Multi-Omics Integration Reveals Metabolic Reprogramming and EMT-Driven Metastasis in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is an aggressive subtype with high metastatic potential and poor prognosis, yet the molecular mechanisms driving metastasis remain incompletely understood. Here, we performed integrated transcriptomic, metabolomic, and imaging mass cytometry (IMC) analyses on tumor tissues from 52 TNBC patients stratified into NonMeta (long-term survival without metastasis, n = 39) and MetaPoor (metastasis-related death within 36 months after metastatic diagnosis, n = 13) groups. Transcriptomic analysis revealed significant enrichment of epithelial-mesenchymal transition (EMT), WNT signaling pathway, and angiogenesis pathways in MetaPoor tumors, with EMT identified as the top enriched hallmark by GSEA. Metabolomic profiling showed decreased branched-chain amino acids (BCAAs) and arginine derivatives, alongside elevated glycerophosphorylcholine (GPC), indicating enhanced metabolic demand and membrane remodeling. IMC-based spatial proteomics identified distinct tumor cell subpopulations, with MetaPoor tumors harboring higher proportions of stem-like and EMT-like cells characterized by upregulated HADHA (BCAA oxidation) and P38, and downregulated ATP5A (oxidative phosphorylation). Multi-omics integration revealed strong correlations between GPC and EMT markers, and between BCAA depletion and HADHA expression. Collectively, our multi-omics study demonstrates that metastatic TNBC is characterized by EMT activation, metabolic reprogramming toward altered BCAA metabolism and oxidative phosphorylation-related protein expression, and remodeling of the tumor immune microenvironment, suggesting candidate molecules that warrant independent validation and further mechanistic investigation.