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Applications of metabolomics and proteomics to the mdx mouse model of Duchenne muscular dystrophy: lessons from downstream of the transcriptome.

Griffin JL, Des Rosiers C - Genome Med (2009)

Bottom Line: This can be contrasted with proteomics, metabolomics and metabolic flux analysis (fluxomics), which have all been much slower in development, despite these techniques each providing a unique viewpoint of what is happening in the overall biological system.Studies using proteomics, metabolomics and fluxomics have characterized perturbations in calcium homeostasis in dystrophic skeletal muscle, provided an understanding of the role of dystrophin in skeletal muscle regeneration, and defined the changes in substrate energy metabolism in the working heart.More importantly, they all point to perturbations in proteins, metabolites and metabolic fluxes reflecting mitochondrial energetic alterations, even in the early stage of the dystrophic pathology.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK.

ABSTRACT
Functional genomic studies are dominated by transcriptomic approaches, in part reflecting the vast amount of information that can be obtained, the ability to amplify mRNA and the availability of commercially standardized functional genomic DNA microarrays and related techniques. This can be contrasted with proteomics, metabolomics and metabolic flux analysis (fluxomics), which have all been much slower in development, despite these techniques each providing a unique viewpoint of what is happening in the overall biological system. Here, we give an overview of developments in these fields 'downstream' of the transcriptome by considering the characterization of one particular, but widely used, mouse model of human disease. The mdx mouse is a model of Duchenne muscular dystrophy (DMD) and has been widely used to understand the progressive skeletal muscle wasting that accompanies DMD, and more recently the associated cardiomyopathy, as well as to unravel the roles of the other isoforms of dystrophin, such as those found in the brain. Studies using proteomics, metabolomics and fluxomics have characterized perturbations in calcium homeostasis in dystrophic skeletal muscle, provided an understanding of the role of dystrophin in skeletal muscle regeneration, and defined the changes in substrate energy metabolism in the working heart. More importantly, they all point to perturbations in proteins, metabolites and metabolic fluxes reflecting mitochondrial energetic alterations, even in the early stage of the dystrophic pathology. Philosophically, these studies also illustrate an important lesson relevant to both functional genomics and the mouse phenotyping in that the knowledge generated has advanced our understanding of cell biology and physiological organization as much as it has advanced our understanding of the disease.

No MeSH data available.


Related in: MedlinePlus

Metabolic flux ratios assessed in working control (C) and mdx mouse heart perfused with 13C-labeled substrates. Data are given as means ± standard errors (indicated in parentheses); n = 4-8 in each group. Reactions are shown in the part of the cell in which they take place. (a) Flux ratios. (i) Flux ratios reflecting the contribution of exogenous fatty acids (oleate) and carbohydrates (CHOs: lactate, pyruvate and glucose) to acetyl-CoA formation (energy) and oxaloacetate (OAA; anaplerosis) via oleate β-oxidation (OLE), pyruvate decarboxylation (PDC) and carboxyation (PC), respectively, and expressed relative to citrate synthesis (CS). (ii) Flux ratios reflecting the contribution of individual CHOs - as indicated by the individual arrows - to pyruvate formation, expressed in percentage of total. (b) Glycolytic rate, which reflects the production of lactate and pyruvate, in μmol × min-1. (c) Tissue concentration of Krebs cycle intermediates, in μmol × g wet weight-1. (d) Tissue aconitase activity, in μmol × min-1 × mg protein-1. *p < 0.05, #p < 0.001 for mdx versus control mouse hearts. Adapted from Khairallah et al. [54].
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Figure 2: Metabolic flux ratios assessed in working control (C) and mdx mouse heart perfused with 13C-labeled substrates. Data are given as means ± standard errors (indicated in parentheses); n = 4-8 in each group. Reactions are shown in the part of the cell in which they take place. (a) Flux ratios. (i) Flux ratios reflecting the contribution of exogenous fatty acids (oleate) and carbohydrates (CHOs: lactate, pyruvate and glucose) to acetyl-CoA formation (energy) and oxaloacetate (OAA; anaplerosis) via oleate β-oxidation (OLE), pyruvate decarboxylation (PDC) and carboxyation (PC), respectively, and expressed relative to citrate synthesis (CS). (ii) Flux ratios reflecting the contribution of individual CHOs - as indicated by the individual arrows - to pyruvate formation, expressed in percentage of total. (b) Glycolytic rate, which reflects the production of lactate and pyruvate, in μmol × min-1. (c) Tissue concentration of Krebs cycle intermediates, in μmol × g wet weight-1. (d) Tissue aconitase activity, in μmol × min-1 × mg protein-1. *p < 0.05, #p < 0.001 for mdx versus control mouse hearts. Adapted from Khairallah et al. [54].

Mentions: In the heart studies described by Khairallah et al. [54] four different substrates uniformly labeled with carbon 13 (U-13C) were used to probe metabolism in the mdx heart: the long-chain fatty acid (LCFA) [U-13C18]oleate and the carbohydrates (CHO) [U-13C3]lactate, [U-13C3]pyruvate and [U-13C6]glucose. Metabolic flux ratios that were assessed revealed cytosolic glycolysis, substrate selection (CHO versus LCFA) for mitochondrial acetyl-CoA formation for citrate synthesis (energy production), and pyruvate partitioning between decarboxylation (oxidation by pyruvate dehydrogenase) and carboxylation (by pyruvate carboxylase); see Figure 2. It is noteworthy that pyruvate carboxylation participates in the refueling of catalytic Krebs cycle intermediates, that is, in anaplerosis, a process that is proposed to have a crucial role in optimal cardiac energy production [77].


Applications of metabolomics and proteomics to the mdx mouse model of Duchenne muscular dystrophy: lessons from downstream of the transcriptome.

Griffin JL, Des Rosiers C - Genome Med (2009)

Metabolic flux ratios assessed in working control (C) and mdx mouse heart perfused with 13C-labeled substrates. Data are given as means ± standard errors (indicated in parentheses); n = 4-8 in each group. Reactions are shown in the part of the cell in which they take place. (a) Flux ratios. (i) Flux ratios reflecting the contribution of exogenous fatty acids (oleate) and carbohydrates (CHOs: lactate, pyruvate and glucose) to acetyl-CoA formation (energy) and oxaloacetate (OAA; anaplerosis) via oleate β-oxidation (OLE), pyruvate decarboxylation (PDC) and carboxyation (PC), respectively, and expressed relative to citrate synthesis (CS). (ii) Flux ratios reflecting the contribution of individual CHOs - as indicated by the individual arrows - to pyruvate formation, expressed in percentage of total. (b) Glycolytic rate, which reflects the production of lactate and pyruvate, in μmol × min-1. (c) Tissue concentration of Krebs cycle intermediates, in μmol × g wet weight-1. (d) Tissue aconitase activity, in μmol × min-1 × mg protein-1. *p < 0.05, #p < 0.001 for mdx versus control mouse hearts. Adapted from Khairallah et al. [54].
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Related In: Results  -  Collection

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Figure 2: Metabolic flux ratios assessed in working control (C) and mdx mouse heart perfused with 13C-labeled substrates. Data are given as means ± standard errors (indicated in parentheses); n = 4-8 in each group. Reactions are shown in the part of the cell in which they take place. (a) Flux ratios. (i) Flux ratios reflecting the contribution of exogenous fatty acids (oleate) and carbohydrates (CHOs: lactate, pyruvate and glucose) to acetyl-CoA formation (energy) and oxaloacetate (OAA; anaplerosis) via oleate β-oxidation (OLE), pyruvate decarboxylation (PDC) and carboxyation (PC), respectively, and expressed relative to citrate synthesis (CS). (ii) Flux ratios reflecting the contribution of individual CHOs - as indicated by the individual arrows - to pyruvate formation, expressed in percentage of total. (b) Glycolytic rate, which reflects the production of lactate and pyruvate, in μmol × min-1. (c) Tissue concentration of Krebs cycle intermediates, in μmol × g wet weight-1. (d) Tissue aconitase activity, in μmol × min-1 × mg protein-1. *p < 0.05, #p < 0.001 for mdx versus control mouse hearts. Adapted from Khairallah et al. [54].
Mentions: In the heart studies described by Khairallah et al. [54] four different substrates uniformly labeled with carbon 13 (U-13C) were used to probe metabolism in the mdx heart: the long-chain fatty acid (LCFA) [U-13C18]oleate and the carbohydrates (CHO) [U-13C3]lactate, [U-13C3]pyruvate and [U-13C6]glucose. Metabolic flux ratios that were assessed revealed cytosolic glycolysis, substrate selection (CHO versus LCFA) for mitochondrial acetyl-CoA formation for citrate synthesis (energy production), and pyruvate partitioning between decarboxylation (oxidation by pyruvate dehydrogenase) and carboxylation (by pyruvate carboxylase); see Figure 2. It is noteworthy that pyruvate carboxylation participates in the refueling of catalytic Krebs cycle intermediates, that is, in anaplerosis, a process that is proposed to have a crucial role in optimal cardiac energy production [77].

Bottom Line: This can be contrasted with proteomics, metabolomics and metabolic flux analysis (fluxomics), which have all been much slower in development, despite these techniques each providing a unique viewpoint of what is happening in the overall biological system.Studies using proteomics, metabolomics and fluxomics have characterized perturbations in calcium homeostasis in dystrophic skeletal muscle, provided an understanding of the role of dystrophin in skeletal muscle regeneration, and defined the changes in substrate energy metabolism in the working heart.More importantly, they all point to perturbations in proteins, metabolites and metabolic fluxes reflecting mitochondrial energetic alterations, even in the early stage of the dystrophic pathology.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QW, UK.

ABSTRACT
Functional genomic studies are dominated by transcriptomic approaches, in part reflecting the vast amount of information that can be obtained, the ability to amplify mRNA and the availability of commercially standardized functional genomic DNA microarrays and related techniques. This can be contrasted with proteomics, metabolomics and metabolic flux analysis (fluxomics), which have all been much slower in development, despite these techniques each providing a unique viewpoint of what is happening in the overall biological system. Here, we give an overview of developments in these fields 'downstream' of the transcriptome by considering the characterization of one particular, but widely used, mouse model of human disease. The mdx mouse is a model of Duchenne muscular dystrophy (DMD) and has been widely used to understand the progressive skeletal muscle wasting that accompanies DMD, and more recently the associated cardiomyopathy, as well as to unravel the roles of the other isoforms of dystrophin, such as those found in the brain. Studies using proteomics, metabolomics and fluxomics have characterized perturbations in calcium homeostasis in dystrophic skeletal muscle, provided an understanding of the role of dystrophin in skeletal muscle regeneration, and defined the changes in substrate energy metabolism in the working heart. More importantly, they all point to perturbations in proteins, metabolites and metabolic fluxes reflecting mitochondrial energetic alterations, even in the early stage of the dystrophic pathology. Philosophically, these studies also illustrate an important lesson relevant to both functional genomics and the mouse phenotyping in that the knowledge generated has advanced our understanding of cell biology and physiological organization as much as it has advanced our understanding of the disease.

No MeSH data available.


Related in: MedlinePlus