Estimation of flux ratios without uptake or release data: Application to serine and methionine metabolism

• DOI: 10.1016/j.ymben.2017.02.005
• Publication Date: 2017-02-21T07:31:26Z
• Authors: Roland Nilsson; Irena Roci; Jeramie Watrous; Mohit Jain
• Keywords: Optimization; 0303 health sciences; Metabolic network; Metabolic flux analysis; Biological Sciences; Simulation studies; Biological; Industrial biotechnology; Cancer metabolism; Models, Biological; Industrial Biotechnology; 3. Good health; 03 medical and health sciences; Methionine; Models; Hela Cells; Biochemistry and cell biology; Isotope Labeling; Neoplasms; Serine; Humans; Cancer; Biotechnology; HeLa Cells

Model-based metabolic flux analysis (MFA) using isotope-labeled substrates has provided great insight into intracellular metabolic activities across a host of organisms. One challenge with applying MFA in mammalian systems, however, is the need for absolute quantification of nutrient uptake, biomass composition, and byproduct release fluxes. Such measurements are often not feasible in complex culture systems or in vivo. One way to address this issue is to estimate flux ratios, the fractional contribution of a flux to a metabolite pool, which are independent of absolute measurements and yet informative for cellular metabolism. Prior work has focused on "local" estimation of a handful of flux ratios for specific metabolites and reactions. Here, we perform systematic, model-based estimation of all flux ratios in a metabolic network using isotope labeling data, in the absence of uptake/release data. In a series of examples, we investigate what flux ratios can be well estimated with reasonably tight confidence intervals, and contrast this with confidence intervals on normalized fluxes. We find that flux ratios can provide useful information on the metabolic state, and is complementary to normalized fluxes: for certain metabolic reactions, only flux ratios can be well estimated, while for others normalized fluxes can be obtained. Simulation studies of a large human metabolic network model suggest that estimation of flux ratios is technically feasible for complex networks, but additional studies on data from actual isotopomer labeling experiments are needed to validate these results. Finally, we experimentally study serine and methionine metabolism in cancer cells using flux ratios. We find that, in these cells, the methionine cycle is truncated with little remethylation from homocysteine, and polyamine synthesis in the absence of methionine salvage leads to loss of 5-methylthioadenosine, suggesting a new mode of overflow metabolism in cancer cells. This work highlights the potential for flux ratio analysis in the absence of absolute quantification, which we anticipate will be important for both in vitro and in vivo studies of cancer metabolism.