INCA 2.0: A tool for integrated,dynamic modeling of NMR- and MS-based isotopomer measurements and rigorous metabolic flux analysis |
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| Affiliation: | 1. Department of Chemical and Biomolecular, Nashville, TN, 37212, USA;2. Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Engineering, Nashville, TN, 37212, USA;3. Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL, USA;4. Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, USA;1. Children''s Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA;2. Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA;3. McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA;4. Departments of Pathology and Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA;5. Department of Pathology and Laboratory Medicine, Children''s Health, 1935 Medical District Drive, Dallas, TX 75235, USA;6. Royal Stoke University Hospital, Newcastle Rd, Stoke-on-Trent, ST4 6QG, United Kingdom;7. University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, USA;1. Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA;2. Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA |
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| Abstract: | Metabolic flux analysis (MFA) combines experimental measurements and computational modeling to determine biochemical reaction rates in live biological systems. Advancements in analytical instrumentation, such as nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), have facilitated chemical separation and quantification of isotopically enriched metabolites. However, no software packages have been previously described that can integrate isotopomer measurements from both MS and NMR analytical platforms and have the flexibility to estimate metabolic fluxes from either isotopic steady-state or dynamic labeling experiments. By applying physiologically relevant cardiac and hepatic metabolic models to assess NMR isotopomer measurements, we herein test and validate new modeling capabilities of our enhanced flux analysis software tool, INCA 2.0. We demonstrate that INCA 2.0 can simulate and regress steady-state 13C NMR datasets from perfused hearts with an accuracy comparable to other established flux assessment tools. Furthermore, by simulating the infusion of three different 13C acetate tracers, we show that MFA based on dynamic 13C NMR measurements can more precisely resolve cardiac fluxes compared to isotopically steady-state flux analysis. Finally, we show that estimation of hepatic fluxes using combined 13C NMR and MS datasets improves the precision of estimated fluxes by up to 50%. Overall, our results illustrate how the recently added NMR data modeling capabilities of INCA 2.0 can enable entirely new experimental designs that lead to improved flux resolution and can be applied to a wide range of biological systems and measurement time courses. |
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| Keywords: | Metabolic flux analysis Metabolomics Metabolic modeling software Mass spectrometry Nuclear magnetic resonance INST-MFA |
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