA study SRP510339. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39996241) ↗
Study design
14 conditions, mostly in duplicate
Ctrl 1-A ×2 Ctrl 3-A ×2 Ctrl 4-A ×2 Ctrl 6-A ×2 Ctrl 7-A ×2 Ctrl 9-A ×2 Ctrl 11-A ×2 MASH 1-A ×2 +17 more

Supports a between-group comparison across 28 samples.

How we read this: 14 replicated groups read from 39 sample titles; they account for 28 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
Datasets on a similar topic

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