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ICOSL, OX40L, and CD30L Control Persistence of Asthmatic CD4 Trm Cells

GSE235059 Mus musculus (mouse) Single-cell RNA-seq 80 samples Submitted 2025/02/13 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 80 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
80 samples: 16 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
ICOSL, OX40L, and CD30L control persistence of asthmatic CD4 tissue-resident memory CD4 T cellsThe Journal of allergy and clinical immunology · 2025
Summary (written by the submitters)
Tissue-resident memory T cells (Trm) are central to maintaining autoimmune and inflammatory disease. Modulation of their continued replenishment in tissues has significant implications for clinical treatment. In a murine model of lung inflammation, scRNA-seq revealed the complexity of antigen-responding CD4+ Trm, encompassing many pathogenic subpopulations including Th2, Th17, Th1 and CTL, but suggested several targets for therapeutic intervention, with significant co-expression of the costimulatory molecules OX40, ICOS, CD30, and CD30L throughout these T cells.
Read the full summary ↓
Inhibiting ICOSL alone, or co-blocking OX40L and CD30L, with neutralizing antibodies, only partially suppressed the response of Trm to recall antigen, whereas inhibiting all three molecules strongly reduced the accumulation of Trm-derived effector memory T cells, and ablated all aspects of lung inflammation. Most importantly, transient therapeutic inhibition of these molecules together prevented the continued accumulation and long-term persistence of induced Trm, leading to a state of tolerance such that subsequent exposure to antigen failed to re-establish a pathogenic inflammatory response. These data show that costimulatory molecules are critical for reactivation and persistence of pathogenic CD4+ Trm, and reveal several therapeutic combinations that are applicable for treatment of lung inflammatory disease and potentially multiple autoimmune diseases.
Published in
ICOSL, OX40L, and CD30L control persistence of asthmatic CD4 tissue-resident memory CD4 T cells
Sethi GS, Ramamoorthy Premlal AL, Chawla A et al. · The Journal of allergy and clinical immunology 2025 · PMID 39921040 · doi:10.1016/j.jaci.2024.12.1097
This dataset
Open GSE235059 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 GSE235059_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 PRJNA984276 and SRA study SRP444175. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39921040) ↗
Study design
16 conditions, mostly in duplicate
Day21 ×10 Day22 ×10 Day23 ×10 Day24 ×10 Day47 ×10 Day48 ×10 Day45_6_GuSe ×2 Day45_8_GuSe ×2 +8 more

Supports a between-group comparison across 80 samples.

How we read this: 16 replicated groups read from 80 sample titles; they account for 80 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

+ 40 more — browse all 80 samples with per-sample file links →

Datasets on a similar topic

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