|Ph.D Student||Lee Won Dong|
|Subject||Characterization of Cancer Metabolism at Subcellular Level:|
An Integrated Experimental-Computational Approach
|Department||Department of Biology||Supervisor||Professor Tomer Shlomi|
|Full Thesis text|
Cancer cells develop remarkably distinct metabolism compared to normal cells. Evidence for alterations in the metabolism of malignant cells goes back a century ago to the discovery of the ‘Warburg effect.’ The recent resurgence of interest in cancer metabolism involved findings of metabolic alterations in a variety of pathways, oncogenes regulating metabolic enzymes, and specific oncogenic mutations in metabolic genes.
Metabolic flux is the rate of metabolic reactions and pathways in living systems, which is not directly measurable. Isotope tracing with computational metabolic flux analysis is the most direct approach for quantifying intracellular metabolic flux that has become a central technique in studies of cancer metabolism. A fundamental limitation in our understanding of cellular metabolism is having little information on subcellular level metabolic activity. Standard isotope tracing techniques are applied to whole-cells, providing no information on metabolic fluxes within subcellular compartments - practically aiming to estimate the “average” flux within the whole-cell. However, accumulating evidence suggests the existence of distinct metabolic activities in different subcellular compartments, including, compartment-specific cycling through malate-aspartate, citrate/α-ketoglutarate, malate/pyruvate, and proline.
Here, I describe a spatial-fluxomics approach for inferring metabolic fluxes in mitochondria and cytosol under physiological conditions, combining isotope tracing, rapid subcellular fractionation, LC-MS-based metabolomics, computational deconvolution, and metabolic network modeling. Applied to study reductive glutamine metabolism in cancer cells, shown to mediate fatty acid biosynthesis under hypoxia and defective mitochondria, I find a previously unappreciated role of reductive IDH1 as the sole net contributor of carbons to fatty acid biosynthesis under standard normoxic conditions in HeLa cells. In murine cells with defective SDH, I find that reductive biosynthesis of citrate in mitochondria is followed by a reversed CS activity, suggesting a new route for supporting pyrimidine biosynthesis.
Overall, the research challenges our current view of cancer metabolism, zooming in from the level of whole-cell level fluxes to a compartmentalized view of metabolic activity. This will profoundly affect our understanding of the phenotypic advantage that metabolic compartmentalization confers to cancer cells. I expect understanding cancer metabolism within and among subcellular compartments will provide novel insights into future therapeutic approaches.