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Human single nuclear RNA sequencing identifies CD47 as a therapeutic target for doxorubicin-induced cardiomyopathy

GSE292067 Homo sapiens (human) Single-nucleus RNA-seq 25 samples Submitted 2025/08/18 Platform GPL24676
At a glance

Single-nucleus RNA-seq · human · 25 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
25 samples: 11 × AJAI-Zhen-DoxT2 vs 8 × AJAI-Zhen-Ctrl1 vs 6 × AJAI-Zhen-DCM4Groups 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
Human Single-Nucleus RNA Sequencing Identifies CD47 as a Therapeutic Target for Doxorubicin-Induced CardiomyopathyCirculation · 2025
Summary (written by the submitters)
Doxorubicin cardiomyopathy (DoxCM) remains a significant clinical problem, yet its underlying mechanisms remain incompletely understood. Identifying DoxCM mechanisms that can be translated into therapeutic interventions may improve patient outcomes. We performed single nuclear RNA-sequencing on left ventricular (LV) myocardial tissue from patients with DoxCM versus non-ischemic cardiomyopathy and non-failing donors.
Read the full summary ↓
This approach aimed to elucidate the transcriptional changes associated with DoxCM. Additionally, we conducted immunostaining, flow cytometry, antibody neutralization, and cell depletion studies to validate our findings and define in vivo mechanisms.Compared to both donors and non-ischemic cardiomyopathy, LV myocardium from DoxCM patients exhibited increased periostin-positive (POSTN+) activated fibroblasts, down-regulation of genes involved in phagocytosis, and increased expression of the anti-phagocytic molecule CD47. Immunostaining of human cardiac sections and murine studies demonstrated increased POSTN+ cells and CD47 in DoxCM and in a murine breast cancer model. CD47 antibody neutralization both prevented and treated Dox-induced reduction in LV ejection fraction and fibrosis. Mechanistically, depletion of resident cardiac macrophages blocked the cardioprotective effects of CD47 neutralization and clearance of cardiac fibroblasts. Our data support CD47 as a disease-specific target and promising therapeutic approach for mitigating cardiac dysfunction in DoxCM
Published in
Human Single-Nucleus RNA Sequencing Identifies CD47 as a Therapeutic Target for Doxorubicin-Induced Cardiomyopathy
Guo Z, Ataran A, Ma P et al. · Circulation 2025 · PMID 40808662 · doi:10.1161/CIRCULATIONAHA.124.071217
This dataset
Open GSE292067 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 GSE292067_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 PRJNA1236641 and SRA study SRP570663. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40808662) ↗
Study design
11 × AJAI-Zhen-DoxT2 vs 8 × AJAI-Zhen-Ctrl1 vs 6 × AJAI-Zhen-DCM4

Supports a between-group comparison across 25 samples.

How we read this: 3 replicated groups read from 25 sample titles; they account for 25 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
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