Proteomics Analysis of Human Skeletal Muscle Reveals Novel Abnormalities in Obesity and Type 2 Diabetes

OBJECTIVE Insulin resistance in skeletal muscle is an early phenomenon in the pathogenesis of type 2 diabetes. Studies of insulin resistance usually are highly focused. However, approaches that give a more global picture of abnormalities in insulin resistance are useful in pointing out new directions for research. In previous studies, gene expression analyses show a coordinated pattern of reduction in nuclear-encoded mitochondrial gene expression in insulin resistance. However, changes in mRNA levels may not predict changes in protein abundance. An approach to identify global protein abundance changes involving the use of proteomics was used here. RESEARCH DESIGN AND METHODS Muscle biopsies were obtained basally from lean, obese, and type 2 diabetic volunteers (n = 8 each); glucose clamps were used to assess insulin sensitivity. Muscle protein was subjected to mass spectrometry–based quantification using normalized spectral abundance factors. RESULTS Of 1,218 proteins assigned, 400 were present in at least half of all subjects. Of these, 92 were altered by a factor of 2 in insulin resistance, and of those, 15 were significantly increased or decreased by ANOVA (P < 0.05). Analysis of protein sets revealed patterns of decreased abundance in mitochondrial proteins and altered abundance of proteins involved with cytoskeletal structure (desmin and alpha actinin-2 both decreased), chaperone function (TCP-1 subunits increased), and proteasome subunits (increased). CONCLUSIONS The results confirm the reduction in mitochondrial proteins in insulin-resistant muscle and suggest that changes in muscle structure, protein degradation, and folding also characterize insulin resistance.

[1]  Akhilesh Pandey,et al.  Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS , 2008, Proceedings of the National Academy of Sciences.

[2]  Tobias Straub,et al.  Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. , 2008, Molecular cell.

[3]  R. Berria,et al.  Global relationship between the proteome and transcriptome of human skeletal muscle. , 2008, Journal of proteome research.

[4]  Costel C. Darie,et al.  Stable Isotopic Labeling by Amino Acids in Cultured Primary Neurons , 2008, Molecular & Cellular Proteomics.

[5]  Norman Pavelka,et al.  Statistical Similarities between Transcriptomics and Quantitative Shotgun Proteomics Data *S , 2008, Molecular & Cellular Proteomics.

[6]  C. Flynn,et al.  Characterization of the Human Skeletal Muscle Proteome by One-dimensional Gel Electrophoresis and HPLC-ESI-MS/MS*S , 2008, Molecular & Cellular Proteomics.

[7]  Maristela L Onozato,et al.  Expression of NG,NG-Dimethylarginine Dimethylaminohydrolase and Protein Arginine N-Methyltransferase Isoforms in Diabetic Rat Kidney , 2008, Diabetes.

[8]  Rebecca L. Frederick,et al.  Moving Mitochondria: Establishing Distribution of an Essential Organelle , 2007, Traffic.

[9]  M. Kirk,et al.  Proteomic analysis of water insoluble proteins from normal and cataractous human lenses. , 2007, Molecular vision.

[10]  L. Mouthon,et al.  A Combined SDS‐PAGE and Proteomics Approach to Identify Target Autoantigens in Healthy Individuals and Patients with Autoimmune Diseases , 2007, Annals of the New York Academy of Sciences.

[11]  X. Papademetris,et al.  The role of skeletal muscle insulin resistance in the pathogenesis of the metabolic syndrome , 2007, Proceedings of the National Academy of Sciences.

[12]  M. Mavroidis,et al.  Muscle intermediate filaments and their links to membranes and membranous organelles. , 2007, Experimental cell research.

[13]  K. Petersen,et al.  Impaired Mitochondrial Substrate Oxidation in Muscle of Insulin-Resistant Offspring of Type 2 Diabetic Patients , 2007, Diabetes.

[14]  M. Washburn,et al.  Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. , 2007, Molecular bioSystems.

[15]  R. DeFronzo,et al.  Paradoxical Changes in Muscle Gene Expression in Insulin-Resistant Subjects After Sustained Reduction in Plasma Free Fatty Acid Concentration , 2007, Diabetes.

[16]  J. Leiper,et al.  Expression of DDAH and PRMT isoforms in the diabetic rat kidney; effects of angiotensin II receptor blocker , 2007 .

[17]  W. Mitch,et al.  Insulin resistance accelerates muscle protein degradation: Activation of the ubiquitin-proteasome pathway by defects in muscle cell signaling. , 2006, Endocrinology.

[18]  Michael K. Coleman,et al.  Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. , 2006, Journal of proteome research.

[19]  P. Cerretelli,et al.  The human muscle proteome in aging. , 2006, Journal of proteome research.

[20]  I. Boldogh,et al.  Interactions of mitochondria with the actin cytoskeleton. , 2006, Biochimica et biophysica acta.

[21]  R. Berria,et al.  Increased collagen content in insulin-resistant skeletal muscle. , 2006, American journal of physiology. Endocrinology and metabolism.

[22]  I. Boldogh,et al.  A Mammalian Actin Substitution in Yeast Actin (H372R) Causes a Suppressible Mitochondria/Vacuole Phenotype* , 2005, Journal of Biological Chemistry.

[23]  E. Hoffman,et al.  Proteome analysis of skeletal muscle from obese and morbidly obese women. , 2005, Diabetes.

[24]  Sylvia Heeneman,et al.  Proteomic analysis of differential protein expression in human atherosclerotic plaque progression , 2005, The Journal of pathology.

[25]  R. DeFronzo,et al.  Lipid Infusion Decreases the Expression of Nuclear Encoded Mitochondrial Genes and Increases the Expression of Extracellular Matrix Genes in Human Skeletal Muscle* , 2005, Journal of Biological Chemistry.

[26]  B. Goodpaster,et al.  Deficiency of subsarcolemmal mitochondria in obesity and type 2 diabetes. , 2005, Diabetes.

[27]  Sui Huang,et al.  Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles , 2003, Bioinform..

[28]  C. Reggiani,et al.  Mitochondrial dysfunction and apoptosis in myopathic mice with collagen VI deficiency , 2003, Nature Genetics.

[29]  M. Nozaki,et al.  Transcriptional Regulation of the Cytosolic Chaperonin θ Subunit Gene, Cctq, by Ets Domain Transcription Factors Elk-1, Sap-1a, and Net in the Absence of Serum Response Factor* , 2003, Journal of Biological Chemistry.

[30]  K. Nair,et al.  Impact of aerobic exercise training on age-related changes in insulin sensitivity and muscle oxidative capacity. , 2003, Diabetes.

[31]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[32]  A. Butte,et al.  Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Aase Handberg,et al.  Proteome Analysis Reveals Phosphorylation of ATP Synthase β-Subunit in Human Skeletal Muscle and Proteins with Potential Roles in Type 2 Diabetes* , 2003, The Journal of Biological Chemistry.

[34]  Y. Capetanaki.  Desmin cytoskeleton: a potential regulator of muscle mitochondrial behavior and function. , 2002, Trends in cardiovascular medicine.

[35]  Jing He,et al.  Dysfunction of mitochondria in human skeletal muscle in type 2 diabetes. , 2002, Diabetes.

[36]  P. Tsao,et al.  Impaired Nitric Oxide Synthase Pathway in Diabetes Mellitus: Role of Asymmetric Dimethylarginine and Dimethylarginine Dimethylaminohydrolase , 2002, Circulation.

[37]  K. Nair,et al.  Synthesis rate of muscle proteins, muscle functions, and amino acid kinetics in type 2 diabetes. , 2002, Diabetes.

[38]  K. Nair,et al.  Gene expression profile in skeletal muscle of type 2 diabetes and the effect of insulin treatment. , 2002, Diabetes.

[39]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[40]  L. Kunkel,et al.  Myozenin: An α-actinin- and γ-filamin-binding protein of skeletal muscle Z lines , 2001 .

[41]  Simon C Watkins,et al.  Myozenin: an alpha-actinin- and gamma-filamin-binding protein of skeletal muscle Z lines. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[42]  J. Zierath,et al.  Characterization of signal transduction and glucose transport in skeletal muscle from type 2 diabetic patients. , 2000, Diabetes.

[43]  C. Kahn,et al.  Insulin resistance differentially affects the PI 3-kinase- and MAP kinase-mediated signaling in human muscle. , 2000, The Journal of clinical investigation.

[44]  R. DeFronzo,et al.  Effects of exercise and insulin on insulin signaling proteins in human skeletal muscle. , 1999, Medicine and science in sports and exercise.

[45]  H. Yanagi,et al.  Structures and co-regulated expression of the genes encoding mouse cytosolic chaperonin CCT subunits. , 1999, European journal of biochemistry.

[46]  P. Tsao,et al.  Asymmetric dimethylarginine (ADMA): a novel risk factor for endothelial dysfunction: its role in hypercholesterolemia. , 1998, Circulation.

[47]  R. Pipek,et al.  Insulin-induced hexokinase II expression is reduced in obesity and NIDDM. , 1998, Diabetes.

[48]  K. Nair,et al.  Protein metabolism in insulin-dependent diabetes mellitus. , 1998, The Journal of nutrition.

[49]  V. Shah,et al.  Nitric oxide synthase inhibitors and hypertension in children and adolescents , 1997, Journal of hypertension.

[50]  Nair Ks.  Muscle Protein Turnover: Methodological Issues and the Effect of Aging , 1995 .

[51]  K. Nair.  Muscle protein turnover: methodological issues and the effect of aging. , 1995, The journals of gerontology. Series A, Biological sciences and medical sciences.

[52]  L. Mandarino,et al.  Intracellular Defects in Glucose Metabolism in Obese Patients With NIDDM , 1992, Diabetes.

[53]  R. DeFronzo.  The Triumvirate: β-Cell, Muscle, Liver: A Collusion Responsible for NIDDM , 1988, Diabetes.

[54]  R. DeFronzo.  Lilly lecture 1987. The triumvirate: beta-cell, muscle, liver. A collusion responsible for NIDDM. , 1988, Diabetes.

[55]  R. DeFronzo,et al.  Glucose clamp technique: a method for quantifying insulin secretion and resistance. , 1979, The American journal of physiology.

[56]  H. W. Lee,et al.  Purification and characterization of protein methylase I (S-adenosylmethionine: protein-arginine methyltransferase; EC 2.1.1.23) from calf brain. , 1978, Methods in cell biology.

[57]  Y. Habib,et al.  Serum electrolytes in diabetic patients and the effect of insulin treatment. , 1959, The Journal of the Egyptian Medical Association.