Identifying and validating hypoxia- and metabolism-related hub genes and cell communication in atherosclerosis.

Background: Atherosclerosis (AS) is a multifactorial disorder characterized by plaque formation, with hypoxia and metabolic pathways playing central roles in its pathogenesis. However, the differentially expressed metabolism-hypoxia-related genes (DE-MH-RGs) contributing to AS remain largely undefined. This study aimed to characterize DE-MH-RGs to uncover their potential regulatory mechanisms in AS. Results: Single-cell sequencing data, AS-related datasets, 200 hypoxia-related genes (HRGs), and 2,752 metabolism-related genes (MRGs) were employed for analysis. Single-cell sequencing identified distinct cell subpopulations, and differential gene expression was assessed between the AS and normal groups in GSE100927. DE-MH-RGs were determined by intersecting differentially expressed HRGs and MRGs. Functional enrichment of DE-MH-RGs was conducted through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, followed by protein-protein interaction (PPI) network construction. Hub genes were identified using least absolute shrinkage and selection operator (LASSO) logistic regression and further validated by gene set enrichment analysis (GSEA) and Gene Set Variation Analysis (GSVA). Immune feature analysis assessed immune cell proportions and identified potential drug candidates. Hub genes were also pinpointed in single-cell data (GSE159677) using ReactomeGSA, cell communication, and pseudotime analyses. Single-cell analysis revealed five distinct subpopulations-T lymphocytes, endothelial cells, macrophages, vascular smooth muscle cells (VSMCs), and B lymphocytes-and 141 DE-MH-RGs. Enrichment analysis highlighted the association of these genes with circulatory system pathways, including vascular functions and responses to oxygen and hypoxia. The hub genes, RYR2, ABCC9, KCNJ2, EGFR, and SLC7A8, exhibited strong diagnostic potential. GSVA analysis linked the hub genes to several metabolic pathways. Thirteen immune cell types showed significant differences between normal and AS samples. Potential therapeutic agents, such as afatinib, were identified. The hub genes were primarily located in VSMCs. Most AS cells displayed low differentiation levels. Conclusions: Transcriptomic data from AS identified key hub genes related to hypoxia and metabolism, offering valuable insights for future research.