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Engineered probiotics limit T-cell driven CNS autoimmunity by activating AHR-KLF4-FADS3 signaling in intestinal dendritic cells

GSE296433 Mus musculus (mouse) Single-cell RNA-seq 40 samples Submitted 2026/05/05 Platform GPL21273
At a glance

Single-cell RNA-seq · mouse · 40 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
40 samples: 10 conditions, mostly with about 4 replicates eachGroups 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.
Summary (written by the submitters)
Dendritic cells (DCs) control the induction of effector immune responses and tolerance. The development and function of DCs is regulated by transcriptional, epigenetic and metabolic programs, but the mechanisms controlling DC metabolism and its impact on autoimmune diseases remain poorly understood.
Read the full summary ↓
Here, using single-cell and bulk RNA-sequencing, in vivo DC-specific gene perturbations, multiple sclerosis (MS) clinical samples and preclinical models, we identified an aryl hydrocarbon receptor (AHR) - Krüppel-like factor 4 (KLF4) - fatty acid desaturase enzyme 3 (FADS3) axis which drives the production of docosahexaenoic acid (DHA) in DCs and limits effector T-cell responses and the development of experimental autoimmune encephalomyelitis (EAE). Furthermore, we used synthetic biology approaches to engineer a probiotic (EcNIAA) that produces the AHR agonist indole-3-acetic acid (IAA) as a tool to limit pathogenic inflammatory responses. EcNIAA administration activates AHR-KLF4-FADS3 signaling in intestinal DCs, increasing DHA production and suppressing encephalitogenic T cells that originate in the gut and migrate to the central nervous system to promote autoimmune pathology. Briefly, we identified a novel immunometabolic axis that operates in DCs to limit effector T-cell responses, and can be targeted with engineered probiotics to treat autoimmunity.
This dataset
Open GSE296433 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 GSE296433_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 PRJNA1259386 and SRA study SRP583308. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
10 conditions, mostly with about 4 replicates each
CNS_WT ×4 CNS_FADS3 ×4 Spleen_WT ×4 Spleen_FADS3 ×4 CMP9_CNS_CTRL ×4 CMP9_CNS_IAA ×4 CMP11_Spleen_WT ×4 CMP11_Spleen_AH ×4 +2 more

Supports a between-group comparison across 40 samples.

How we read this: 10 replicated groups read from 40 sample titles; they account for 40 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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