Identification of the metabolic state of surviving cardiomyocytes in the human infarcted heart by spatial single-cell transcriptomics

Abstract

Background and purpose: The metabolic status of surviving cardiomyocytes (CM) in the myocardial tissues of patients who sustained myocardial infarction (MI) is largely unknown. Spatial single-cell RNA-sequencing (scRNA-seq) is a novel tool that enables the unbiased analysis of RNA signatures within intact tissues. We employed this tool to assess the metabolic profiles of surviving CM in the myocardial tissues of patients post-MI.Methods: A spatial scRNA-seq dataset was used to compare the genetic profiles of CM from patients with MI and control patients; we analyzed the metabolic adaptations of surviving CM within the ischemic niche. A standard pipeline in Seurat was used for data analysis, including normalization, feature selection, and identification of highly variable genes using principal component analysis (PCA). Harmony was used to remove batch effects and integrate the CM samples based on annotations. Uniform manifold approximation and projection (UMAP) was used for dimensional reduction. The Seurat "FindMarkers" function was used to identify differentially expressed genes (DEGs), which were analyzed by the Gene Ontology (GO) enrichment pathway. Finally, the scMetabolism R tool pipeline with parameters method = VISION (Vision is a flexible system that utilizes a high-throughput pipeline and an interactive web-based report to annotate and explore scRNA-seq datasets in a dynamic manner) and metabolism.type = Kyoto Encyclopedia of Genes and Genomes (KEGG) was used to quantify the metabolic activity of each CM.Results: Analysis of spatial scRNA-seq data showed fewer surviving CM in infarcted hearts than in control hearts. GO analysis revealed repressed pathways in oxidative phosphorylation, cardiac cell development, and activated pathways in response to stimuli and macromolecular metabolic processes. Metabolic analysis showed downregulated energy and amino acid pathways and increased purine, pyrimidine, and one-carbon pool by folate pathways in surviving CM.Conclusions: Surviving CM within the infarcted myocardium exhibited metabolic adaptations, as evidenced by the downregulation of most pathways linked to oxidative phosphorylation, glucose, fatty acid, and amino acid metabolism. In contrast, pathways linked to purine and pyrimidine metabolism, fatty acid biosynthesis, and one-carbon metabolism were upregulated in surviving CM. These novel findings have implications for the development of effective strategies to improve the survival of hibernating CM within the infarcted heart.

Being Eaten Alive: How Energy-Deprived Cells Are Disposed of, Mediated by C-Reactive Protein—Including a Treatment Option

“…In the ischemic tissue, there is no immediate tissue necrosis, but a switch of energy metabolism to anaerobic glycolysis, leading to a marked shortage of energy in the individual cardiomyocytes. After this, the cardiomyocytes go into a state of hibernation (myocardial hibernation) or stunning up to the time when metabolism returns to the aerobic mode, which resolves the energy shortage [ 45 , 46 ]. In principle, these cardiomyocytes survive only if they are not labeled by CRP and are consequently removed by phagocytes.…”

Metabolism, inflammation, and cardiovascular diseases from basic research to clinical practice

“…A combination of single-cell RNA-sequencing and spatial transcriptomics analysis allows investigation of the changes at the single cell level, and is helpful in understanding the basis of global changes [5] . Using spatial single-cell transcriptomics, Dr. Shen, Prof. Tang (Augusta University, USA) and his colleagues [6] demonstrated severe metabolic shift in cardiomyocytes that survived myocardial infarction in human subjects in their study. The changes included downregulation of fatty acid oxidation, mitochondrial oxidative phosphorylation (OXPHOS) and tricarboxylic acid cycle (TCA) activities, and a concomitant increase in the biosynthesis of fatty acids; these changes are known to protect membrane integrity and inhibit ROS generation upon inflammatory injury.…”