Mass flux balance-based model and metabolic flux analysis for collagen synthesis in the fibrogenesis process of human liver

Çalı́k, Pınar; Akbay, Ayşegül

doi:10.1054/mehy.1999.0958

Cited by 15 publications

(13 citation statements)

References 22 publications

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“…Isotopomer analysis of heart and liver metabolism has been used to quantify metabolic fluxes in the tricarboxylic acid (TCA) cycle and gluconeogenic pathway (Jeffrey et al, 1996;Jones et al, 1998;Katz et al, 1989Katz et al, , 1991Large et al, 1997;Yarmush et al, 1999). More recently, our laboratory has used nonisotopic metabolic flux analysis (MFA) to quantify flux changes in perfused livers (Arai et al, 2001;Lee et al, 2000), and an MFA model for human liver has been reported by Ç alik and Akbay (2000). The advantage of this approach over that which uses a given set of labeled tracers is that the MFA model predicts fluxes throughout the metabolic network, which includes the TCA and urea cycles, gluconeogenesis, pentose phosphate pathway, and amino acid degradation and transamination reactions.…”

Section: Introductionmentioning

confidence: 99%

Metabolic flux analysis of cultured hepatocytes exposed to plasma

Chan

Berthiaume

Lee

et al. 2002

Biotech & Bioengineering

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Hepatic metabolism can be investigated using metabolic flux analysis (MFA), which provides a comprehensive overview of the intracellular metabolic flux distribution. The characterization of intermediary metabolism in hepatocytes is important for all biotechnological applications involving liver cells, including the development of bioartificial liver (BAL) devices. During BAL operation, hepatocytes are exposed to plasma or blood from the patient, at which time they are prone to accumulate intracellular lipids and exhibit poor liver-specific functions. In a prior study, we found that preconditioning the primary rat hepatocytes in culture medium containing physiological levels of insulin, as opposed to the typical supraphysiological levels found in standard hepatocyte culture media, reduced lipid accumulation during subsequent plasma exposure. Furthermore, supplementing the plasma with amino acids restored hepatospecific functions. In the current study, we used MFA to quantify the changes in intracellular pathway fluxes of primary rat hepatocytes in response to low-insulin preconditioning and amino acid supplementation. We found that culturing hepatocytes in medium containing lower physiological levels of insulin decreased the clearance of glucose and glycerol with a concomitant decrease in glycolysis. These findings are consistent with the general notion that low insulin, especially in the presence of high glucagon levels, downregulates glycolysis in favor of gluconeogenesis in hepatocytes. The MFA model shows that, during subsequent plasma exposure, low-insulin preconditioning upregulated gluconeogenesis, with lactate as the primary precursor in unsupplemented plasma, with a greater contribution from deaminated amino acids in amino acid-supplemented plasma. Concomitantly, low-insulin preconditioning increased fatty acid oxidation, an effect that was further enhanced by amino acid supplementation to the plasma. The increase in fatty acid oxidation reduced intracellular triglyceride accumulation. Overall, these findings are consistent with the notion that the insulin level in medium culture presets the metabolic machinery of hepatocytes such that it directly impacts on their metabolic behavior during subsequent plasma culture.

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Section: Introductionmentioning

confidence: 99%

Metabolic flux analysis of cultured hepatocytes exposed to plasma

Chan

Berthiaume

Lee

et al. 2002

Biotech & Bioengineering

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“…Despite numerous applications of FBA [46][47][48][49][50][51][52][53][54][55][56] based on this criterion, a direct demonstration of its feasibility by comparison with measured flux rates was only provided in ref. [57].…”

Section: Discussionmentioning

confidence: 99%

Computational Design of Reduced Metabolic Networks

Holzhütter

2004

ChemBioChem

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Cellular functions are based on thousands of chemical reactions and transport processes, most of them being catalysed and regulated by specific proteins. Systematic gene knockouts have provided evidence that this complex reaction network possesses considerable redundancy, that is, alternative routes exist along which signals and metabolic fluxes may be directed to accomplish an identical output behaviour. This property is of particular importance in cases where parts of the reaction network are transiently or permanently impaired, for example, due to an infection or genetic alterations. Here we present a computational concept to determine enzyme-reduced metabolic networks that are still sufficient to accomplish a given set of cellular functions. Our approach consists of defining an objective function that expresses the compromise that has to be made between successive reduction of the network by omission of enzymes and its decreasing thermodynamic and kinetic feasibility. Optimisation of this objective function results in a linear mixed-integer program. With increasing weight given to the reduction of the number of enzymes, the total flux in the network increases and some of the reactions have to proceed in thermodynamically unfavourable directions. The approach was applied to two metabolic schemes: the energy and redox metabolism of red blood cells and the carbon metabolism of Methylobacterium extorquens. For these two example networks, we determined various variants of reduced networks differing in the number and types of disabled enzymes and disconnected reactions. Using a comprehensive kinetic model of the erythrocyte metabolism, we assess the kinetic feasibility of enzyme-reduced subnetworks. The number of enzymes predicted to be indispensable amounts to 14 (out of 28) for the erythrocyte scheme and 13 (out of 77) for the bacterium scheme, the largest group of enzymes predicted to be simultaneously dispensable amounts to 3 and 37 for these two systems. Our approach might contribute to identifying potential target enzymes for rational drug design, to rationalising gene-expression profiles of metabolic enzymes and to designing synthetic networks with highly specialised metabolic functions.

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“…These objective functions are generally based on the physiological properties of the liver. Calik and Akbay [67] calculated flux distributions in the fibrotic and healthy liver cells by maximizing respectively the collagen and palmitate synthesis. Yang et al .…”

Section: Stoichiometric Models For Hepatic Networkmentioning

confidence: 99%

“…The liver has a very robust metabolic network affected by metabolites and hormones; therefore, it exhibits different phenotypes depending on the environmental conditions. Different objective functions based on the topological and physiological properties of the liver have been used in the literature [64,67,68]. Focusing on consistent results predicted by different objective functions might reveal potentially important properties of liver metabolism [64].…”

Section: Current Challengesmentioning

confidence: 99%

“…, constant metabolite production or consumption rates) [1,2,3,4,5,6,7], implying that the perfused liver was metabolically stable for the duration of the perfusion, the pseudo steady-state assumption is reasonably valid. However, for hepatocytes cultured in vitro , flux measurements have been performed every 24 h [66,67,68,69,84]. Therefore, these studies do not guarantee whether or not metabolic switches between the pathways in hepatocytes take place within a 24 h period.…”

Section: Current Challengesmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2012

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: 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.

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Mass flux balance-based model and metabolic flux analysis for collagen synthesis in the fibrogenesis process of human liver

Cited by 15 publications

References 22 publications

Metabolic flux analysis of cultured hepatocytes exposed to plasma

Metabolic flux analysis of cultured hepatocytes exposed to plasma

Computational Design of Reduced Metabolic Networks

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

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