CE-MS Metabolomic and LC-MS Proteomic Analyses of Breast Cancer Exosomes Reveal Alterations in Purine and Carnitine Metabolism

A nano sheath-flow capillary electrophoresis mass spectrometry (CE-MS) system with electrospray ionization was used to profile cationic metabolite cargo in exosomes secreted by non-tumorigenic MCF-10A and tumorigenic MDA-MB-231 breast epithelial cells. CE-MS-based metabolomics revealed increased purine synthesis intermediates and increased carnitine synthesis metabolites in MDA-MB-231-derived exosomes, with pathway enrichment indicating activation of de novo purine pathways and upregulating of carnitine metabolism. In addition, nanoLC-MS-based proteomics revealed differential expression of ecto-5’-nucleotidase (NT5E) and mitochondrial aldehyde dehydrogenase (ALDH9A1) demonstrated metabolic alterations in related enzymatic steps. This study demonstrates the application of nano sheath-flow CE-MS for comprehensive and quantitative exosome metabolomics, uncovering metabolic reprogramming in purine and carnitine pathways between normal and cancerous breast cell lines and providing insight into exosome-mediated signaling of breast cancer metabolism.