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Involvement of Naïve CD4+ T cells in the Pathogenesis of Osimertinib-induced Pneumonitis

GSE248539 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2025/10/23 Platform GPL28457
At a glance

RNA-seq (gene expression) · mouse · 11 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
11 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
Involvement of naïve T cells in the pathogenesis of osimertinib-induced pneumonitisScientific reports · 2025
Summary (written by the submitters)
Background: Osimertinib, a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI), has exhibited significant efficacy in the treatment of EGFR-mutated non-small cell lung cancer. Drug-induced interstitial lung disease is a potentially fatal complication of osimertinib therapy. Although there is often an elevated number of lymphocytes in the bronchoalveolar lavage fluid (BALF) in patients with drug-induced pneumonitis, the precise involvement of lymphocytes in osimertinib-induced pneumonitis remains unclear.
Read the full summary ↓
Therefore, we investigated the pathogenesis of osimertinib-induced pneumonitis using BALF obtained from patients with osimertinib-induced pneumonitis and a mouse model of osimertinib-induced pneumonitis. Methods: Mass cytometry was used to analyze BALF cells obtained from patients with osimertinib-induced pneumonitis. A mouse model of osimertinib-induced pneumonitis was established by the administration of naphthalene and osimertinib. Histopathological evaluation, body weight measurements, BALF analysis, and RNA sequencing were performed to investigate immune cell involvement and the mechanisms underlying osimertinib-induced pneumonitis. Results: Analysis of BALF cells obtained from patients with osimertinib-induced pneumonitis revealed the expansion of CCR7+ CD45RA+ naïve T cells. In the mouse model, osimertinib administration following naphthalene-induced club cell injury exacerbated lung inflammation, leading to increased inflammatory cell infiltration and body weight loss. BALF analysis revealed elevated proportions of T cells, including CD4+ and double-negative T cells, in mice administered osimertinib after naphthalene treatment. Bulk RNA sequencing identified upregulation of chemokine-related biological processes, with increased the expression of C-C motif chemokine ligand 21 (Ccl21) and C-C motif chemokine ligand 8 (Ccl8) in lung tissue, and immunostaining confirmed elevated expression of Ccl21 and Ccl8 in the distal bronchiolar epithelium. Conclusion: This study provides insights into the immune mechanisms underlying osimertinib-induced pneumonitis, which are crucial for overcoming this fatal complication in EGFR-positive non-small cell lung cancer.
Published in
Involvement of naïve T cells in the pathogenesis of osimertinib-induced pneumonitis
Ando H, Tsubouchi K, Yanagihara T et al. · Scientific reports 2025 · PMID 40148432 · doi:10.1038/s41598-025-95271-9
This dataset
Open GSE248539 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 GSE248539_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 PRJNA1044723 and SRA study SRP473963. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40148432) ↗
Samples in this study

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