Systems lipidomics reveals sesamin-driven suppression of lipid metabolic reprogramming via AMPK activation in triple-negative breast cancer cells

Abstract

Triple-negative breast cancer (TNBC), the most aggressive breast cancer (BC) subtype, exhibits profound metabolic plasticity, with cancer-linked lipid metabolic reprogramming (CLMR) supporting membrane remodeling, energy generation, and oncogenic signaling. Targeting CLMR, therefore, represents a promising strategy for therapeutic intervention. To validate sesamin's (SE) interactions with lipid metabolism reprogramming (LMR)-related targets, an integrated in silico-in vitro approach was employed. Molecular docking (AutoDock Vina) and 100 ns molecular dynamics (MD) simulations (GROMACS) were conducted on the top 10 hub proteins identified from a dbCLMR-based PPI network, along with AMPK pathway targets. For in vitro validation, MDA-MB-231 cells were treated with SE and subjected to untargeted lipidomic profiling using Orbitrap high-resolution LC-MS, LipidSearch, and LipidSig 2.0, which were used for lipid identification, quantification, and analysis. Lipid class distribution, hierarchical clustering, and differential abundance profiling revealed SE-driven lipid alterations. Enrichment analyses and multi-layered pathway mapping identified dysregulated lipid metabolic networks. Functional assays included Oil Red O staining for lipid droplets, MitoSOX/DCF-DA-based flow cytometry for mitochondrial and cellular ROS, and qRT-PCR for AMPK-pathway gene expression, confirming the anticancer potential of SE through transcriptional and metabolic reprogramming in TNBC cells. Lipidomic profiling showed significant depletion of lipogenic lipid classes, mainly triacylglycerols, phosphatidylcholines, and sphingomyelins, alongside enrichment of polyunsaturated and long-chain fatty acids, indicative of suppressed lipid anabolism and altered membrane dynamics. SE activated AMPKA1/2 and downregulated fatty acid mobilization genes (CPT1A, LIPE, ACSL1, and PCK1). SE treatment also increased cellular and mitochondrial ROS and reduced lipid droplet accumulation, consistent with AMPK-mediated metabolic stress. In conclusion, this study identifies SE as a nutraceutical modulator of CLMR and establishes a systems biology-lipidomics framework for precision nutraceutical discovery in TNBC.

Keywords: Cancer; Lipid metabolism reprogramming; Lipidomics; Molecular docking; Molecular dynamics; Network pharmacology; Sesamin.