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Research paper thumbnail of ABCC9 mutations identified in human dilated cardiomyopathy disrupt catalytic KATP channel gating

Research paper thumbnail of Compartmentation of membrane processes and nucleotide dynamics in diffusion-restricted cardiac cell microenvironment

Journal of Molecular and Cellular Cardiology, 2012

Orchestrated excitation-contraction coupling in heart muscle requires adequate spatial arrangemen... more Orchestrated excitation-contraction coupling in heart muscle requires adequate spatial arrangement of systems responsible for ion movement and metabolite turnover. Co-localization of regulatory and transporting proteins into macromolecular complexes within an environment of microanatomical cell components raises intracellular diffusion barriers that hamper the mobility of metabolites and signaling molecules. Compared to substrate diffusion in the cytosol, diffusional restrictions underneath the sarcolemma are much larger and could impede ion and nucleotide movement by a factor of 10 3 -10 5 . Diffusion barriers thus seclude metabolites within the submembrane space enabling rapid and vectorial effector targeting, yet hinder energy supply from the bulk cytosolic space implicating the necessity for a shunting transfer mechanism. Here, we address principles of membrane protein compartmentation, phosphotransfer enzymefacilitated interdomain energy transfer, and nucleotide signal dynamics at the subsarcolemma-cytosol interface. This article is part of a Special Issue entitled "Local Signaling in Myocytes".

Research paper thumbnail of Nucleotide-gated K ATP channels integrated with creatine and adenylate kinases: Amplification, tuning and sensing of energetic signals in the compartmentalized cellular environment

Molecular and Cellular Biochemistry, 2000

Research paper thumbnail of Acceptor substrate inhibits transketolase competitively with respect to donor substrate

Biochemistry. Biokhimii͡a, 2000

Two substrates of the transketolase reaction are known to bind with the enzyme according to a pin... more Two substrates of the transketolase reaction are known to bind with the enzyme according to a ping-pong mechanism [1]. It is shown in this work that high concentrations of ribose-5-phosphate (acceptor substrate) compete with xylulose-5-phosphate (donor substrate), suppressing the transketolase activity (Ki = 3.8 mM). However, interacting with the donor-substrate binding site on the protein molecule, the acceptor substrate, unlike the donor substrate, does not cause any change in the active site of the enzyme. The data are interesting in terms of studying the regulatory mechanism of the transketolase activity and the structure of the enzyme-substrate complex.

Research paper thumbnail of Energy metabolism of human muscle and training

Research paper thumbnail of LIGHT-INDUCED-CHANGES IN PH AND BUFFERING CAPACITY IN A SUSPENSION OF PHOTOSYNTHETIC REACTION CENTERS FROM RHODOPSEUDOMONAS-SPHAEROIDES

Research paper thumbnail of Optimal Experimental Design for Isotopic Tracing Experiments of Tumour Metabolism

... yannis@rci.rutgers.edu. Co-Chair: Matt H. Bassett Email: mhbassett@dow.com. - indicates paper... more ... yannis@rci.rutgers.edu. Co-Chair: Matt H. Bassett Email: mhbassett@dow.com. - indicates paper has an Extended Abstract file available on CD. 3:15 PM. (714a) Optimal Experimental Design for Isotopic Tracing Experiments of Tumour Metabolism Constantinos Theodoropoulos, ...

Research paper thumbnail of Oxygen Pathway Modeling Estimates High Reactive Oxygen Species Production

The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of m... more The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of many fundamental processes governing the balance between health and disease. It is well known that ROS are necessary signaling molecules in gene expression, yet when expressed at high levels, ROS may cause oxidative stress and cell damage. Both hypoxia and hyperoxia may alter ROS production by changing mitochondrial Po2 (PmO2). Because PmO2 depends on the balance between O2 transport and utilization, we formulated an integrative mathematical model of O2 transport and utilization in skeletal muscle to predict conditions to cause abnormally high ROS generation. Simulations using data from healthy subjects during maximal exercise at sea level reveal little mitochondrial ROS production. However, altitude triggers high mitochondrial ROS production in muscle regions with high metabolic capacity but limited O2 delivery. This altitude roughly coincides with the highest location of permanent human habitation. Above 25,000 ft., more than 90% of exercising muscle is predicted to produce abnormally high levels of ROS, corresponding to the "death zone" in mountaineering.

Research paper thumbnail of Oxygen pathway modeling estimates high Reactive oxygen species production above the highest permanent human habitation

The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of m... more The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of many fundamental processes governing the balance between health and disease. It is well known that ROS are necessary signaling molecules in gene expression, yet when expressed at high levels, ROS may cause oxidative stress and cell damage. Both hypoxia and hyperoxia may alter ROS production by changing mitochondrial Po2 (PmO2). Because PmO2 depends on the balance between O2 transport and utilization, we formulated an integrative mathematical model of O2 transport and utilization in skeletal muscle to predict conditions to cause abnormally high ROS generation. Simulations using data from healthy subjects during maximal exercise at sea level reveal little mitochondrial ROS production. However, altitude triggers high mitochondrial ROS production in muscle regions with high metabolic capacity but limited O2 delivery. This altitude roughly coincides with the highest location of permanent human habitation. Above 25,000 ft., more than 90% of exercising muscle is predicted to produce abnormally high levels of ROS, corresponding to the "death zone" in mountaineering.

Research paper thumbnail of Effects of Free Ca2+ on Kinetic Characteristics of Holotransketolase

Catalytic activity has been demonstrated for holotransketolase in the absence of free bivalent ca... more Catalytic activity has been demonstrated for holotransketolase in the absence of free bivalent cations in the medium. The two active centers of the enzyme are equivalent in both the catalytic activity and the affinity for the substrates. In the presence of free Ca 2? (added to the medium from an external source), this equivalence is lost: negative cooperativity is induced on binding of either xylulose 5-phosphate (donor substrate) or ribose 5-phosphate (acceptor substrate), whereupon the catalytic conversion of the bound substrates causes the interaction between the centers to become positively cooperative. Moreover, the enzyme total activity increase is observed.

Research paper thumbnail of Ramos-Montoy ante, M.(2004) a, A., Lee, PW and Casc An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites

Research paper thumbnail of Light-induced changes in pH and buffer capacity in reaction center preparations of Rhodopseudomonas spheroides

In experiments with reaction centers (RC) preparations of Rps. sphaeroides, strain 1760-1, pH of ... more In experiments with reaction centers (RC) preparations of Rps. sphaeroides, strain 1760-1, pH of the suspension medium was found to change under continuous light excitation. The concentration of hydrogen ions starts to decrease fastly (t1/2 = 2--4 s) after the light is on, whereupon it increases slowly, to a steady-state level, within t1/2 = 5--7 min. During the fast phase 0.3 microM H+/1 microM of RC are absorbed and 7--8 microM H+/1 microM of RC are released under the slow phase. The fast phase is suppressed by ortho-phenantroline (10 mM)--an inhibitor of electron transfer from the primary (Fe-quinone complex) to the secondary (quinone) electron acceptors. Glutaraldehyde which is known to modify a protein structure of the RC inhibits the slow phase. The obtained data suggest that fast light-induced pH changes are due to a H+ uptake by the secondary quinoid anion-radical products; slow pH changes are ascribed to structural changes within the RC complex, which lead to a pK shift and/or changes in the amount of dissociating groups on the protein interfacial surface. The conclusion was supported by an observation of light-induced changes in buffer capacity of an RC suspension and by a light-induced increase in the amount of SH-groups titrated by 5.5-dithio-bis(2 nitro)-benzoic acid. The role of conformational dynamics of photoactive pigment--protein complexes in the functions of the RC is discussed.

Research paper thumbnail of Determination of constants of substrate primary binding with baker's yeast transketolase by kinetic modelling

A kinetic model of bisubstrate reaction catalyzed by baker's yeast transketolase ... more A kinetic model of bisubstrate reaction catalyzed by baker's yeast transketolase is proposed. The model considers individual stages of substrates reversible primary binding. The model corresponds to the observed kinetics of product accumulation within a wide range of initial substrate concentrations. Kinetic parameters for the best simulation of the experimental data are defined. The equilibrium constants of the primary binding of both the initial and produced ketose and also the initial aldose were unequivocally determined by varying the initial substrate concentrations. The dissociation constants of the primary enzyme-substrate complex for the initial ketose (xylulose 5-phosphate) and the reaction product (sedoheptulose 7-phosphate) were found to differ by more than by two orders of magnitude. The result is discussed in the context of the hypothesis of flip-flop functioning of the transketolase active sites.

Research paper thumbnail of Kinetic investigation of cooperativity in coenzyme binding by transketolase active sites

The two-step mechanism of coenzyme (thiamine diphosphate, ThDP) binding with two initially identi... more The two-step mechanism of coenzyme (thiamine diphosphate, ThDP) binding with two initially identical active sites of apotransketolase has been examined with a kinetic model. Cooperativity between sites in the primary ThDP binding and in the following conformational transition has been analyzed. The only reliable difference between sites is shown to be the tenfold difference in the backward rate constants of the conformational transition; this means that the cooperative interaction between sites takes place only after termination of both steps of ThDP binding in both sites.

Research paper thumbnail of Analysis of the control exerted by glucokinase and glucose-6-phosphatase on glycerol metabolism of liver cells using different systems biology frameworks

Research paper thumbnail of Characterisation of the metabolic fluxes in the adipocyte differentiation process using bioinformatics tools

Research paper thumbnail of Systems Medicine In Complex Chronic Diseases: Chronic Obstructive Pulmonary Disease (COPD) As A Use Case

C98. OF MEN AND MICE: BETTER UNDERSTANDING OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE, 2010

C98 OF MEN AND MICE: BETTER UNDERSTANDING OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE Tuesday, May 1... more C98 OF MEN AND MICE: BETTER UNDERSTANDING OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE Tuesday, May 18/1:30 PM-4:00 PM / Room 286-287 (Second Level), Morial Convention Center ... Systems Medicine In Complex Chronic Diseases: Chronic Obstructive ...

Research paper thumbnail of Systems Medicine: from molecular features and models to the clinic in COPD

Journal of Translational Medicine, 2014

Chronic Obstructive Pulmonary Disease (COPD) patients are characterized by heterogeneous clinical... more Chronic Obstructive Pulmonary Disease (COPD) patients are characterized by heterogeneous clinical manifestations and patterns of disease progression. Two major factors that can be used to identify COPD subtypes are muscle dysfunction/wasting and co-morbidity patterns. We hypothesized that COPD heterogeneity is in part the result of complex interactions between several genes and pathways. We explored the possibility of using a Systems Medicine approach to identify such pathways, as well as to generate predictive computational models that may be used in clinic practice. Our overarching goal is to generate clinically applicable predictive models that characterize COPD heterogeneity through a Systems Medicine approach. To this end we have developed a general framework, consisting of three steps/objectives: (1) feature identification, (2) model generation and statistical validation, and (3) application and validation of the predictive models in the clinical scenario. We used muscle dysfunction and co-morbidity as test cases for this framework. In the study of muscle wasting we identified relevant features (genes) by a network analysis and generated predictive models that integrate mechanistic and probabilistic models. This allowed us to characterize muscle wasting as a general de-regulation of pathway interactions. In the co-morbidity analysis we identified relevant features (genes/pathways) by the integration of gene-disease and disease-disease associations. We further present a detailed characterization of co-morbidities in COPD patients that was implemented into a predictive model. In both use cases we were able to achieve predictive modeling but we also identified several key challenges, the most pressing being the validation and implementation into actual clinical practice. The results confirm the potential of the Systems Medicine approach to study complex diseases and generate clinically relevant predictive models. Our study also highlights important obstacles and bottlenecks for such approaches (e.g. data availability and normalization of frameworks among others) and suggests specific proposals to overcome them.

Research paper thumbnail of 13C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes

BackgroundIt has been suggested that the adipokine resistin links obesity and insulin resistance,... more BackgroundIt has been suggested that the adipokine resistin links obesity and insulin resistance, although how resistin acts on muscle metabolism is controversial. We aimed to quantitatively analyse the effects of resistin on the glucose metabolic flux profile and on insulin response in L6E9 myotubes at the metabolic level using a tracer-based metabolomic approach and our in-house developed software, Isodyn.ResultsResistin significantly increased glucose uptake and glycolysis, altering pyruvate utilisation by the cell. In the presence of resistin, insulin only slightly increased glucose uptake and glycolysis, and did not alter the flux profile around pyruvate induced by resistin. Resistin prevented the increase in gene expression in pyruvate dehydrogenase-E1 and the sharp decrease in gene expression in cytosolic phosphoenolpyruvate carboxykinase-1 induced by insulin.ConclusionsThese data suggest that resistin impairs the metabolic activation of insulin. This impairment cannot be explained by the activity of a single enzyme, but instead due to reorganisation of the whole metabolic flux distribution.

Research paper thumbnail of Application of tracer-based metabolomics and flux analysis in targeted cancer drug design

Research paper thumbnail of ABCC9 mutations identified in human dilated cardiomyopathy disrupt catalytic KATP channel gating

Research paper thumbnail of Compartmentation of membrane processes and nucleotide dynamics in diffusion-restricted cardiac cell microenvironment

Journal of Molecular and Cellular Cardiology, 2012

Orchestrated excitation-contraction coupling in heart muscle requires adequate spatial arrangemen... more Orchestrated excitation-contraction coupling in heart muscle requires adequate spatial arrangement of systems responsible for ion movement and metabolite turnover. Co-localization of regulatory and transporting proteins into macromolecular complexes within an environment of microanatomical cell components raises intracellular diffusion barriers that hamper the mobility of metabolites and signaling molecules. Compared to substrate diffusion in the cytosol, diffusional restrictions underneath the sarcolemma are much larger and could impede ion and nucleotide movement by a factor of 10 3 -10 5 . Diffusion barriers thus seclude metabolites within the submembrane space enabling rapid and vectorial effector targeting, yet hinder energy supply from the bulk cytosolic space implicating the necessity for a shunting transfer mechanism. Here, we address principles of membrane protein compartmentation, phosphotransfer enzymefacilitated interdomain energy transfer, and nucleotide signal dynamics at the subsarcolemma-cytosol interface. This article is part of a Special Issue entitled "Local Signaling in Myocytes".

Research paper thumbnail of Nucleotide-gated K ATP channels integrated with creatine and adenylate kinases: Amplification, tuning and sensing of energetic signals in the compartmentalized cellular environment

Molecular and Cellular Biochemistry, 2000

Research paper thumbnail of Acceptor substrate inhibits transketolase competitively with respect to donor substrate

Biochemistry. Biokhimii͡a, 2000

Two substrates of the transketolase reaction are known to bind with the enzyme according to a pin... more Two substrates of the transketolase reaction are known to bind with the enzyme according to a ping-pong mechanism [1]. It is shown in this work that high concentrations of ribose-5-phosphate (acceptor substrate) compete with xylulose-5-phosphate (donor substrate), suppressing the transketolase activity (Ki = 3.8 mM). However, interacting with the donor-substrate binding site on the protein molecule, the acceptor substrate, unlike the donor substrate, does not cause any change in the active site of the enzyme. The data are interesting in terms of studying the regulatory mechanism of the transketolase activity and the structure of the enzyme-substrate complex.

Research paper thumbnail of Energy metabolism of human muscle and training

Research paper thumbnail of LIGHT-INDUCED-CHANGES IN PH AND BUFFERING CAPACITY IN A SUSPENSION OF PHOTOSYNTHETIC REACTION CENTERS FROM RHODOPSEUDOMONAS-SPHAEROIDES

Research paper thumbnail of Optimal Experimental Design for Isotopic Tracing Experiments of Tumour Metabolism

... yannis@rci.rutgers.edu. Co-Chair: Matt H. Bassett Email: mhbassett@dow.com. - indicates paper... more ... yannis@rci.rutgers.edu. Co-Chair: Matt H. Bassett Email: mhbassett@dow.com. - indicates paper has an Extended Abstract file available on CD. 3:15 PM. (714a) Optimal Experimental Design for Isotopic Tracing Experiments of Tumour Metabolism Constantinos Theodoropoulos, ...

Research paper thumbnail of Oxygen Pathway Modeling Estimates High Reactive Oxygen Species Production

The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of m... more The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of many fundamental processes governing the balance between health and disease. It is well known that ROS are necessary signaling molecules in gene expression, yet when expressed at high levels, ROS may cause oxidative stress and cell damage. Both hypoxia and hyperoxia may alter ROS production by changing mitochondrial Po2 (PmO2). Because PmO2 depends on the balance between O2 transport and utilization, we formulated an integrative mathematical model of O2 transport and utilization in skeletal muscle to predict conditions to cause abnormally high ROS generation. Simulations using data from healthy subjects during maximal exercise at sea level reveal little mitochondrial ROS production. However, altitude triggers high mitochondrial ROS production in muscle regions with high metabolic capacity but limited O2 delivery. This altitude roughly coincides with the highest location of permanent human habitation. Above 25,000 ft., more than 90% of exercising muscle is predicted to produce abnormally high levels of ROS, corresponding to the "death zone" in mountaineering.

Research paper thumbnail of Oxygen pathway modeling estimates high Reactive oxygen species production above the highest permanent human habitation

The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of m... more The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of many fundamental processes governing the balance between health and disease. It is well known that ROS are necessary signaling molecules in gene expression, yet when expressed at high levels, ROS may cause oxidative stress and cell damage. Both hypoxia and hyperoxia may alter ROS production by changing mitochondrial Po2 (PmO2). Because PmO2 depends on the balance between O2 transport and utilization, we formulated an integrative mathematical model of O2 transport and utilization in skeletal muscle to predict conditions to cause abnormally high ROS generation. Simulations using data from healthy subjects during maximal exercise at sea level reveal little mitochondrial ROS production. However, altitude triggers high mitochondrial ROS production in muscle regions with high metabolic capacity but limited O2 delivery. This altitude roughly coincides with the highest location of permanent human habitation. Above 25,000 ft., more than 90% of exercising muscle is predicted to produce abnormally high levels of ROS, corresponding to the "death zone" in mountaineering.

Research paper thumbnail of Effects of Free Ca2+ on Kinetic Characteristics of Holotransketolase

Catalytic activity has been demonstrated for holotransketolase in the absence of free bivalent ca... more Catalytic activity has been demonstrated for holotransketolase in the absence of free bivalent cations in the medium. The two active centers of the enzyme are equivalent in both the catalytic activity and the affinity for the substrates. In the presence of free Ca 2? (added to the medium from an external source), this equivalence is lost: negative cooperativity is induced on binding of either xylulose 5-phosphate (donor substrate) or ribose 5-phosphate (acceptor substrate), whereupon the catalytic conversion of the bound substrates causes the interaction between the centers to become positively cooperative. Moreover, the enzyme total activity increase is observed.

Research paper thumbnail of Ramos-Montoy ante, M.(2004) a, A., Lee, PW and Casc An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites

Research paper thumbnail of Light-induced changes in pH and buffer capacity in reaction center preparations of Rhodopseudomonas spheroides

In experiments with reaction centers (RC) preparations of Rps. sphaeroides, strain 1760-1, pH of ... more In experiments with reaction centers (RC) preparations of Rps. sphaeroides, strain 1760-1, pH of the suspension medium was found to change under continuous light excitation. The concentration of hydrogen ions starts to decrease fastly (t1/2 = 2--4 s) after the light is on, whereupon it increases slowly, to a steady-state level, within t1/2 = 5--7 min. During the fast phase 0.3 microM H+/1 microM of RC are absorbed and 7--8 microM H+/1 microM of RC are released under the slow phase. The fast phase is suppressed by ortho-phenantroline (10 mM)--an inhibitor of electron transfer from the primary (Fe-quinone complex) to the secondary (quinone) electron acceptors. Glutaraldehyde which is known to modify a protein structure of the RC inhibits the slow phase. The obtained data suggest that fast light-induced pH changes are due to a H+ uptake by the secondary quinoid anion-radical products; slow pH changes are ascribed to structural changes within the RC complex, which lead to a pK shift and/or changes in the amount of dissociating groups on the protein interfacial surface. The conclusion was supported by an observation of light-induced changes in buffer capacity of an RC suspension and by a light-induced increase in the amount of SH-groups titrated by 5.5-dithio-bis(2 nitro)-benzoic acid. The role of conformational dynamics of photoactive pigment--protein complexes in the functions of the RC is discussed.

Research paper thumbnail of Determination of constants of substrate primary binding with baker's yeast transketolase by kinetic modelling

A kinetic model of bisubstrate reaction catalyzed by baker's yeast transketolase ... more A kinetic model of bisubstrate reaction catalyzed by baker's yeast transketolase is proposed. The model considers individual stages of substrates reversible primary binding. The model corresponds to the observed kinetics of product accumulation within a wide range of initial substrate concentrations. Kinetic parameters for the best simulation of the experimental data are defined. The equilibrium constants of the primary binding of both the initial and produced ketose and also the initial aldose were unequivocally determined by varying the initial substrate concentrations. The dissociation constants of the primary enzyme-substrate complex for the initial ketose (xylulose 5-phosphate) and the reaction product (sedoheptulose 7-phosphate) were found to differ by more than by two orders of magnitude. The result is discussed in the context of the hypothesis of flip-flop functioning of the transketolase active sites.

Research paper thumbnail of Kinetic investigation of cooperativity in coenzyme binding by transketolase active sites

The two-step mechanism of coenzyme (thiamine diphosphate, ThDP) binding with two initially identi... more The two-step mechanism of coenzyme (thiamine diphosphate, ThDP) binding with two initially identical active sites of apotransketolase has been examined with a kinetic model. Cooperativity between sites in the primary ThDP binding and in the following conformational transition has been analyzed. The only reliable difference between sites is shown to be the tenfold difference in the backward rate constants of the conformational transition; this means that the cooperative interaction between sites takes place only after termination of both steps of ThDP binding in both sites.

Research paper thumbnail of Analysis of the control exerted by glucokinase and glucose-6-phosphatase on glycerol metabolism of liver cells using different systems biology frameworks

Research paper thumbnail of Characterisation of the metabolic fluxes in the adipocyte differentiation process using bioinformatics tools

Research paper thumbnail of Systems Medicine In Complex Chronic Diseases: Chronic Obstructive Pulmonary Disease (COPD) As A Use Case

C98. OF MEN AND MICE: BETTER UNDERSTANDING OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE, 2010

C98 OF MEN AND MICE: BETTER UNDERSTANDING OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE Tuesday, May 1... more C98 OF MEN AND MICE: BETTER UNDERSTANDING OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE Tuesday, May 18/1:30 PM-4:00 PM / Room 286-287 (Second Level), Morial Convention Center ... Systems Medicine In Complex Chronic Diseases: Chronic Obstructive ...

Research paper thumbnail of Systems Medicine: from molecular features and models to the clinic in COPD

Journal of Translational Medicine, 2014

Chronic Obstructive Pulmonary Disease (COPD) patients are characterized by heterogeneous clinical... more Chronic Obstructive Pulmonary Disease (COPD) patients are characterized by heterogeneous clinical manifestations and patterns of disease progression. Two major factors that can be used to identify COPD subtypes are muscle dysfunction/wasting and co-morbidity patterns. We hypothesized that COPD heterogeneity is in part the result of complex interactions between several genes and pathways. We explored the possibility of using a Systems Medicine approach to identify such pathways, as well as to generate predictive computational models that may be used in clinic practice. Our overarching goal is to generate clinically applicable predictive models that characterize COPD heterogeneity through a Systems Medicine approach. To this end we have developed a general framework, consisting of three steps/objectives: (1) feature identification, (2) model generation and statistical validation, and (3) application and validation of the predictive models in the clinical scenario. We used muscle dysfunction and co-morbidity as test cases for this framework. In the study of muscle wasting we identified relevant features (genes) by a network analysis and generated predictive models that integrate mechanistic and probabilistic models. This allowed us to characterize muscle wasting as a general de-regulation of pathway interactions. In the co-morbidity analysis we identified relevant features (genes/pathways) by the integration of gene-disease and disease-disease associations. We further present a detailed characterization of co-morbidities in COPD patients that was implemented into a predictive model. In both use cases we were able to achieve predictive modeling but we also identified several key challenges, the most pressing being the validation and implementation into actual clinical practice. The results confirm the potential of the Systems Medicine approach to study complex diseases and generate clinically relevant predictive models. Our study also highlights important obstacles and bottlenecks for such approaches (e.g. data availability and normalization of frameworks among others) and suggests specific proposals to overcome them.

Research paper thumbnail of 13C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes

BackgroundIt has been suggested that the adipokine resistin links obesity and insulin resistance,... more BackgroundIt has been suggested that the adipokine resistin links obesity and insulin resistance, although how resistin acts on muscle metabolism is controversial. We aimed to quantitatively analyse the effects of resistin on the glucose metabolic flux profile and on insulin response in L6E9 myotubes at the metabolic level using a tracer-based metabolomic approach and our in-house developed software, Isodyn.ResultsResistin significantly increased glucose uptake and glycolysis, altering pyruvate utilisation by the cell. In the presence of resistin, insulin only slightly increased glucose uptake and glycolysis, and did not alter the flux profile around pyruvate induced by resistin. Resistin prevented the increase in gene expression in pyruvate dehydrogenase-E1 and the sharp decrease in gene expression in cytosolic phosphoenolpyruvate carboxykinase-1 induced by insulin.ConclusionsThese data suggest that resistin impairs the metabolic activation of insulin. This impairment cannot be explained by the activity of a single enzyme, but instead due to reorganisation of the whole metabolic flux distribution.

Research paper thumbnail of Application of tracer-based metabolomics and flux analysis in targeted cancer drug design