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Consistent lack of efficacy of nintedanib in a spirometry-confirmed and bleomycin-induced mouse model of idiopathic pulmonary fibrosis

GSE308578 Mus musculus (mouse) RNA-seq (gene expression) 43 samples Submitted 2026/03/18 Platform GPL21626
At a glance

RNA-seq (gene expression) · mouse · 43 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
43 samples: 17 × BLEO-IPF Nintedanib Sample vs 16 × BLEO-IPF Nintedanib Vehicle Sample vs 10 × CTRL Vehicle SampleGroups 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
Nintedanib Lacks Efficacy in a Spirometry-Confirmed and Bleomycin-Induced Mouse Model of Idiopathic Pulmonary FibrosisBasic & clinical pharmacology & toxicology · 2026
Summary (written by the submitters)
Nintedanib, a multitargeted tyrosine kinase inhibitor, is approved for idiopathic pulmonary fibrosis (IPF) for its ability to slow lung function decline. This study systematically evaluated the effects of nintedanib across three independent treatment intervention studies in the single-dose bleomycin (BLEO) mouse model of IPF.
Read the full summary ↓
In each study, male C57BL/6J mice received a single intratracheal instillation of BLEO (n=15-18 per study) or saline (n=10 per study) and were randomized and stratified to treatment according to body weight and non-invasive whole-body plethysmography measured seven days after BLEO administration. BLEO-IPF mice were administered (PO, BID) vehicle, nintedanib (50 or 60 mg/kg), or an activin receptor-like kinase 5 inhibitor (ALK5i, SB525334, 60 mg/kg) for up to 21 days. In all studies, nintedanib consistently failed to improve lung health, as evaluated by lung function tests, biochemistry, histology and RNA sequencing. Plasma concentrations of nintedanib showed no correlation to any efficacy endpoint applied. Lung transcriptome signatures in nintedanib-treated BLEO-mice indicated upregulated mRNA expression of p-glycoprotein (P-gp), a known nintedanib efflux transporter, suggesting limited lung bioavailability of nintedanib in the model. In comparison, ALK5i significantly improved lung function and exhibited robust anti-fibrotic efficacy in the model. Collectively, these findings challenge the use of nintedanib as a benchmarking drug in the BLEO-IPF model.
Published in
Nintedanib Lacks Efficacy in a Spirometry-Confirmed and Bleomycin-Induced Mouse Model of Idiopathic Pulmonary Fibrosis
Bousamaki J, Maciag G, Petersen AG et al. · Basic & clinical pharmacology & toxicology 2026 · PMID 41826148 · doi:10.1111/bcpt.70220
This dataset
Open GSE308578 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 GSE308578_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 PRJNA1331575 and SRA study SRP622264. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41826148) ↗
Study design
17 × BLEO-IPF Nintedanib Sample vs 16 × BLEO-IPF Nintedanib Vehicle Sample vs 10 × CTRL Vehicle Sample

Supports a between-group comparison across 43 samples.

How we read this: 3 replicated groups read from 43 sample titles; they account for 43 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

+ 3 more — browse all 43 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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