Stoichiometry Based Steady-State Hepatic Flux Analysis: Computational and Experimental Aspects

Abstract

: The liver has many complex physiological functions, including lipid, protein and carbohydrate metabolism, as well as bile and urea production. It detoxifies toxic substances and medicinal products. It also plays a key role in the onset and maintenance of abnormal metabolic patterns associated with various disease states, such as burns, infections and major traumas. Liver cells have been commonly used in in vitro experiments to elucidate the toxic effects of drugs and metabolic changes caused by aberrant metabolic conditions, and to improve the functions of existing systems, such as bioartificial liver. More recently, isolated liver perfusion systems have been increasingly used to characterize intrinsic metabolic changes in the liver caused by various perturbations, including systemic injury, hepatotoxin exposure and warm ischemia. Metabolic engineering tools have been widely applied to these systems to identify metabolic flux distributions using metabolic flux analysis or flux balance analysis and to characterize the topology of the networks using metabolic pathway analysis. In this context, hepatic metabolic models, together with experimental methodologies where hepatocytes or perfused livers are mainly investigated, are described in detail in this review. The challenges and opportunities are also discussed extensively.

Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME

“…As the choice of the independent fluxes is not unequivocal, the modeler and the experimentalist together can agree on a list of independent fluxes that can be comfortably determined (preferentially exchange fluxes that can be easily measured by monitoring the respective concentration changes in the external medium) and which from the computational point of view allow to infer the remaining fluxes with a minimal error. Numerous examples for MFA applied to liver cells can be found in the report by Orman et al (2012). Note that if the number of measured fluxes is smaller than the number of independent fluxes N *, MFA has to be complemented by flux-balance analysis (see below) to determine all fluxes.…”

Isotope-Assisted Metabolic Flux Analysis: A Powerful Technique to Gain New Insights into the Human Metabolome in Health and Disease

“…Tissue-specific models consider the specific metabolism and function of each cell type when constructing the iMFA metabolic map. For example, gluconeogenic pathways are important in hepatocytes [99] and should be included in hepatocyte iMFA models. In contrast, the core metabolic model should be pruned when studying red blood cells, which lack mitochondria and therefore do not use the TCA cycle [100].…”

Influence of plasma macronutrient levels on hepatic metabolism: role of regulatory networks in homeostasis and disease states

“…However, it should be noted that there are several models that specically model signaling or the metabolic pathways independently. [30][31][32][33][34][35][36][37][38][39][40][41] We have integrated these several published models as components of our comprehensive model along with a module for whole body plasma metabolite homeostasis. We applied a system level approach that is composed of four modules such as blood, metabolism, signaling and transcription.…”