J Vis Exp. 2026 Aug 25;(234). doi: 10.3791/72286.
ABSTRACT
Dilated cardiomyopathy (DCM) is characterized by left ventricular dilation and systolic dysfunction and is associated with mitochondrial dysfunction and immune-inflammatory activation. However, aging-related molecular signatures and mitochondrial regulatory pathways in DCM remain incompletely understood. This study analyzed six bulk transcriptomic datasets and one single-cell RNA sequencing dataset from the Gene Expression Omnibus database. After data normalization, batch correction, and cell-type annotation, aging- and mitochondria-related candidate genes were identified using differential expression analysis, weighted gene co-expression network analysis, and protein-protein interaction network construction. Core genes were further screened using least absolute shrinkage and selection operator regression, random forest, and support vector machine-recursive feature elimination. Immune-cell infiltration, cell-cell communication, and molecular subtyping analyses were performed to characterize the cardiac immune microenvironment in DCM. A total of 66 aging-related genes and 16 mitochondria-related genes were associated with DCM and were mainly enriched in hypoxia-inducible factor-1 signaling, oxidative phosphorylation, and nitric oxide synthase-related pathways. Machine learning and single-cell RNA sequencing analyses identified SERPINE1, TGFB2, CYBB, and TLR2 as core genes. CYBB and TLR2 were highly expressed in monocytes and macrophages, whereas SERPINE1 and TGFB2 were predominantly expressed in stromal cells. Immune landscape analysis showed increased pro-inflammatory macrophage activation and altered cell-cell communication in DCM samples. Based on core gene expression, DCM samples were divided into two molecular subtypes associated with vascular endothelial growth factor signaling and primary bile acid biosynthesis, respectively. This protocol provides an integrated framework for identifying candidate biomarkers and molecular subtypes in DCM.
PMID:42644501 | DOI:10.3791/72286