Five hub genes (VAMP8, STX2, MCOLN1, DERL1, and PTP4A2) were identified as candidate molecular markers of heart failure reflecting alterations in a lysophagy- and vesicular-transport-related program associated with FOLR2+ tissue-resident macrophages.
Key Findings
Results
Five hub genes—VAMP8, STX2, MCOLN1, DERL1, and PTP4A2—were consistently and markedly decreased in failing myocardial tissue.
Hub genes were identified by integrating bulk transcriptome datasets (GSE16499, GSE57338, GSE76701) with differential expression analysis
Candidate genes were screened using two machine learning approaches: support vector machine-recursive feature elimination (SVM-RFE) and least absolute shrinkage and selection operator (LASSO) regression
These genes were primarily linked to SNARE-dependent vesicle trafficking and lysophagy regulation
Decreased expression was validated in a murine HF model at the mRNA level for all five genes, and at the protein level for VAMP8, MCOLN1, and DERL1
Results
A diagnostic model incorporating the five hub genes demonstrated good discriminatory performance in both the training dataset and a small independent validation cohort.
The model was built using the bulk myocardial transcriptome datasets GSE16499, GSE57338, and GSE76701 as training data
An independent validation cohort was used to assess generalizability, though the cohort was described as small
The authors note the results support 'further evaluation of their potential diagnostic value' rather than confirming clinical utility
Discriminatory performance was characterized as 'good' by the authors
Results
Single-cell transcriptomic analysis indicated that the five hub genes were primarily enriched in cardiac FOLR2+ tissue-resident macrophages (TRMs).
Single-cell analysis used the human cardiac dataset GSE145154
FOLR2+ TRMs represent a specific tissue-resident macrophage subpopulation within the cardiac immune microenvironment
Pseudotime analysis associated this gene module with FOLR2+ TRM cell states
Cell-cell communication analyses predicted interactions between this macrophage subpopulation and cardiac stromal cells
Results
VAMP8 overexpression in Ang II/LLOMe-induced H9c2 cardiomyocytes was associated with reduced cellular injury and attenuation of lysosomal and autophagic dysfunction.
H9c2 cells were used as an in vitro cardiomyocyte model, stimulated with angiotensin II (Ang II) and LLOMe to induce lysosomal damage
VAMP8 overexpression was associated with reduced cardiomyocyte injury markers
Overexpression attenuated changes in the abundance of lysosome- and autophagy-related proteins
Fewer ultrastructural abnormalities were observed under electron microscopy in VAMP8-overexpressing cells
The authors describe this as suggesting 'a potential cardioprotective effect'
Results
Immune infiltration assessment and functional enrichment analysis linked the hub gene module to alterations in the cardiac immune microenvironment in heart failure.
Gene Set Enrichment Analysis (GSEA) and functional enrichment analysis were performed on the differentially expressed lysophagy-related genes
Immune infiltration assessment was conducted as part of the multi-omic integration pipeline
Regulatory network analysis was also performed to characterize upstream regulators of the hub genes
The module was connected to SNARE-dependent vesicle trafficking pathways in addition to lysophagy regulation
Background
Lysosomal impairment and loss of autophagic homeostasis are recognized contributors to myocardial damage and ventricular remodeling in heart failure.
The study was motivated by increasing recognition of lysophagy's role in HF pathology
Lysophagy refers to the selective autophagic clearance of damaged lysosomes
The study integrated bulk and single-cell transcriptomics to investigate this pathway's gene-level manifestations in human HF tissue
Three bulk RNA datasets (GSE16499, GSE57338, GSE76701) were integrated to improve robustness of differential expression findings
What This Means
This research suggests that heart failure involves significant disruption of a cellular cleanup system called lysophagy—the process by which cells identify and dispose of damaged lysosomes (the cell's recycling centers). By analyzing gene activity data from human heart tissue and combining it with single-cell data that can identify which specific cell types are involved, researchers identified five genes (VAMP8, STX2, MCOLN1, DERL1, and PTP4A2) that are consistently reduced in failing hearts. These genes are involved in how cells transport and clear damaged material, and their reduction may impair the heart's ability to maintain healthy cellular function.
A particularly notable finding is that these five genes appear to be most active in a specific type of immune cell called FOLR2+ tissue-resident macrophages—immune cells that permanently reside in heart tissue rather than being recruited from the bloodstream. This suggests that the failure of cellular cleanup processes in heart disease may be closely tied to changes in the heart's resident immune cell population, and that these macrophages may communicate with other structural cells in the heart in ways that contribute to disease progression. The researchers also found that artificially increasing levels of one of these genes (VAMP8) in lab-grown heart cells appeared to reduce damage and preserve normal cellular structure under stress conditions.
This research suggests that monitoring these five genes could eventually help in identifying or characterizing heart failure, and that the lysophagy pathway in cardiac immune cells may represent a new direction for understanding—and potentially targeting—heart failure mechanisms. However, the diagnostic model was validated only in a small cohort, and the cell experiments were conducted in a lab setting, so further research in larger human studies and animal models would be needed before these findings could have clinical applications.
Cheng Q, Wang Y, Wang D, Wu G, Liu B, Yuan Q, et al.. (2026). Integrated Bulk and Single-Cell Transcriptomic Analyses Identify a FOLR2+ Tissue-Resident Macrophage-Associated Lysophagy Gene Module in Heart Failure.. Genes. https://doi.org/10.3390/genes17080957