HepatoDyn: A Dynamic Model of Hepatocyte Metabolism That Integrates 13C Isotopomer Data

Abstract

The liver performs many essential metabolic functions, which can be studied using computational models of hepatocytes. Here we present HepatoDyn, a highly detailed dynamic model of hepatocyte metabolism. HepatoDyn includes a large metabolic network, highly detailed kinetic laws, and is capable of dynamically simulating the redox and energy metabolism of hepatocytes. Furthermore, the model was coupled to the module for isotopic label propagation of the software package IsoDyn, allowing HepatoDyn to integrate data derived from 13C based experiments. As an example of dynamical simulations applied to hepatocytes, we studied the effects of high fructose concentrations on hepatocyte metabolism by integrating data from experiments in which rat hepatocytes were incubated with 20 mM glucose supplemented with either 3 mM or 20 mM fructose. These experiments showed that glycogen accumulation was significantly lower in hepatocytes incubated with medium supplemented with 20 mM fructose than in hepatocytes incubated with medium supplemented with 3 mM fructose. Through the integration of extracellular fluxes and 13C enrichment measurements, HepatoDyn predicted that this phenomenon can be attributed to a depletion of cytosolic ATP and phosphate induced by high fructose concentrations in the medium.

Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease

“…Supporting our results are data from a recently published kinetic model comprising 88 reactions and 81 metabolites of hepatocyte core metabolism capable of simulating energy and redox metabolism. 43 The model of Fouget and colleagues was parametrised with 13 C labelled glucose and fructose based experimental (GC-MS) data from primary rat hepatocytes treated with 20 mM of glucose supplemented with either 3 or 20 mM of fructose for 2 h. The results show that while 20 mM of fructose inhibited glycogen synthesis, the addition of 3 mM of fructose, a physiological relevant portal concentration (0.2–2 mM 44 ), showed no adverse effects on intracellular energy status. Moreover, the authors observe there was very little flux going through fatty acid synthesis in both experimental models of 3 and 20 mM fructose.…”

“…While the in vitro experiments performed here did not take into account glycogen synthesis; similarly, our experimental HepG2 cells fed glucose and fructose had no differential effects in intracellular lipid over longer periods of exposure. It might be of interest to implement the stoichiometric data produced from Foguet and colleagues 43 into our metabolic model in order to incorporate specific rates of hepatic fructose and glucose metabolism. However, whereas our data are from a human hepatoma cell line, the Foguet data are derived from rat primary hepatocytes; ultimately human kinetic data would be preferable.…”

p13CMFA: Parsimonious 13C metabolic flux analysis

“…13 C MFA is a well-established technique and has proven to be an extremely valuable tool in quantifying metabolic fluxes[9–18]. However, to fully determine fluxes through a large metabolic network, parallel labeling experiments must be performed and 13 C propagation must be quantified in many metabolites in the network[19].…”

Metabolic Alterations in Cardiopulmonary Vascular Dysfunction

“…For medium-scale metabolic network models, among the main approaches used to model metabolic pathways are those based on the use of stable-isotope tracers (such as 13 C labeled metabolites). Computational tools to reconstruct metabolic flux maps from the quantification of the incorporation of 13 C-atoms into metabolites have been developed in recent years (e.g., Young, 2014; Antoniewicz, 2015; Foguet et al, 2016).…”