Abstract 3831: A molecular landscape of epithelial to mesenchymal transition reveals dependencies on lysosomes and nutrient scavenging
Authors: Michal J. Nagiec, Paola M. Cavaliere, Friederike Dundar, Joana C. Nunes, Sejeong Shin, Derrick Spencer, Nikolaos Koundouros, Julie Han, Andre Chavez, Olivia Kester, Asara John, Steven P. Gygi, Doron Betel, Noah Dephoure, John Blenis
Journal: Cancer Research (2025)

Abstract Metastatic cancer cells invade into surrounding tissue, overcome nutrient stress, and survive the journey to distant sites. Many of the mechanisms that support these processes are incompatible with proliferation which is required for metastatic outgrowth. How cells balance proliferative and invasive programs has remained a complex question considering the heterogeneity of cancer cells. Here we define the cellular transition states associated with loss of proliferation and acquisition of invasive proficiency in non-tumorigenic breast epithelial cells. We measure dynamic changes to the transcriptome, proteome and metabolome in response to drivers of epithelial-mesenchymal transition (EMT), ERK2 and TGF-β. Our analysis identifies a cellular network of reversable metabolic adaptations that support the transition between proliferative and invasive states anchored by a switch from glycolysis to increased mitochondrial respiration that closely follows the dynamics of proliferative deceleration and acquisition of invasive capacity. Analysis of proteomics data revealed a robust upregulation of the endolysosomal system during this cellular reconfiguration. These cells become dependent on amino acid scavenging through upregulating macropinocytosis, a process requiring lysosomal activity. We find that this EMT-driven scavenging is associated with a decreased requirement for free amino acid transport at the plasma membrane. This is highlighted by the suppression of LAT1/SLC7A5 and ASCT2/SLC1A5 and increased expression of the lysosomal glutamine transporter SNAT7/SLC38A7. We also find that macropinocytosis is associated with increased intracellular amino acid storage, which supports survival during amino acid deprivation. Notably, highly metastatic triple negative breast cancer cells, that are better adapted at balancing elevated proliferation with invasive capacity also exhibit a dependency on lysosomes and macropinocytosis. We find the metabolic transition to be dependent on loss of c-MYC expression, an early event in the EMT reconfiguration process. Engineered expression of c-MYC in the presence of ERK2 and TGF-β signaling suppresses the metabolic switch, endolysosomal induction, macropinocytosis, changes to amino acid transporters and reverses the transition from proliferation to migration. This study provides critical insights into how cells dynamically balance proliferation and invasion tradeoffs that are difficult to capture in models of breast cancer metastasis. Citation Format: Michal J. Nagiec, Paola M. Cavaliere, Friederike Dundar, Joana C. Nunes, Sejeong Shin, Derrick Spencer, Nikolaos Koundouros, Julie Han, Andre Chavez, Olivia Kester, Asara John, Steven P. Gygi, Doron Betel, Noah Dephoure, John Blenis. A molecular landscape of epithelial to mesenchymal transition reveals dependencies on lysosomes and nutrient scavenging [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3831.