Systems-Level Multi-Omics Analysis Resolves the Mechanism of Action of a Novel Multifunctional Nanosystem Against Triple-Negative Breast Cancer

Background/Objectives: Triple-negative breast cancer remains a major therapeutic challenge due to its aggressive behavior and limited treatment options. Methods: In this study, an integrated multi-omics strategy combining SILAC-based quantitative proteomics, shotgun lipidomics, and targeted metabolomics was applied to characterize the biomolecular response of MDA-MB-231 cells following exposure to the Ag@MSN-Tf-SeNPs nanosystem. Results and Conclusions: The complementary analytical platforms provided a comprehensive and system-level view of the cytotoxic effects induced by the nanosystem, highlighting its potential as an antitumoral nanotherapeutic approach. Exposure resulted in reduced cell growth and metastatic potential, associated with DNA damage-induced cell-cycle arrest, disruption of protein biosynthesis, and impaired protein quality control linked to Ca2+ homeostasis imbalance. In addition, significant alterations in lipid metabolism were observed, including disruption of cholesterol biosynthesis. These changes, together with disturbances in glycolysis and the tricarboxylic acid cycle, and alterations in NAD+/NADH balance, indicate the induction of oxidative stress driven by reactive oxygen species accumulation. Furthermore, the integration of multi-omics data revealed the activation of compensatory mechanisms aimed at restoring cellular homeostasis, including metabolic rewiring and stress-response pathways, although these responses were insufficient to counteract nanosystem-induced cytotoxicity.