title: Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow.
abstract: Skeletal muscle has emerged as an important secretory organ that produces so-called myokines, regulating energy metabolism via autocrine, paracrine, and endocrine actions; however, the nature and extent of the muscle secretome has not been fully elucidated. Mass spectrometry (MS)-based proteomics, in principle, allows an unbiased and comprehensive analysis of cellular secretomes; however, the distinction of bona fide secreted proteins from proteins released upon lysis of a small fraction of dying cells remains challenging. Here we applied highly sensitive MS and streamlined bioinformatics to analyze the secretome of lipid-induced insulin-resistant skeletal muscle cells. Our workflow identified 1073 putative secreted proteins including 32 growth factors, 25 cytokines, and 29 metalloproteinases. In addition to previously reported proteins, we report hundreds of novel ones. Intriguingly, ∼40% of the secreted proteins were regulated under insulin-resistant conditions, including a protein family with signal peptide and EGF-like domain structure that had not yet been associated with insulin resistance. Finally, we report that secretion of IGF and IGF-binding proteins was down-regulated under insulin-resistant conditions. Our study demonstrates an efficient combined experimental and bioinformatics workflow to identify putative secreted proteins from insulin-resistant skeletal muscle cells, which could easily be adapted to other cellular models.
authors.affiliation: Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany.|The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Blegdamsvej 3B, Building 6.1, DK-2200 Copenhagen, Denmark.
authors.forename: Atul S
authors.initials: AS
authors.lastname: Deshmukh
authors.affiliation: Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany.
authors.forename: Juergen
authors.initials: J
authors.lastname: Cox
authors.affiliation: The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Blegdamsvej 3B, Building 6.1, DK-2200 Copenhagen, Denmark.
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
authors.affiliation: Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany.
authors.forename: Felix
authors.initials: F
authors.lastname: Meissner
authors.affiliation: Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany.|The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Blegdamsvej 3B, Building 6.1, DK-2200 Copenhagen, Denmark.
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002454:Cell Differentiation; D002460:Cell Line; D019295:Computational Biology / Q000379:methods; D016207:Cytokines / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D005786:Gene Expression Regulation; D005947:Glucose / Q000378:metabolism / Q000494:pharmacology; D007328:Insulin / Q000378:metabolism / Q000494:pharmacology; D007333:Insulin Resistance; D018969:Insulin-Like Growth Factor Binding Proteins / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D045726:Metalloproteases / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D051379:Mice; D008969:Molecular Sequence Data; D018485:Muscle Fibers, Skeletal / Q000166:cytology / Q000187:drug effects / Q000378:metabolism*; D032446:Myoblasts / Q000166:cytology / Q000187:drug effects / Q000378:metabolism*; D019308:Palmitic Acid / Q000494:pharmacology; D021382:Protein Sorting Signals / Q000235:genetics; D017434:Protein Structure, Tertiary; D012710:Serum Albumin, Bovine / Q000737:chemistry
chemical_list: D016207:Cytokines; D007328:Insulin; D018969:Insulin-Like Growth Factor Binding Proteins; D036341:Intercellular Signaling Peptides and Proteins; D021382:Protein Sorting Signals; D012710:Serum Albumin, Bovine; D019308:Palmitic Acid; D045726:Metalloproteases; D005947:Glucose
keywords: diabetes; glucose uptake; insulin signaling; mass spectrometry; metabolism; myokines; obesity; palmitic acid; quantitative proteomics; secretome