Gene expression

What cell programs mark ischemic cardiomyopathy?

Simonson B, Chaffin M, Hill MC, et al. · Cell reports · 2023

Open access · cc by · source: Europe PMC

snRNA-seq of ~100k cardiac nuclei showed fewer cardiomyocytes and more specialized endothelial states in ICM, overlapping other end-stage cardiomyopathy programs.

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Study at a glance

Design: Case-control — snRNA-seq of non-infarct LV from ICM transplant recipients vs NF controls
N: N=15 · 7 ICM + 8 NF; 99,684 nuclei after QC
Population: Human LV nuclei from ICM and non-failing hearts
Outcome: Cell-composition and transcriptional differences in ICM vs NF

Structured fields used in claim comparison tables when every cited study has a complete layer.

Key findings

99,684 QC nuclei in 16 clusters. ICM had fewer cardiomyocytes and more lymphatic/angiogenic/arterial endothelial cells; transcriptional changes resembled HCM/DCM datasets.

Methodology

Profiled non-infarct LV nuclei from ICM transplant recipients and non-failing controls with snRNA-seq.

Limitations

End-stage transplant tissue may not represent early ICM; composition shifts are associative.

How this study connects

Role on claims

Each row is a claim on a concept or method page where this paper supports, challenges, or qualifies the statement. Roles are hand-checked — not a model guess.

SupportsSingle-cell RNA-seq (scRNA-seq)method
snRNA-seq maps end-stage ischemic cardiomyopathy cell states.
Profiling ~100k human cardiac nuclei showed fewer cardiomyocytes and more specialized endothelial states in ICM versus non-failing controls, with programs overlapping other end-stage cardiomyopathies.
Evidence for the claim as stated.
SupportsSingle-cell QC (mitochondrial filtering)method
Disease atlases depend on QC’d nuclei before cell-state claims.
ICM snRNA-seq profiles ~100k QC’d cardiac nuclei before composition claims—reminding students that atlas biology sits atop filtering decisions.
Evidence for the claim as stated.
SupportsSingle-cell QC (mitochondrial filtering)method
A mito-filter methods result, a foundation-model benchmark, and a disease atlas answer different layers of the single-cell stack.
Evidence for the claim as stated.

Open questions

Tensions this paper is part of

From concept pages' “where studies disagree.” Disagreement means the same question; scope means different assays, populations, or outcomes.

Scope difference — different assays, populations, or outcomes
SupportsSingle-cell QC (mitochondrial filtering)
A mito-filter methods result, a foundation-model benchmark, and a disease atlas answer different layers of the single-cell stack.
Also on this tension
- Supports · High-mito filters can discard living cancer cell states
- Supports · Simple baselines beat cell foundation models on Perturb-seq

History

When this study was placed

Dated entries from the concept change log — when this paper was added or removed as support, challenge, or qualifier on a claim.

2026-09-15
Placed as supporting evidence on Single-cell RNA-seq (scRNA-seq)
Profiling ~100k human cardiac nuclei showed fewer cardiomyocytes and more specialized endothelial states in ICM versus non-failing controls, with programs overlapping other end-stage cardiomyopathies.