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High-Fat Diet Causes Rapid Loss of Intestinal Group 3 Innate Lymphoid Cells Through Microbiota-Driven Inflammation

GSE317764 Homo sapiens (human) RNA-seq (gene expression) 270 samples Submitted 2026/05/26 Platform GPL19057Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 270 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
270 samples: 81 conditions, mostly in triplicateGroups 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
High-fat diet causes rapid loss of intestinal group 3 innate lymphoid cells through microbiota-driven inflammation and mitochondrial stressImmunity · 2026
Summary (written by the submitters)
Group 3 innate lymphoid cells (ILC3s) are critical sensory hubs to maintain intestinal immunity while adapting to environmental changes, including food intake and microbiota composition. Nutritional stress such as feeding on a high-fat diet (HFD) impairs ILC3s homeostasis, but the drivers underlying this phenotype remain elusive. Here, we found that intestinal ILC3s are depleted in overweight and obese humans, similarly to HFD-induced obese mice.
Read the full summary ↓
However, we identified that ILC3s loss is not dependent on excessive calorie intake, weight gain, or glucose intolerance. Instead, we found that ILC3s impairment starts upon hours of HFD consumption, inducing microbial efflux. As a result, tissue-resident mononuclear phagocytes (MNPs) become proinflammatory, driving ILC3 cell death. We determined that the microbiota-driven stimulation overrides lipid-laden ILC3s ability to perform fatty acid oxidation, causing mitochondrial damage due to the accumulation of lipid peroxides. Collectively, our findings define the mechanism driving ILC3s maladaptation to fat-microbiota crosstalk and raise new considerations for understanding intestinal homeostasis and inflammation.
Published in
High-fat diet causes rapid loss of intestinal group 3 innate lymphoid cells through microbiota-driven inflammation and mitochondrial stress
Torrico EC, Kaptein P, Laalouhmi F et al. · Immunity 2026 · PMID 41916320 · doi:10.1016/j.immuni.2026.02.014
This dataset
Open GSE317764 in finder → Find more 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 GSE317764_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 PRJNA1415199 and SRA study SRP667836. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41916320) ↗
Study design
81 conditions, mostly in triplicate
Duodenum, Chow diet, 1Wk, Sample ×6 Duodenum, HFD, 1Wk, Sample ×6 Jejunum, Chow diet, 1Wk, Sample ×6 Jejunum, HFD, 1Wk, Sample ×6 Ileum, Chow diet, 1Wk, Sample ×6 Ileum, HFD, 1Wk, Sample ×6 Colon, Chow diet, 1Wk, Sample ×6 Colon, HFD, 1Wk, Sample ×6 +82 more

Supports a case/control comparison: 9 samples read as cases, 10 as controls.

How we read this: 81 replicated groups read from 270 sample titles; they account for 261 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

+ 230 more — browse all 270 samples with per-sample file links →

Datasets on a similar topic

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