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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.

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Applications of metabolomics and proteomics to the mdx mouse. (a) A typical high-resolution 1H NMR spectrum from an aqueous extract of cardiac tissue from the mdx mouse. The chemical shift and splitting pattern of a given resonance (peak) enables the identification of the metabolite it belongs to, and the area under the resonance determines the concentration of that metabolite. (b) An orthogonal signal corrected partial least squares discriminate analysis plot of various mouse models of cardiac disease using solution state NMR spectroscopy. Key: circles, control + mdx; diamonds, model of cardiac hypertrophy (MLPKO); squares, model of cardiac arrhythmia (Scn-/+); triangles, model of cardiac arrhythmia (ScnΔ /+). (c) Correlation analysis between identified proteins in a proteomic study of heart tissue from mdx mice and the intracellular concentration of taurine. When detected by 1H NMR spectroscopy (bottom graph), taurine can be identified by two triple peaks at δ 3.25-3.27 and δ 3.42-3.46. The correlation heat map between spectral intensity and protein expression was used to determine which proteomic changes were associated with the increase in taurine in dystrophic muscle. The x axis is the chemical shift region containing the resonances from taurine; the y axis consists of protein spots detected in the two-dimensional gel electrophoresis. The color scale displays the correlation coefficients between the two sets of data (concentration of taurine against concentration of protein).
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Figure 1: Applications of metabolomics and proteomics to the mdx mouse. (a) A typical high-resolution 1H NMR spectrum from an aqueous extract of cardiac tissue from the mdx mouse. The chemical shift and splitting pattern of a given resonance (peak) enables the identification of the metabolite it belongs to, and the area under the resonance determines the concentration of that metabolite. (b) An orthogonal signal corrected partial least squares discriminate analysis plot of various mouse models of cardiac disease using solution state NMR spectroscopy. Key: circles, control + mdx; diamonds, model of cardiac hypertrophy (MLPKO); squares, model of cardiac arrhythmia (Scn-/+); triangles, model of cardiac arrhythmia (ScnΔ /+). (c) Correlation analysis between identified proteins in a proteomic study of heart tissue from mdx mice and the intracellular concentration of taurine. When detected by 1H NMR spectroscopy (bottom graph), taurine can be identified by two triple peaks at δ 3.25-3.27 and δ 3.42-3.46. The correlation heat map between spectral intensity and protein expression was used to determine which proteomic changes were associated with the increase in taurine in dystrophic muscle. The x axis is the chemical shift region containing the resonances from taurine; the y axis consists of protein spots detected in the two-dimensional gel electrophoresis. The color scale displays the correlation coefficients between the two sets of data (concentration of taurine against concentration of protein).

Mentions: Applying techniques developed for following drug toxicity using a combination of 1H NMR spectroscopy and principal components analysis [58], Griffin and co-workers [7] examined a range of tissues from the mdx mouse, including cardiac (Figure 1a), diaphragm, soleus (calf muscle), cerebral cortex and cerebellum at 6 months of age. Dystrophic muscle tissue from heart, diaphragm and soleus were similarly perturbed metabolically by a failure to express dystrophin, despite being very different types of muscle; this was characterized by an increase in taurine and lactate and a decrease in creatine in tissue extracts from dystrophic tissue. This is in keeping with the single protein isoform known to be involved in all these tissue types, and that presumably has a similar role in all these tissues. These changes could be detected even in intact tissue using high-resolution magic angle spinning 1H NMR spectroscopy, which also identified a significant increase in lipid infiltration in dystrophic tissue [59]. Similarly, extracts of cerebellum tissue from mdx mice were readily distinguished from wild-type controls by their metabolic profiles, including a characteristic increase in phosphocholine. The approach even found a weak separation in cortical tissue extracts, although this had not been detected by previous studies. The changes in profiles of dystrophic muscle, cortex and cerebellum tissue were all distinct, suggesting very different roles for the three iso-forms of dystrophin in the tissues.


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)

Applications of metabolomics and proteomics to the mdx mouse. (a) A typical high-resolution 1H NMR spectrum from an aqueous extract of cardiac tissue from the mdx mouse. The chemical shift and splitting pattern of a given resonance (peak) enables the identification of the metabolite it belongs to, and the area under the resonance determines the concentration of that metabolite. (b) An orthogonal signal corrected partial least squares discriminate analysis plot of various mouse models of cardiac disease using solution state NMR spectroscopy. Key: circles, control + mdx; diamonds, model of cardiac hypertrophy (MLPKO); squares, model of cardiac arrhythmia (Scn-/+); triangles, model of cardiac arrhythmia (ScnΔ /+). (c) Correlation analysis between identified proteins in a proteomic study of heart tissue from mdx mice and the intracellular concentration of taurine. When detected by 1H NMR spectroscopy (bottom graph), taurine can be identified by two triple peaks at δ 3.25-3.27 and δ 3.42-3.46. The correlation heat map between spectral intensity and protein expression was used to determine which proteomic changes were associated with the increase in taurine in dystrophic muscle. The x axis is the chemical shift region containing the resonances from taurine; the y axis consists of protein spots detected in the two-dimensional gel electrophoresis. The color scale displays the correlation coefficients between the two sets of data (concentration of taurine against concentration of protein).
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Related In: Results  -  Collection

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Figure 1: Applications of metabolomics and proteomics to the mdx mouse. (a) A typical high-resolution 1H NMR spectrum from an aqueous extract of cardiac tissue from the mdx mouse. The chemical shift and splitting pattern of a given resonance (peak) enables the identification of the metabolite it belongs to, and the area under the resonance determines the concentration of that metabolite. (b) An orthogonal signal corrected partial least squares discriminate analysis plot of various mouse models of cardiac disease using solution state NMR spectroscopy. Key: circles, control + mdx; diamonds, model of cardiac hypertrophy (MLPKO); squares, model of cardiac arrhythmia (Scn-/+); triangles, model of cardiac arrhythmia (ScnΔ /+). (c) Correlation analysis between identified proteins in a proteomic study of heart tissue from mdx mice and the intracellular concentration of taurine. When detected by 1H NMR spectroscopy (bottom graph), taurine can be identified by two triple peaks at δ 3.25-3.27 and δ 3.42-3.46. The correlation heat map between spectral intensity and protein expression was used to determine which proteomic changes were associated with the increase in taurine in dystrophic muscle. The x axis is the chemical shift region containing the resonances from taurine; the y axis consists of protein spots detected in the two-dimensional gel electrophoresis. The color scale displays the correlation coefficients between the two sets of data (concentration of taurine against concentration of protein).
Mentions: Applying techniques developed for following drug toxicity using a combination of 1H NMR spectroscopy and principal components analysis [58], Griffin and co-workers [7] examined a range of tissues from the mdx mouse, including cardiac (Figure 1a), diaphragm, soleus (calf muscle), cerebral cortex and cerebellum at 6 months of age. Dystrophic muscle tissue from heart, diaphragm and soleus were similarly perturbed metabolically by a failure to express dystrophin, despite being very different types of muscle; this was characterized by an increase in taurine and lactate and a decrease in creatine in tissue extracts from dystrophic tissue. This is in keeping with the single protein isoform known to be involved in all these tissue types, and that presumably has a similar role in all these tissues. These changes could be detected even in intact tissue using high-resolution magic angle spinning 1H NMR spectroscopy, which also identified a significant increase in lipid infiltration in dystrophic tissue [59]. Similarly, extracts of cerebellum tissue from mdx mice were readily distinguished from wild-type controls by their metabolic profiles, including a characteristic increase in phosphocholine. The approach even found a weak separation in cortical tissue extracts, although this had not been detected by previous studies. The changes in profiles of dystrophic muscle, cortex and cerebellum tissue were all distinct, suggesting very different roles for the three iso-forms of dystrophin in the tissues.

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