Integrated Omics Approach to Delineate the Mechanisms of Doxorubicin-Induced Cardiotoxicity

Abstract Doxorubicin (DOX) is an effective chemotherapy whose clinical utility is limited by cardiotoxicity. To investigate underlying mechanisms, we employed a multi-omics approach integrating transcriptomic and proteomic profiling leveraging established mouse models of chronic DOX- induced cardiotoxicity. Five-week-old male mice received weekly DOX (4 mg/kg) or saline injections for six weeks, with heart tissues harvested 4 days post-treatment. Differentially expressed genes (DEGs) and proteins (DEPs) were identified by bulk RNA-seq and proteomics, validated via qPCR and western blot, respectively Key DEPs were validated in plasma samples from DOX-treated breast cancer patients. Additionally, a temporal comparison was conducted between DEPs in the mice hearts 4 days and 6 weeks post-DOX. RNA-seq revealed upregulation of stress-responsive genes ( Phlda3, Trp53inp1 ) and circadian regulators ( Nr1d1 ), with downregulation of Apelin and Cd74 . Proteomics identified upregulation of serpina3n, thrombospondin-1, and epoxide hydrolase 1. Plasma SERPINA3 concentrations were significantly elevated in breast cancer patients 24 hours post-DOX. Gene set enrichment analysis (GSEA) revealed upregulated pathways including p53 signaling, apoptosis, and unfolded protein response. Integrated omics analysis revealed 2,089 gene-protein pairs. GSEA of concordant gene-protein pairs implicated p53 signaling, apoptosis, and epithelial-mesenchymal transition in upregulated pathways, while oxidative phosphorylation and metabolic pathways were downregulated. Temporal comparison with a delayed timepoint (6 weeks post-DOX) uncovered dynamic remodeling of cardiac signaling, with early response dominated by inflammatory and apoptotic responses, and delayed response marked by cell cycle and DNA repair pathway activation. This integrated-omics study reveals key molecular pathways and temporal changes in DOX-induced cardiotoxicity, identifying potential biomarkers for future cardioprotective strategies.