GEO series

Prenatal VEGF Nano-Delivery Reverses Congenital Diaphragmatic Hernia-Associated Pulmonary Abnormalities

GSE267778 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2025/05/17 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 12 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: 12 samples: 4 × Day0_control vs 4 × Day2_control vs 4 × Day2_compressionGroups 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: Prenatal VEGF Nanodelivery Reverses Congenital Diaphragmatic Hernia-associated Pulmonary AbnormalitiesAmerican journal of respiratory and critical care medicine · 2025

Summary (written by the submitters)

Congenital diaphragmatic hernia (CDH) affects 1-2 in 5,000 neonates who are born with hypoplastic lungs leading to significant morbidity and mortality. In severe cases tracheal occlusion (TO) can be offered to promote lung growth through airway stretch, but such growth remains limited. Vascular endothelial growth factor (VEGF), a key mediator of normal lung development, is downregulated in animal models of CDH, but its role in CDH-associated lung pathology in humans is not known.

Read the full summary ↓

Using 18-22 post-conception week fetal lungs from CDH patients, we demonstrated for the first time that lung hypoplasia in this setting is associated with impaired VEGF expression and reduced pulmonary epithelial cell proliferation. We then developed a human ex vivo model of fetal lung compression relevant to CDH, in which a mechanical constraint was added to cultured lung fragments. Our model recapitulated impaired branching morphogenesis observed in CDH fetal lungs, and scRNAseq revealed significant reduction of the proliferative potential of terminal bud epithelial progenitors with concomitant reduction in expression of VEGF. Importantly, the exogenous supplementation of recombinant VEGF in this setting induced a significant increase of terminal bud progenitor cell proliferation, comparable to non-compressed control tissue. Finally, we developed a novel therapeutic agent delivery platform by conjugating recombinant VEGF on the surface of nanoparticles (nanodiamonds; ND-VEGF). In utero, intratracheal administration of ND-VEGF into the in vivo TO Nitrofen rat model of CDH resulted in lung growth as well as pulmonary arterial remodelling leading to histological appearances comparable to healthy controls. The beneficial effects of ND-VEGF were abrogated by co-administration of a selective VEGF-receptor-2 (KDR/Flk1) inhibitor and were not observed when unconjugated VEGF was delivered. This innovative approach could have a significant impact on the treatment of CDH.

Published in

Prenatal VEGF Nanodelivery Reverses Congenital Diaphragmatic Hernia-associated Pulmonary Abnormalities

Loukogeorgakis SP, Michielin F, Al-Juffali N et al. · American journal of respiratory and critical care medicine 2025 · PMID 39965074 · doi:10.1164/rccm.202401-0161OC

This dataset

Open GSE267778 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 GSE267778_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 PRJNA1112851 and SRA study SRP508403. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39965074) ↗

Study design

4 × Day0_control vs 4 × Day2_control vs 4 × Day2_compression

Supports a between-group comparison across 12 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 12 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

GSM8278611 Day0_control_rep1 Day0_control
GSM8278612 Day0_control_rep2 Day0_control
GSM8278613 Day0_control_rep3 Day0_control
GSM8278614 Day0_control_rep4 Day0_control
GSM8278615 Day2_control_rep1 Day2_control
GSM8278616 Day2_control_rep2 Day2_control
GSM8278617 Day2_control_rep3 Day2_control
GSM8278618 Day2_control_rep4 Day2_control
GSM8278619 Day2_compression_rep1 Day2_compression
GSM8278620 Day2_compression_rep2 Day2_compression
GSM8278621 Day2_compression_rep3 Day2_compression
GSM8278622 Day2_compression_rep4 Day2_compression

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