GEO series

Proliferative diabetic retinopathy subtypes defined by immune defense and endothelial mitochondrial dysfunction

GSE307925 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/09/19 Platform GPL34281

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples: 7 × PDR, CD31high, sample vs 5 × PDR, CD31low, 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: Proliferative diabetic retinopathy subtypes defined by immune defense and endothelial mitochondrial dysfunctionSignal transduction and targeted therapy · 2025

Summary (written by the submitters)

Proliferative diabetic retinopathy (PDR) is a major complication of diabetes characterized by pathological angiogenesis in the retina. Standard treatment includes vitrectomy to remove these abnormal vessels, and the resulting clinical specimens provide an opportunity to define drivers of PDR. Here, we profiled endothelial and immune cells from such samples to identify disease mechanisms.

Read the full summary ↓

In some patients, endothelial cells were more abundant, whereas in others, immune cells predominated. Immune cells exhibit gene expression programs directed against pathological endothelium, suggesting an endogenous defense that may explain the scarcity of endothelial cells in certain cases. Preoperative anti-vascular endothelial growth factor (VEGF) therapy altered transcriptional programs in both endothelial and immune cells, indicating that its effects extend beyond the vasculature. A comparison of endothelial signatures from PDR patients and nondiabetic donor retinas revealed a distinct molecular program in PDR, prominently marked by mitochondrial dysfunction. In contrast, endothelial cells from the murine oxygen-induced retinopathy (OIR) model lacked mitochondrial dysfunction, although other features of pathological angiogenesis were shared. These findings suggest that PDR is not a uniform disease but comprises distinct types characterized by either immune-mediated clearance of pathological vessels or endothelial mitochondrial dysfunction. They also revealed that anti-VEGF therapy influences both endothelial and immune compartments, with implications for treatment strategies. Finally, the data clarify both the relevance and limitations of the OIR model for preclinical testing of new therapeutic targets.

Published in

Proliferative diabetic retinopathy subtypes defined by immune defense and endothelial mitochondrial dysfunction

McCann MA, Baccouche B, Li Y et al. · Signal transduction and targeted therapy 2025 · PMID 41120275 · doi:10.1038/s41392-025-02448-9

This dataset

Open GSE307925 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 GSE307925_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 PRJNA1327830 and SRA study SRP619673. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41120275) ↗

Study design

7 × PDR, CD31high, sample vs 5 × PDR, CD31low, sample

Supports a between-group comparison across 12 samples.

How we read this: 2 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

GSM9234046 PDR, CD31low, sample1 PDR, CD31low, sample
GSM9234047 PDR, CD31low, sample2 PDR, CD31low, sample
GSM9234048 PDR, CD31low, sample3 PDR, CD31low, sample
GSM9234049 PDR, CD31low, sample4 PDR, CD31low, sample
GSM9234050 PDR, CD31low, sample5 PDR, CD31low, sample
GSM9234051 PDR, CD31high, sample1 PDR, CD31high, sample
GSM9234052 PDR, CD31high, sample2 PDR, CD31high, sample
GSM9234053 PDR, CD31high, sample3 PDR, CD31high, sample
GSM9234054 PDR, CD31high, sample4 PDR, CD31high, sample
GSM9234055 PDR, CD31high, sample5 PDR, CD31high, sample
GSM9234056 PDR, CD31high, sample6 PDR, CD31high, sample
GSM9234057 PDR, CD31high, sample7 PDR, CD31high, sample

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