GEO series

Epithelial RXRα activity induced by Westernization of diet instigates enteritis in Crohn’s disease

GSE284139 Mus musculus (mouse) RNA-seq (gene expression) 19 samples Submitted 2025/12/12 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 19 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: 19 samples
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: Metabolic stress sensing by epithelial RXRα links westernization of diet with Crohn's diseaseCell metabolism · 2026

Summary (written by the submitters)

Westernization of diet, partly characterised by excess of long-chain fatty acids, provides a risk for developing Crohn’s disease (CD), and perturbs the function of specialized intestinal epithelium termed Paneth cells. The lack of a cellular and molecular framework of lipid sensing in intestinal inflammation poses a constraint to understanding detrimental effects of Western diets.

Read the full summary ↓

Here, we report how Paneth cell sensing of lipid excess in a Western diet is translated into CD-like intestinal inflammation. Small intestinal transcriptional profiling of CD patients from three independent cohorts identified increased activity of the transcription factor retinoid x receptor alpha (RXRα) specifically in intestinal epithelium. Intestinal epithelial RXRα activity was induced by polyunsaturated fatty acid (PUFA) excess in a Western diet in mice with CD-like enteritis. PUFA-induced RXRα activity in Paneth cells governed chronic transmural enteritis by enabling the expression of the interleukin 8 homologue CXCL1. Blockade of PUFA-induced RXRα activity by 9-cis retinoic acid ameliorated CXCL1 production and enteritis, and patients receiving isotretinoin therapy (a precursor for 9-cis retinoic acid) displayed reduced odds of developing CD. Collectively, we identify Paneth cells as gatekeepers of lipid stress that exploit RXRα to sense and translate PUFA excess into enteritis, which could be targeted to prevent or treat CD.

Published in

Metabolic stress sensing by epithelial RXRα links westernization of diet with Crohn's disease

Meyer M, Grabherr F, Plattner C et al. · Cell metabolism 2026 · PMID 41365295 · doi:10.1016/j.cmet.2025.11.008

This dataset

Open GSE284139 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 GSE284139_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 PRJNA1197431 and SRA study SRP551092. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41365295) ↗

Samples in this study

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+ 19 more — browse all 19 samples with per-sample file links →

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