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Endothelial Sensitivity to Pro-Fibrotic Signals Links Systemic exposure to Pulmonary Fibrosis

GSE286040 Homo sapiens (human) RNA-seq (gene expression) 96 samples Submitted 2025/05/26 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 96 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
96 samples: 24 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.
Paper
Endothelial sensitivity to pro-fibrotic signals links systemic exposure to pulmonary fibrosisCell death & disease · 2025
Summary (written by the submitters)
Pulmonary fibrosis (PF) is a life-threatening condition characterised by excessive extracellular matrix deposition and tissue scarring. While much of PF research has focused on alveolar epithelial cells and fibroblasts, endothelial cells have emerged as active contributors to the disease initiation, especially in the context of systemic exposure to pro-fibrotic substances.
Read the full summary ↓
Here, we investigate early transcriptomic and secretory responses of human umbilical vein endothelial cells (HUVEC) to subtoxic doses of bleomycin, a known pro-fibrotic agent, and TGF-beta, a key cytokine in fibrosis. Bleomycin exposure induced a rapid and extensive shift in the endothelial transcriptional programme, including signatures of endothelial to mesenchymal transition, cellular senescence, and immune cell recruitment. These findings suggest endothelial cells as early initiators of pro-fibrotic signals, independent of contributions from other cell types. In contrast, TGF-beta effects were limited and transient, indicating its pro-fibrotic action may require another initial stimulus and interplay with other cells like fibroblasts. This study highlights the sensitivity of endothelial cells to systemic pro-fibrotic exposure and provides a blueprint of early pro-fibrotic mechanisms, emphasising their pivotal role in PF pathogenesis.
Published in
Endothelial sensitivity to pro-fibrotic signals links systemic exposure to pulmonary fibrosis
Möbus L, Ylä-Outinen L, Mannino L et al. · Cell death & disease 2025 · PMID 40623988 · doi:10.1038/s41419-025-07824-5
This dataset
Open GSE286040 in finder → Find more human 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 GSE286040_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 PRJNA1207535 and SRA study SRP555832. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40623988) ↗
Study design
24 conditions, mostly with about 4 replicates each
HUVEC cells exposed to 0 µg/ml bleomycin for … ×4 HUVEC cells exposed to 7 µg/ml bleomycin for … ×4 HUVEC cells exposed to 21 µg/ml bleomycin for… ×4 HUVEC cells exposed to 14 µg/ml bleomycin for… ×4 HUVEC cells exposed to 7 µg/ml bleomycin for … ×4 HUVEC cells exposed to 21 µg/ml bleomycin for… ×4 HUVEC cells exposed to 14 µg/ml bleomycin for… ×4 HUVEC cells exposed to 0 µg/ml bleomycin for … ×4 +16 more

Supports a between-group comparison across 96 samples.

How we read this: 24 replicated groups read from 96 sample titles; they account for 96 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

+ 56 more — browse all 96 samples with per-sample file links →

Datasets on a similar topic

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