Lysosomal Alkalinization Selects for Metabolically Plastic, Motile Cancer Cells under Nutrient Stress.

Cancer cells exposed to nutrient deprivation activate adaptive programs to survive metabolic stress, often acquiring enhanced plasticity and motility. We have previously reported that colon cancer cell lines that survived nutrient depletion underwent partial epithelial-mesenchymal transition (pEMT), which was further exacerbated when these cells also underwent lysosomal alkalinization. Here, we have attempted to dissect the molecular mechanisms that drive the motility and shape change from cobblestone to elongated in subpopulations of cells. Using RNA-seq-based bioinformatic analyses integrated with pathway scoring, protein-protein interaction networks, probabilistic modeling and confirmatory experimental data, we have identified the coordinated activation of sublethal apoptotic signaling, fatty acid oxidation, mitochondrial ROS generation, and Ca{superscript 2}-dependent lysosomal exocytosis in the nutrient-depleted cells. Among these phenotypes, the cells undergoing starvation and lysosomal alkalinization exclusively mediated lysosomal exocytosis and cell motility. Probabilistic modeling further revealed non-linear relationships between metabolic stress signals and cell fate transitions, highlighting heterogeneous lysosomal functions as a key determinant of the altered phenotype of cells under nutrient depletion. Overall, our study has identified that aberrant lysosomal functioning in cells under nutrient depletion can specifically select for a subpopulation of cells that are highly viable, metabolically plastic and capable of motility.