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Tamir TY, Chaudhary S, Li AX, Trojan SE, Flower CT, Vo P, Cui Y, Davis JC, Mukkamala RS, Venditti FN, Hillis AL, Toker A, Vander Heiden MG, Spinelli JB, Kennedy NJ, Davis RJ, White FM. Structural and systems characterization of phosphorylation on metabolic enzymes identifies sex-specific metabolic reprogramming in obesity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.609894. [PMID: 39257804 PMCID: PMC11383994 DOI: 10.1101/2024.08.28.609894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Coordination of adaptive metabolism through cellular signaling networks and metabolic response is essential for balanced flow of energy and homeostasis. Post-translational modifications such as phosphorylation offer a rapid, efficient, and dynamic mechanism to regulate metabolic networks. Although numerous phosphorylation sites have been identified on metabolic enzymes, much remains unknown about their contribution to enzyme function and systemic metabolism. In this study, we stratify phosphorylation sites on metabolic enzymes based on their location with respect to functional and dimerization domains. Our analysis reveals that the majority of published phosphosites are on oxidoreductases, with particular enrichment of phosphotyrosine (pY) sites in proximity to binding domains for substrates, cofactors, active sites, or dimer interfaces. We identify phosphosites altered in obesity using a high fat diet (HFD) induced obesity model coupled to multiomics, and interrogate the functional impact of pY on hepatic metabolism. HFD induced dysregulation of redox homeostasis and reductive metabolism at the phosphoproteome and metabolome level in a sex-specific manner, which was reversed by supplementing with the antioxidant butylated hydroxyanisole (BHA). Partial least squares regression (PLSR) analysis identified pY sites that predict HFD or BHA induced changes of redox metabolites. We characterize predictive pY sites on glutathione S-transferase pi 1 (GSTP1), isocitrate dehydrogenase 1 (IDH1), and uridine monophosphate synthase (UMPS) using CRISPRi-rescue and stable isotope tracing. Our analysis revealed that sites on GSTP1 and UMPS inhibit enzyme activity while the pY site on IDH1 induces activity to promote reductive carboxylation. Overall, our approach provides insight into the convergence points where cellular signaling fine-tunes metabolism.
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Affiliation(s)
- Tigist Y Tamir
- Koch Institute for Integrative Cancer Research
- Center for Precision Cancer Medicine
- Department of Biological Engineering
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shreya Chaudhary
- Koch Institute for Integrative Cancer Research
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Annie X Li
- Koch Institute for Integrative Cancer Research
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sonia E Trojan
- Koch Institute for Integrative Cancer Research
- Department of Biology
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cameron T Flower
- Koch Institute for Integrative Cancer Research
- Center for Precision Cancer Medicine
- Program in Computational and Systems Biology
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paula Vo
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yufei Cui
- Koch Institute for Integrative Cancer Research
- Department of Biological Engineering
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey C Davis
- Koch Institute for Integrative Cancer Research
- Department of Biology
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rachit S Mukkamala
- Koch Institute for Integrative Cancer Research
- Department of Biological Engineering
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Francesca N Venditti
- Koch Institute for Integrative Cancer Research
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alissandra L Hillis
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Alex Toker
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research
- Center for Precision Cancer Medicine
- Department of Biology
- Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jessica B Spinelli
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Norman J Kennedy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Roger J Davis
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Forest M White
- Koch Institute for Integrative Cancer Research
- Center for Precision Cancer Medicine
- Department of Biological Engineering
- Program in Computational and Systems Biology
- Massachusetts Institute of Technology, Cambridge, MA, USA
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2
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Kioumourtzoglou D, Black HL, Al Tobi M, Livingstone R, Petrie JR, Boyle JG, Gould GW, Bryant NJ. Phosphorylation of Syntaxin 4 by the Insulin Receptor Drives Exocytic SNARE Complex Formation to Deliver GLUT4 to the Cell Surface. Biomolecules 2023; 13:1738. [PMID: 38136609 PMCID: PMC10741561 DOI: 10.3390/biom13121738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
A major consequence of insulin binding its receptor on fat and muscle cells is the stimulation of glucose transport into these tissues. This is achieved through an increase in the exocytic trafficking rate of the facilitative glucose transporter GLUT4 from intracellular stores to the cell surface. Delivery of GLUT4 to the cell surface requires the formation of functional SNARE complexes containing Syntaxin 4, SNAP23, and VAMP2. Insulin stimulates the formation of these complexes and concomitantly causes phosphorylation of Syntaxin 4. Here, we use a combination of biochemistry and cell biological approaches to provide a mechanistic link between these observations. We present data to support the hypothesis that Tyr-115 and Tyr-251 of Syntaxin 4 are direct substrates of activated insulin receptors, and that these residues modulate the protein's conformation and thus regulate the rate at which Syntaxin 4 forms SNARE complexes that deliver GLUT4 to the cell surface. This report provides molecular details on how the cell regulates SNARE-mediated membrane traffic in response to an external stimulus.
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Affiliation(s)
| | - Hannah L. Black
- Department of Biology, University of York, Heslington YO10 5DD, UK; (D.K.)
| | - Mohammed Al Tobi
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (M.A.T.)
| | - Rachel Livingstone
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (M.A.T.)
| | - John R. Petrie
- Institute of Cardiovascular and Medical Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - James G. Boyle
- School of Medicine, Dentistry & Nursing, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Gwyn W. Gould
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 ORE, UK
| | - Nia J. Bryant
- Department of Biology, University of York, Heslington YO10 5DD, UK; (D.K.)
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Abstract
Nutrient intake is obligatory for animal growth and development, but nutrients alone are not sufficient. Indeed, insulin and homologous hormones are required for normal growth even in the presence of nutrients. These hormones communicate nutrient status between organs, allowing animals to coordinate growth and metabolism with nutrient supply. Insulin and related hormones, such as insulin-like growth factors and insulin-like peptides, play important roles in development and metabolism, with defects in insulin production and signaling leading to hyperglycemia and diabetes. Here, we describe the insulin hormone family and the signal transduction pathways activated by these hormones. We highlight the roles of insulin signaling in coordinating maternal and fetal metabolism and growth during pregnancy, and we describe how secretion of insulin is regulated at different life stages. Additionally, we discuss the roles of insulin signaling in cell growth, stem cell proliferation and cell differentiation. We provide examples of the role of insulin in development across multiple model organisms: Caenorhabditis elegans, Drosophila, zebrafish, mouse and human.
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Affiliation(s)
- Miyuki Suzawa
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Michelle L. Bland
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
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Roy PK, Islam J, Lalhlenmawia H. Prospects of potential adipokines as therapeutic agents in obesity-linked atherogenic dyslipidemia and insulin resistance. Egypt Heart J 2023; 75:24. [PMID: 37014444 PMCID: PMC10073393 DOI: 10.1186/s43044-023-00352-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND In normal circumstances, AT secretes anti-inflammatory adipokines (AAKs) which regulates lipid metabolism, insulin sensitivity, vascular hemostasis, and angiogenesis. However, during obesity AT dysfunction occurs and leads to microvascular imbalance and secretes several pro-inflammatory adipokines (PAKs), thereby favoring atherogenic dyslipidemia and insulin resistance. Literature suggests decreased levels of circulating AAKs and increased levels of PAKs in obesity-linked disorders. Importantly, AAKs have been reported to play a vital role in obesity-linked metabolic disorders mainly insulin resistance, type-2 diabetes mellitus and coronary heart diseases. Interestingly, AAKs counteract the microvascular imbalance in AT and exert cardioprotection via several signaling pathways such as PI3-AKT/PKB pathway. Although literature reviews have presented a number of investigations detailing specific pathways involved in obesity-linked disorders, literature concerning AT dysfunction and AAKs remains sketchy. In view of the above, in the present contribution an effort has been made to provide an insight on the AT dysfunction and role of AAKs in modulating the obesity and obesity-linked atherogenesis and insulin resistance. MAIN BODY "Obesity-linked insulin resistance", "obesity-linked cardiometabolic disease", "anti-inflammatory adipokines", "pro-inflammatory adipokines", "adipose tissue dysfunction" and "obesity-linked microvascular dysfunction" are the keywords used for searching article. Google scholar, Google, Pubmed and Scopus were used as search engines for the articles. CONCLUSIONS This review offers an overview on the pathophysiology of obesity, management of obesity-linked disorders, and areas in need of attention such as novel therapeutic adipokines and their possible future perspectives as therapeutic agents.
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Affiliation(s)
- Probin Kr Roy
- Department of Pharmacy, Regional Institute of Paramedical and Nursing Sciences (RIPANS), Aizawl, Mizoram, 796017, India.
| | - Johirul Islam
- Coromandel International Limited, Hyderabad, Telangana, 500101, India
| | - Hauzel Lalhlenmawia
- Department of Pharmacy, Regional Institute of Paramedical and Nursing Sciences (RIPANS), Aizawl, Mizoram, 796017, India
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Huang H, Drici L, Lassen PS, Palmisano G, Larsen MR. TiCPG - a strategy for the simultaneous enrichment of reversibly modified cysteine peptides, phosphopeptides, and sialylated N-Glycopeptides to study cytokines stimulated beta-cells. J Proteomics 2023; 273:104796. [PMID: 36538968 DOI: 10.1016/j.jprot.2022.104796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022]
Abstract
Diverse post-translational modifications (PTMs) regulate protein function and interaction to fine-tune biological processes. Reversible phosphorylation, cysteines (Cys) modifications, and N-linked glycosylation are all essentially involved in cellular signaling pathways, such as those initiated by the action of pro-inflammatory cytokines, which can induce pancreatic β-cell death and diabetes. Here we have developed a novel strategy for the simultaneous and comprehensive characterization of the proteome and three PTMs including reversibly modified Cysteines (rmCys), phosphorylation, and sialylated N-linked glycosylation from low amount of sample material. This strategy, termed TiCPG, is based on a combination of chemical labeling and titanium dioxide (TiO2) chromatography. We applied the TiCPG strategy to study the proteome and the three PTMs changes in β-cells subject to pro-inflammatory cytokines stimulation. It enabled quantitative analysis of 8346 rmCys sites, 10,321 phosphosites and 962 sialylated N-glycosites from 5496 proteins. Significant regulation was found on 100 proteins at the expression level, while 3020 PTM peptide isoforms from 1468 proteins were significantly regulated. The three PTMs were involved in cytokine mediated β-cell apoptosis, such as the NFκB and the inducible NO synthase signaling pathways. Overall, the TiCPG strategy is a cheap, straightforward, and powerful tool for studies targeting the three PTMs described above. SIGNIFICANCE: The present study presents a fast and easy method for quantitative assessment of the proteome and three PTMs from minimal amount of sample material. This simple method provides comprehensive and significant knowledge on biological systems and cellular signaling with relatively low analysis time, suitable for younger researchers and researchers that do not have direct access to LC-MSMS in their laboratories. From sub-milligram amount of material, we were able to map known cellular signaling events of proinflammatory cytokine effect on beta-cells and to discover novel PTMs involved in several known signaling pathways.
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Affiliation(s)
- Honggang Huang
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Lylia Drici
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Pernille S Lassen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Giuseppe Palmisano
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; Departament of Parasitology, Institute of Biomedical Sciences - University of São Paulo, Avenida Prof. Lineu Prestes, 1374 - Edifício Biomédicas II, Cidade Universitária "Armando Salles Oliveira" - CEP, 05508-000 São Paulo, Brazil
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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Li B, Li W, Liu T, Zha L. Extracellular vesicles regulate the transmission of insulin resistance and redefine noncommunicable diseases. Front Mol Biosci 2023; 9:1024786. [PMID: 36699697 PMCID: PMC9868246 DOI: 10.3389/fmolb.2022.1024786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
Noncommunicable diseases (NCDs), such as diabetes and related neurological disorders, are considered to not be directly transmissible from one person to another. However, NCDs may be transmissible in vivo through extracellular vesicles (EVs). A long-term high-fat diet (HFD) can induce a series of health issues like hyperlipidemia, type 2 diabetes mellitus (T2DM), and diabetic peripheral neuropathy (DPN) due to insulin resistance. Multiple molecular signaling changes can stimulate insulin resistance, especially blocking insulin signaling by increased insulin resistance inducer (phosphorylation of negative regulatory sites of insulin receptor substrate (IRS) proteins) and decreased tyrosine phosphorylation of insulin receptor substrate (phosphorylation of positive regulatory sites of IRS), thus leading to reduced phosphorylation of AKT enzymes. Current efforts to treat T2DM and prevent its complications mainly focus on improving insulin sensitivity, enhancing insulin secretion, or supplementing exogenous insulin based on a common assumption that insulin resistance is noncommunicable. However, insulin resistance is transmissible within multiple tissues or organs throughout the body. Exploring the regulatory roles of EVs in developing insulin resistance may provide novel and effective preventive and therapeutic strategies.
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Affiliation(s)
- Biao Li
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration Key Laboratory of Cosmetic Safety Evaluation, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Wan Li
- School of Physical Education, Hubei Minzu University, Enshi, China
| | - Tiancai Liu
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Longying Zha
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, National Medical Products Administration Key Laboratory of Cosmetic Safety Evaluation, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
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7
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Hwang J, Thurmond DC. Exocytosis Proteins: Typical and Atypical Mechanisms of Action in Skeletal Muscle. Front Endocrinol (Lausanne) 2022; 13:915509. [PMID: 35774142 PMCID: PMC9238359 DOI: 10.3389/fendo.2022.915509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022] Open
Abstract
Insulin-stimulated glucose uptake in skeletal muscle is of fundamental importance to prevent postprandial hyperglycemia, and long-term deficits in insulin-stimulated glucose uptake underlie insulin resistance and type 2 diabetes. Skeletal muscle is responsible for ~80% of the peripheral glucose uptake from circulation via the insulin-responsive glucose transporter GLUT4. GLUT4 is mainly sequestered in intracellular GLUT4 storage vesicles in the basal state. In response to insulin, the GLUT4 storage vesicles rapidly translocate to the plasma membrane, where they undergo vesicle docking, priming, and fusion via the high-affinity interactions among the soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) exocytosis proteins and their regulators. Numerous studies have elucidated that GLUT4 translocation is defective in insulin resistance and type 2 diabetes. Emerging evidence also links defects in several SNAREs and SNARE regulatory proteins to insulin resistance and type 2 diabetes in rodents and humans. Therefore, we highlight the latest research on the role of SNAREs and their regulatory proteins in insulin-stimulated GLUT4 translocation in skeletal muscle. Subsequently, we discuss the novel emerging role of SNARE proteins as interaction partners in pathways not typically thought to involve SNAREs and how these atypical functions reveal novel therapeutic targets for combating peripheral insulin resistance and diabetes.
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Affiliation(s)
| | - Debbie C. Thurmond
- Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute at City of Hope, Duarte, CA, United States
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8
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Gök C, Robertson AD, Fuller W. Insulin-induced palmitoylation regulates the Cardiac Na+/Ca2+ exchanger NCX1. Cell Calcium 2022; 104:102567. [DOI: 10.1016/j.ceca.2022.102567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/02/2022]
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Fazakerley DJ, Koumanov F, Holman GD. GLUT4 On the move. Biochem J 2022; 479:445-462. [PMID: 35147164 PMCID: PMC8883492 DOI: 10.1042/bcj20210073] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/16/2022]
Abstract
Insulin rapidly stimulates GLUT4 translocation and glucose transport in fat and muscle cells. Signals from the occupied insulin receptor are translated into downstream signalling changes in serine/threonine kinases within timescales of seconds, and this is followed by delivery and accumulation of the glucose transporter GLUT4 at the plasma membrane. Kinetic studies have led to realisation that there are distinct phases of this stimulation by insulin. There is a rapid initial burst of GLUT4 delivered to the cell surface from a subcellular reservoir compartment and this is followed by a steady-state level of continuing stimulation in which GLUT4 recycles through a large itinerary of subcellular locations. Here, we provide an overview of the phases of insulin stimulation of GLUT4 translocation and the molecules that are currently considered to activate these trafficking steps. Furthermore, we suggest how use of new experimental approaches together with phospho-proteomic data may help to further identify mechanisms for activation of these trafficking processes.
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Affiliation(s)
- Daniel J Fazakerley
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, U.K
| | - Francoise Koumanov
- Department for Health, Centre for Nutrition, Exercise, and Metabolism, University of Bath, Bath, Somerset BA2 7AY, U.K
| | - Geoffrey D Holman
- Department of Biology and Biochemistry, University of Bath, Bath, Somerset BA2 7AY, U.K
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10
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Liao Z, Zhang C, Ding L, Moyers JS, Tang JX, Beals JM. Comprehensive insulin receptor phosphorylation dynamics profiled by mass spectrometry. FEBS J 2021; 289:2657-2671. [PMID: 34826178 DOI: 10.1111/febs.16299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 11/09/2021] [Accepted: 11/25/2021] [Indexed: 02/03/2023]
Abstract
Insulin receptor (IR) phosphorylation is critical for the assessment of the extent of IR agonism and nuances in the downstream signaling cascade. A thorough identification and monitoring of the phosphorylation events is important for understanding the process of insulin signaling transduction and regulation. Although IR phosphorylation has been studied extensively in the past decades, only a handful of phosphorylation sites can be identified by either traditional antibody-based assays or recent large-scale mass spectrometry-based phosphoproteomics approaches. In the present study, the most exhaustive assessment of the IR phosphorylation was conducted using nano-liquid chromatography-tandem mass spectrometry, in which 13 IR phosphorylation sites and 22 combinations thereof were analyzed. The kinetic analysis included Y965, Y972, S968/969, and S974/976 in the juxtamembrane region; Y1158, Y1162, and Y1163 in the kinase domain; and Y1328, Y1334, S1278, S1320, S1321, and T1348 in the C-terminal region. Employing two different receptor agonists (i.e. insulin and an IR peptide agonist), the data revealed contrasting phosphorylation kinetics across these sites with dynamics far more diverse than expected for known IR agonists. Notably, cell trafficking experiments revealed that the IR peptide agonist was incapable of inducing IR to the early endosome, which is probably linked to a difference in IR phosphorylation. The present study provides a powerful tool for investigating IR signaling and trafficking that will benefit the design of IR agonists with improved therapeutic utility.
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Affiliation(s)
- Zhongping Liao
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Chen Zhang
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Liyun Ding
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Julie S Moyers
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Jason X Tang
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - John M Beals
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
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11
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Gerritsen JS, White FM. Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells. Expert Rev Proteomics 2021; 18:661-674. [PMID: 34468274 PMCID: PMC8628306 DOI: 10.1080/14789450.2021.1976152] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Many pathologies, including cancer, have been associated with aberrant phosphorylation-mediated signaling networks that drive altered cell proliferation, migration, metabolic regulation, and can lead to systemic inflammation. Phosphoproteomics, the large-scale analysis of protein phosphorylation sites, has emerged as a powerful tool to define signaling network regulation and dysregulation in normal and pathological conditions. AREAS COVERED We provide an overview of methodology for global phosphoproteomics as well as enrichment of specific subsets of the phosphoproteome, including phosphotyrosine and phospho-motif enrichment of kinase substrates. We review quantitative methods, advantages and limitations of different mass spectrometry acquisition formats, and computational approaches to extract biological insight from phosphoproteomics data. Throughout, we discuss various applications and their challenges in implementation. EXPERT OPINION Over the past 20 years the field of phosphoproteomics has advanced to enable deep biological and clinical insight through the quantitative analysis of signaling networks. Future areas of development include Clinical Laboratory Improvement Amendments (CLIA)-approved methods for analysis of clinical samples, continued improvements in sensitivity to enable analysis of small numbers of rare cells and tissue microarrays, and computational methods to integrate data resulting from multiple systems-level quantitative analytical methods.
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Affiliation(s)
- Jacqueline S Gerritsen
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
| | - Forest M White
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
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12
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Unluhizarci K, Karaca Z, Kelestimur F. Role of insulin and insulin resistance in androgen excess disorders. World J Diabetes 2021; 12:616-629. [PMID: 33995849 PMCID: PMC8107978 DOI: 10.4239/wjd.v12.i5.616] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/13/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Insulin has complex effects on cell growth, metabolism and differentiation, and these effects are mediated by a cell-surface bound receptor and eventually a cascade of intracellular signaling events. Among the several metabolic and growth-promoting effects of insulin, insulin resistance is defined as an attenuated effect of insulin on glucose metabolism, primarily the limited export of blood glucose into skeletal muscle and adipose tissue. On the other hand, not all the signaling pathways and insulin-responsive tissues are equally affected, and some effects other than the metabolic actions of insulin are overexpressed. Ovaries and the adrenal glands are two examples of tissues remaining sensitive to insulin actions where insulin may contribute to increased androgen secretion. Polycystic ovary syndrome (PCOS) is the most common form of androgen excess disorder (AED), and its pathogenesis is closely associated with insulin resistance. Patients with idiopathic hirsutism also exhibit insulin resistance, albeit lower than patients with PCOS. Although it is not as evident as in PCOS, patients with congenital adrenal hyperplasia may have insulin resistance, which may be further exacerbated with glucocorticoid overtreatment and obesity. Among patients with severe insulin resistance syndromes, irrespective of the type of disease, hyperinsulinemia promotes ovarian androgen synthesis independently of gonadotropins. It is highly debated in whom and how insulin resistance should be diagnosed and treated among patients with AEDs, including PCOS. It is not suitable to administer an insulin sensitizer relying on only some mathematical models used for estimating insulin resistance. Instead, the treatment decision should be based on the constellation of the signs, symptoms and presence of obesity; acanthosis nigricans; and some laboratory abnormalities such as impaired glucose tolerance and impaired fasting glucose.
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Affiliation(s)
- Kursad Unluhizarci
- Department of Endocrinology, Erciyes University Medical School, Kayseri, 38039, Turkey
| | - Zuleyha Karaca
- Department of Endocrinology, Erciyes University Medical School, Kayseri, 38039, Turkey
| | - Fahrettin Kelestimur
- Department of Endocrinology, Yeditepe University Medical School, Istanbul, 34755, Turkey
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13
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Chamberlain LH, Shipston MJ, Gould GW. Regulatory effects of protein S-acylation on insulin secretion and insulin action. Open Biol 2021; 11:210017. [PMID: 33784857 PMCID: PMC8061761 DOI: 10.1098/rsob.210017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/02/2021] [Indexed: 12/23/2022] Open
Abstract
Post-translational modifications (PTMs) such as phosphorylation and ubiquitination are well-studied events with a recognized importance in all aspects of cellular function. By contrast, protein S-acylation, although a widespread PTM with important functions in most physiological systems, has received far less attention. Perturbations in S-acylation are linked to various disorders, including intellectual disability, cancer and diabetes, suggesting that this less-studied modification is likely to be of considerable biological importance. As an exemplar, in this review, we focus on the newly emerging links between S-acylation and the hormone insulin. Specifically, we examine how S-acylation regulates key components of the insulin secretion and insulin response pathways. The proteins discussed highlight the diverse array of proteins that are modified by S-acylation, including channels, transporters, receptors and trafficking proteins and also illustrate the diverse effects that S-acylation has on these proteins, from membrane binding and micro-localization to regulation of protein sorting and protein interactions.
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Affiliation(s)
- Luke H. Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Michael J. Shipston
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Gwyn W. Gould
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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14
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Inhalation of ammonium sulfate and ammonium nitrate adversely affect sperm function. Reprod Toxicol 2020; 96:424-431. [PMID: 32866586 DOI: 10.1016/j.reprotox.2020.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/19/2020] [Accepted: 08/22/2020] [Indexed: 01/09/2023]
Abstract
Among the components of air pollution in developing countries and Asia, (NH4)2SO4 and NH4NO3 are known as major water-soluble in-organic compounds that cause particulate matter. Several researchers have been reported that the (NH4)2SO4 and NH4NO3 induce abnormal decreases in body weight, as well as pneumotoxic, and immunotoxic. Moreover, while it has been reported that (NH4)2SO4 and NH4NO3 have detrimental effects on reproduction, specific effects on male fertility have not been addressed in depth. Therefore, the present study evaluated the reproductive toxicity of (NH4)2SO4 and NH4NO3 in spermatozoa under the capacitation condition. Results showed that various sperm motion parameters were significantly altered after inhalation of (NH4)2SO4 and NH4NO3. In particular, alterations to a range of motion kinematic parameters and to capacitation status were observed after capacitation. In addition, protein kinase A (PKA) activity and tyrosine phosphorylation were altered by (NH4)2SO4 and NH4NO3 regardless of capacitation. Taken together, our results show that inhalation of (NH4)2SO4 and NH4NO3 may induce adverse effects on male fertility such as sperm motility, motion kinematics, and capacitation status via unusual tyrosine phosphorylation by abnormal PKA activity. Therefore, we suggest that exposure to (NH4)2SO4 and NH4NO3 should be highlighted as a health risk, as it may lead to male reproductive toxicity in humans and animals.
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15
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Naberhuis JK, Suryawan A, Nguyen HV, Hernandez-Garcia A, Cruz SM, Lau PE, Olutoye OO, Stoll B, Burrin DG, Fiorotto ML, Davis TA. Prematurity blunts the feeding-induced stimulation of translation initiation signaling and protein synthesis in muscle of neonatal piglets. Am J Physiol Endocrinol Metab 2019; 317:E839-E851. [PMID: 31503514 PMCID: PMC6879862 DOI: 10.1152/ajpendo.00151.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Postnatal growth of lean mass is commonly blunted in preterm infants and may contribute to short- and long-term morbidities. To determine whether preterm birth alters the protein anabolic response to feeding, piglets were delivered at term or preterm, and fractional protein synthesis rates (Ks) were measured at 3 days of age while fasted or after an enteral meal. Activation of signaling pathways that regulate protein synthesis and degradation were determined. Relative body weight gain was lower in preterm than in term. Gestational age at birth (GAB) did not alter fasting plasma glucose or insulin, but when fed, plasma insulin and glucose rose more slowly, and reached peak value later, in preterm than in term. Feeding increased Ks in longissimus dorsi (LD) and gastrocnemius muscles, heart, pancreas, and kidney in both GAB groups, but the response was blunted in preterm. In diaphragm, lung, jejunum, and brain, feeding increased Ks regardless of GAB. Liver Ks was greater in preterm than term and increased with feeding regardless of GAB. In all tissues, changes in 4EBP1, S6K1, and PKB phosphorylation paralleled changes in Ks. In LD, eIF4E·eIF4G complex formation, phosphorylation of TSC2, mTOR, and rpS6, and association of mammalian target of rapamycin (mTOR1) complex with RagA, RagC, and Rheb were increased by feeding and blunted by prematurity. There were no differences among groups in LD protein degradation markers. Our results demonstrate that preterm birth reduces weight gain and the protein synthetic response to feeding in muscle, pancreas, and kidney, and this is associated with blunted insulin- and/or amino acid-induced translation initiation signaling.
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Affiliation(s)
- Jane K Naberhuis
- United States Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Agus Suryawan
- United States Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Hanh V Nguyen
- United States Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Adriana Hernandez-Garcia
- United States Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Stephanie M Cruz
- Division of Pediatric Surgery, Michael E. DeBakey Department of Surgery, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Patricio E Lau
- Division of Pediatric Surgery, Michael E. DeBakey Department of Surgery, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Oluyinka O Olutoye
- Division of Pediatric Surgery, Michael E. DeBakey Department of Surgery, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Barbara Stoll
- United States Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Douglas G Burrin
- United States Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Marta L Fiorotto
- United States Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Teresa A Davis
- United States Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
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16
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Emdal KB, Pedersen AK, Bekker-Jensen DB, Lundby A, Claeys S, De Preter K, Speleman F, Francavilla C, Olsen JV. Integrated proximal proteomics reveals IRS2 as a determinant of cell survival in ALK-driven neuroblastoma. Sci Signal 2018; 11:11/557/eaap9752. [PMID: 30459283 DOI: 10.1126/scisignal.aap9752] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oncogenic anaplastic lymphoma kinase (ALK) is one of the few druggable targets in neuroblastoma, and therapy resistance to ALK-targeting tyrosine kinase inhibitors (TKIs) comprises an inevitable clinical challenge. Therefore, a better understanding of the oncogenic signaling network rewiring driven by ALK is necessary to improve and guide future therapies. Here, we performed quantitative mass spectrometry-based proteomics on neuroblastoma cells treated with one of three clinically relevant ALK TKIs (crizotinib, LDK378, or lorlatinib) or an experimentally used ALK TKI (TAE684) to unravel aberrant ALK signaling pathways. Our integrated proximal proteomics (IPP) strategy included multiple signaling layers, such as the ALK interactome, phosphotyrosine interactome, phosphoproteome, and proteome. We identified the signaling adaptor protein IRS2 (insulin receptor substrate 2) as a major ALK target and an ALK TKI-sensitive signaling node in neuroblastoma cells driven by oncogenic ALK. TKI treatment decreased the recruitment of IRS2 to ALK and reduced the tyrosine phosphorylation of IRS2. Furthermore, siRNA-mediated depletion of ALK or IRS2 decreased the phosphorylation of the survival-promoting kinase Akt and of a downstream target, the transcription factor FoxO3, and reduced the viability of three ALK-driven neuroblastoma cell lines. Collectively, our IPP analysis provides insight into the proximal architecture of oncogenic ALK signaling by revealing IRS2 as an adaptor protein that links ALK to neuroblastoma cell survival through the Akt-FoxO3 signaling axis.
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Affiliation(s)
- Kristina B Emdal
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.,Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Anna-Kathrine Pedersen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Dorte B Bekker-Jensen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Alicia Lundby
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Shana Claeys
- Center for Medical Genetics Ghent, Cancer Research Institute Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics Ghent, Cancer Research Institute Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics Ghent, Cancer Research Institute Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Chiara Francavilla
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark. .,Division of Molecular and Cellular Functions, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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17
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Guo XX, An S, Yang Y, Liu Y, Hao Q, Tang T, Xu TR. Emerging role of the Jun N-terminal kinase interactome in human health. Cell Biol Int 2018; 42:756-768. [DOI: 10.1002/cbin.10948] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/03/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Xiao-Xi Guo
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming Yunnan 650500 China
| | - Su An
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming Yunnan 650500 China
| | - Yang Yang
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming Yunnan 650500 China
| | - Ying Liu
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming Yunnan 650500 China
| | - Qian Hao
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming Yunnan 650500 China
| | - Tao Tang
- Faculty of Medicine; Kunming University of Science and Technology; Kunming Yunnan 650500 China
| | - Tian-Rui Xu
- Faculty of Life Science and Technology; Kunming University of Science and Technology; Kunming Yunnan 650500 China
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18
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Li Z, Lai ZW, Christiano R, Gazos-Lopes F, Walther TC, Farese RV. Global Analyses of Selective Insulin Resistance in Hepatocytes Caused by Palmitate Lipotoxicity. Mol Cell Proteomics 2018; 17:836-849. [PMID: 29414761 DOI: 10.1074/mcp.ra117.000560] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/02/2018] [Indexed: 12/11/2022] Open
Abstract
Obesity is tightly linked to hepatic steatosis and insulin resistance. One feature of this association is the paradox of selective insulin resistance: insulin fails to suppress hepatic gluconeogenesis but activates lipid synthesis in the liver. How lipid accumulation interferes selectively with some branches of hepatic insulin signaling is not well understood. Here we provide a resource, based on unbiased approaches and established in a simple cell culture system, to enable investigations of the phenomenon of selective insulin resistance. We analyzed the phosphoproteome of insulin-treated human hepatoma cells and identified sites in which palmitate selectively impairs insulin signaling. As an example, we show that palmitate interferes with insulin signaling to FoxO1, a key transcription factor regulating gluconeogenesis, and identify altered FoxO1 cellular compartmentalization as a contributing mechanism for selective insulin resistance. This model system, together with our comprehensive characterization of the proteome, phosphoproteome, and lipidome changes in response to palmitate treatment, provides a novel and useful resource for unraveling the mechanisms underlying selective insulin resistance.
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Affiliation(s)
- Zhihuan Li
- From the ‡Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, 02115.,§Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115.,¶Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02124
| | - Zon Weng Lai
- From the ‡Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, 02115.,§Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115.,¶Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02124
| | - Romain Christiano
- From the ‡Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, 02115.,§Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115.,¶Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02124
| | - Felipe Gazos-Lopes
- ‖Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, 02115
| | - Tobias C Walther
- From the ‡Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, 02115; .,§Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115.,¶Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02124.,**Howard Hughes Medical Institute, Boston, Massachusetts, 02115
| | - Robert V Farese
- From the ‡Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, 02115.,§Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115.,¶Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02124
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19
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Haeusler RA, McGraw TE, Accili D. Biochemical and cellular properties of insulin receptor signalling. Nat Rev Mol Cell Biol 2018; 19:31-44. [PMID: 28974775 PMCID: PMC5894887 DOI: 10.1038/nrm.2017.89] [Citation(s) in RCA: 428] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The mechanism of insulin action is a central theme in biology and medicine. In addition to the rather rare condition of insulin deficiency caused by autoimmune destruction of pancreatic β-cells, genetic and acquired abnormalities of insulin action underlie the far more common conditions of type 2 diabetes, obesity and insulin resistance. The latter predisposes to diseases ranging from hypertension to Alzheimer disease and cancer. Hence, understanding the biochemical and cellular properties of insulin receptor signalling is arguably a priority in biomedical research. In the past decade, major progress has led to the delineation of mechanisms of glucose transport, lipid synthesis, storage and mobilization. In addition to direct effects of insulin on signalling kinases and metabolic enzymes, the discovery of mechanisms of insulin-regulated gene transcription has led to a reassessment of the general principles of insulin action. These advances will accelerate the discovery of new treatment modalities for diabetes.
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Affiliation(s)
- Rebecca A Haeusler
- Columbia University College of Physicians and Surgeons, Department of Pathology and Cell Biology, New York, New York 10032, USA
| | - Timothy E McGraw
- Weill Cornell Medicine, Departments of Biochemistry and Cardiothoracic Surgery, New York, New York 10065, USA
| | - Domenico Accili
- Columbia University College of Physicians & Surgeons, Department of Medicine, New York, New York 10032, USA
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20
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SNARE phosphorylation: a control mechanism for insulin-stimulated glucose transport and other regulated exocytic events. Biochem Soc Trans 2017; 45:1271-1277. [PMID: 29101310 DOI: 10.1042/bst20170202] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 11/17/2022]
Abstract
Trafficking within eukaryotic cells is a complex and highly regulated process; events such as recycling of plasma membrane receptors, formation of multivesicular bodies, regulated release of hormones and delivery of proteins to membranes all require directionality and specificity. The underpinning processes, including cargo selection, membrane fusion, trafficking flow and timing, are controlled by a variety of molecular mechanisms and engage multiple families of lipids and proteins. Here, we will focus on control of trafficking processes via the action of the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) family of proteins, in particular their regulation by phosphorylation. We will describe how these proteins are controlled in a range of regulated trafficking events, with particular emphasis on the insulin-stimulated delivery of glucose transporters to the surface of adipose and muscle cells. Here, we focus on a few examples of SNARE phosphorylation which exemplify distinct ways in which SNARE machinery phosphorylation may regulate membrane fusion.
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21
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Understanding Alzheimer's disease by global quantification of protein phosphorylation and sialylated N-linked glycosylation profiles: A chance for new biomarkers in neuroproteomics? J Proteomics 2017; 161:11-25. [DOI: 10.1016/j.jprot.2017.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/24/2017] [Accepted: 04/03/2017] [Indexed: 12/13/2022]
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22
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Rabiee A, Schwämmle V, Sidoli S, Dai J, Rogowska-Wrzesinska A, Mandrup S, Jensen ON. Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators. Proteomics 2016; 17. [PMID: 27717184 DOI: 10.1002/pmic.201600248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/07/2016] [Accepted: 09/20/2016] [Indexed: 01/16/2023]
Abstract
Adipocytes (fat cells) are important endocrine and metabolic cells critical for systemic insulin sensitivity. Both adipose excess and insufficiency are associated with adverse metabolic function. Adipogenesis is the process whereby preadipocyte precursor cells differentiate into lipid-laden mature adipocytes. This process is driven by a network of transcriptional regulators (TRs). We hypothesized that protein PTMs, in particular phosphorylation, play a major role in activating and propagating signals within TR networks upon induction of adipogenesis by extracellular stimulus. We applied MS-based quantitative proteomics and phosphoproteomics to monitor the alteration of nuclear proteins during the early stages (4 h) of preadipocyte differentiation. We identified a total of 4072 proteins including 2434 phosphorylated proteins, a majority of which were assigned as regulators of gene expression. Our results demonstrate that adipogenic stimuli increase the nuclear abundance and/or the phosphorylation levels of proteins involved in gene expression, cell organization, and oxidation-reduction pathways. Furthermore, proteins acting as negative modulators involved in negative regulation of gene expression, insulin stimulated glucose uptake, and cytoskeletal organization showed a decrease in their nuclear abundance and/or phosphorylation levels during the first 4 h of adipogenesis. Among 288 identified TRs, 49 were regulated within 4 h of adipogenic stimulation including several known and many novel potential adipogenic regulators. We created a kinase-substrate database for 3T3-L1 preadipocytes by investigating the relationship between protein kinases and protein phosphorylation sites identified in our dataset. A majority of the putative protein kinases belong to the cyclin-dependent kinase family and the mitogen-activated protein kinase family including P38 and c-Jun N-terminal kinases, suggesting that these kinases act as orchestrators of early adipogenesis.
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Affiliation(s)
- Atefeh Rabiee
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Simone Sidoli
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Jie Dai
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
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23
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Chen J, Shinde S, Subedi P, Wierzbicka C, Sellergren B, Helling S, Marcus K. Validation of molecularly imprinted polymers for side chain selective phosphopeptide enrichment. J Chromatogr A 2016; 1471:45-50. [DOI: 10.1016/j.chroma.2016.10.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 09/12/2016] [Accepted: 10/08/2016] [Indexed: 01/13/2023]
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24
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White FM, Wolf-Yadlin A. Methods for the Analysis of Protein Phosphorylation-Mediated Cellular Signaling Networks. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:295-315. [PMID: 27049636 DOI: 10.1146/annurev-anchem-071015-041542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein phosphorylation-mediated cellular signaling networks regulate almost all aspects of cell biology, including the responses to cellular stimulation and environmental alterations. These networks are highly complex and comprise hundreds of proteins and potentially thousands of phosphorylation sites. Multiple analytical methods have been developed over the past several decades to identify proteins and protein phosphorylation sites regulating cellular signaling, and to quantify the dynamic response of these sites to different cellular stimulation. Here we provide an overview of these methods, including the fundamental principles governing each method, their relative strengths and weaknesses, and some examples of how each method has been applied to the analysis of complex signaling networks. When applied correctly, each of these techniques can provide insight into the topology, dynamics, and regulation of protein phosphorylation signaling networks.
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Affiliation(s)
- Forest M White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
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25
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Sun Y, Côté JF, Du K. Elmo2 Is a Regulator of Insulin-dependent Glut4 Membrane Translocation. J Biol Chem 2016; 291:16150-61. [PMID: 27226625 DOI: 10.1074/jbc.m116.731521] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/06/2022] Open
Abstract
Elmo2, a member of the Elmo protein family, has been implicated in the regulation of Rac1 and Akt activation. Recently, we found that Elmo2 specifically interacts with ClipR-59. Because Akt and Rac1 have been implicated in insulin dependent Glut4 membrane translocation, we hypothesize here that Elmo2 may play a role in insulin-dependent Glut4 membrane translocation. Accordingly, we found that overexpression of Elmo2 enhanced, whereas its knockdown suppressed, insulin-dependent Glut4 membrane translocation in both 3T3-L1 adipocytes and L6 skeletal muscle cells. We also examined whether Elmo2 contributes to the insulin-mediated activation of Rac1 and Akt. We found that Elmo2 is required for insulin-induced Rac1 GTP loading, but not AKT activation, in L6 cells induced by insulin. Instead, Elmo2 is required to promote the insulin-induced membrane association of Akt. Together, our studies demonstrate that Elmo2 is a new regulator of insulin-dependent Glut4 membrane translocation through modulating Rac1 activity and Akt membrane compartmentalization.
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Affiliation(s)
- Yingmin Sun
- From the Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts 02111 and
| | - Jean-François Côté
- the Institut de Recherches Cliniques de Montréal, Université de Montréal, Montréal, Québec H2W 1R7, Canada
| | - Keyong Du
- From the Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts 02111 and
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26
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Bergeron JJM, Di Guglielmo GM, Dahan S, Dominguez M, Posner BI. Spatial and Temporal Regulation of Receptor Tyrosine Kinase Activation and Intracellular Signal Transduction. Annu Rev Biochem 2016; 85:573-97. [PMID: 27023845 DOI: 10.1146/annurev-biochem-060815-014659] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Epidermal growth factor (EGF) and insulin receptor tyrosine kinases (RTKs) exemplify how receptor location is coupled to signal transduction. Extracellular binding of ligands to these RTKs triggers their concentration into vesicles that bud off from the cell surface to generate intracellular signaling endosomes. On the exposed cytosolic surface of these endosomes, RTK autophosphorylation selects the downstream signaling proteins and lipids to effect growth factor and polypeptide hormone action. This selection is followed by the recruitment of protein tyrosine phosphatases that inactivate the RTKs and deliver them by membrane fusion and fission to late endosomes. Coincidentally, proteinases inside the endosome cleave the EGF and insulin ligands. Subsequent inward budding of the endosomal membrane generates multivesicular endosomes. Fusion with lysosomes then results in RTK degradation and downregulation. Through the spatial positioning of RTKs in target cells for EGF and insulin action, the temporal extent of signaling, attenuation, and downregulation is regulated.
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Affiliation(s)
- John J M Bergeron
- Department of Medicine, McGill University Hospital Research Institute, Montreal, Quebec, Canada H4A 3J1; , , ,
| | - Gianni M Di Guglielmo
- Department of Physiology and Pharmacology, Western University, London, Ontario, Canada N6A 5C1;
| | - Sophie Dahan
- Department of Medicine, McGill University Hospital Research Institute, Montreal, Quebec, Canada H4A 3J1; , , ,
| | - Michel Dominguez
- Department of Medicine, McGill University Hospital Research Institute, Montreal, Quebec, Canada H4A 3J1; , , ,
| | - Barry I Posner
- Department of Medicine, McGill University Hospital Research Institute, Montreal, Quebec, Canada H4A 3J1; , , ,
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27
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Platt TL, Beckett TL, Kohler K, Niedowicz DM, Murphy MP. Obesity, diabetes, and leptin resistance promote tau pathology in a mouse model of disease. Neuroscience 2015; 315:162-74. [PMID: 26701291 DOI: 10.1016/j.neuroscience.2015.12.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 01/22/2023]
Abstract
Obesity and type 2 diabetes mellitus (T2DM) convey an increased risk for developing dementia. The microtubule-associated protein tau is implicated in neurodegenerative disease by undergoing hyperphosphorylation and aggregation, leading to cytotoxicity and neurodegeneration. Enzymes involved in the regulation of tau phosphorylation, such as GSK3β, are tightly associated with pathways found to be dysregulated in T2DM. We have shown previously that leptin-resistant mice, which develop obesity and a diabetic phenotype, display elevated levels of tau phosphorylation. Here we show cells cultured with leptin, an adipokine shown to have neuroprotective effects, reduces tau phosphorylation. To explore how this mechanism works in vivo we transduced an existing diabetic mouse line (Lepr(db/db)) with a tau mutant (tau(P301L)) via adeno-associated virus (AAV). The resulting phenotype included a striking increase in tau phosphorylation and the number of neurofibrillary tangles (NFTs) found within the hippocampus. We conclude that leptin resistance-induced obesity and diabetes accelerates the development of tau pathology. This model of metabolic dysfunction and tauopathy provides a new system in which to explore the mechanisms underlying the ways in which leptin resistance and diabetes influence development of tau pathology, and may ultimately be related to the development of NFTs.
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Affiliation(s)
- T L Platt
- Department of Molecular and Cellular Biochemistry, University of Kentucky, United States
| | - T L Beckett
- Sanders Brown Center on Aging, University of Kentucky, United States
| | - K Kohler
- Sanders Brown Center on Aging, University of Kentucky, United States
| | - D M Niedowicz
- Department of Molecular and Cellular Biochemistry, University of Kentucky, United States; Sanders Brown Center on Aging, University of Kentucky, United States
| | - M P Murphy
- Department of Molecular and Cellular Biochemistry, University of Kentucky, United States; Sanders Brown Center on Aging, University of Kentucky, United States.
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28
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Walker GE, Marzullo P, Ricotti R, Bona G, Prodam F. The pathophysiology of abdominal adipose tissue depots in health and disease. Horm Mol Biol Clin Investig 2015; 19:57-74. [PMID: 25390016 DOI: 10.1515/hmbci-2014-0023] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 08/11/2014] [Indexed: 12/22/2022]
Abstract
Obesity is currently the most important contributor to ill health and expenditure worldwide. More alarming is the fact that the pediatric population parallels adults, with obesity closely associated to type 2 diabetes mellitus (T2D), cardiovascular disease, hypertension, non-alcoholic fatty liver disease, vitamin D deficiency (VDD) and certain types of cancer. The observation in the early 1950s that android or truncal adipose tissue (AT) distribution compared to gynoid had a greater association with metabolic dysfunction, in particular T2D and cardiovascular disease risk, led to the hypothesis that obesity-associated complications are not associated with fat mass per se, but the pattern of fat distribution. This concept was further supported by groups of individuals with metabolic dysfunction despite a lean phenotype, and healthy obese people protected from metabolic dysfunction. It is now well recognized that an increase in visceral AT is an independent risk factor for the development of obesity-associated comorbidities with AT depot distribution, their anatomic, cellular and molecular features defining their role. The differences and the plasticity of subcutaneous, visceral and ectopic ATs to store and release fatty acids and to synthesize and secrete adipokines, defines the metabolic outcomes. The present review will examine the phenotypic and pathophysiological differences between the different AT depots, with a particular focus on the abdominal depots and their link to metabolic complications.
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Bryson BD, White FM. Quantitative Profiling of Lysine Acetylation Reveals Dynamic Crosstalk between Receptor Tyrosine Kinases and Lysine Acetylation. PLoS One 2015; 10:e0126242. [PMID: 25978619 PMCID: PMC4433260 DOI: 10.1371/journal.pone.0126242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/20/2015] [Indexed: 12/02/2022] Open
Abstract
Lysine acetylation has been primarily investigated in the context of transcriptional regulation, but a role for acetylation in mediating other cellular responses has emerged. Multiple studies have described global lysine acetylation profiles for particular biological states, but none to date have investigated the temporal dynamics regulating cellular response to perturbation. Reasoning that lysine acetylation may be altered in response to growth factors, we implemented quantitative mass spectrometry-based proteomics to investigate the temporal dynamics of lysine acetylation in response to growth factor stimulation in cultured carcinoma cell lines. We found that lysine acetylation changed rapidly in response to activation of several different receptor tyrosine kinases by their respective ligands. To uncover the effects of lysine acetylation dynamics on tyrosine phosphorylation signaling networks, cells were treated with an HDAC inhibitor. This short-term pharmacological inhibition of histone deacetylase activity modulated signaling networks involving phosphorylated tyrosine and thereby altered the response to receptor tyrosine kinase activation. This result highlights the interconnectivity of lysine acetylation and tyrosine phosphorylation signaling networks and suggests that HDAC inhibition may influence cellular responses by affecting both types of post-translational modifications.
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Affiliation(s)
- Bryan D. Bryson
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Forest M. White
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
- * E-mail:
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30
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Adaptive protein and phosphoprotein networks which promote therapeutic sensitivity or acquired resistance. Biochem Soc Trans 2015; 42:758-64. [PMID: 25109954 DOI: 10.1042/bst20140038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Despite the emergence of dozens of oncogenic targets and corresponding molecularly targeted therapies, in most cases tumours continue to progress or recur due to therapeutic resistance. In the present review, we highlight the ability of MS-based phosphoproteomics to quantify oncogenic signalling networks driving tumour growth and invasion, as well as those networks enabling tumour cell survival in the presence of chemotherapeutics. Quantitative protein phosphorylation profiling will facilitate the design and development of optimal therapeutic strategies targeting the initial tumour while simultaneously blocking the predominant resistance mechanisms.
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31
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Glade MJ, Smith K. A glance at … exercise and glucose uptake. Nutrition 2015; 31:893-7. [PMID: 25933500 DOI: 10.1016/j.nut.2014.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022]
Affiliation(s)
| | - Kyl Smith
- Progressive Laboratories Inc., Irving, Texas
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32
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Peng Q, Jia SH, Parodo J, Ai Y, Marshall JC. Pre-B cell colony enhancing factor induces Nampt-dependent translocation of the insulin receptor out of lipid microdomains in A549 lung epithelial cells. Am J Physiol Endocrinol Metab 2015; 308:E324-33. [PMID: 25516545 DOI: 10.1152/ajpendo.00006.2014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pre-B cell colony-enhancing factor (PBEF) is a highly conserved pleiotropic protein reported to be an alternate ligand for the insulin receptor (IR). We sought to clarify the relationship between PBEF and insulin signaling by evaluating the effects of PBEF on the localization of the IRβ chain to lipid rafts in A549 epithelial cells. We isolated lipid rafts from A549 cells and detected the IR by immunoprecipitation from raft fractions or whole cell lysates. Cells were treated with rPBEF, its enzymatic product nicotinamide adenine dinucleotide (NAD), or the Nampt inhibitor daporinad to study the effect of PBEF on IRβ movement. We used coimmunoprecipitation studies in cells transfected with PBEF and IRβ constructs to detect interactions between PBEF, the IRβ, and caveolin-1 (Cav-1). PBEF was present in both lipid raft and nonraft fractions, whereas the IR was found only in lipid raft fractions of resting A549 cells. The IR-, PBEF-, and Cav-1-coimmunoprecipitated rPBEF treatment resulted in the movement of IRβ- and tyrosine-phosphorylated Cav-1 from lipid rafts to nonrafts, an effect that could be blocked by daporinad, suggesting that this effect was facilitated by the Nampt activity of PBEF. The addition of PBEF to insulin-treated cells resulted in reduced Akt phosphorylation of both Ser⁴⁷³ and Thr³⁰⁸. We conclude that PBEF can inhibit insulin signaling through the IR by Nampt-dependent promotion of IR translocation into the nonraft domains of A549 epithelial cells. PBEF-induced alterations in the spatial geometry of the IR provide a mechanistic explanation for insulin resistance in inflammatory states associated with upregulation of PBEF.
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Affiliation(s)
- Qianyi Peng
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, and the Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario, Canada; and Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Song Hui Jia
- Department of Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, and the Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario, Canada; and
| | - Jean Parodo
- Department of Surgery, Keenan Research Centre for Biomedical Science, St. Michael's Hospital, and the Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario, Canada; and
| | - Yuhang Ai
- Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - John C Marshall
- Department of Surgery, Department of Critical Care Medicine, and Keenan Research Centre for Biomedical Science, St. Michael's Hospital, and the Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario, Canada; and
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33
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Govers R. Molecular mechanisms of GLUT4 regulation in adipocytes. DIABETES & METABOLISM 2014; 40:400-10. [DOI: 10.1016/j.diabet.2014.01.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/24/2014] [Accepted: 01/26/2014] [Indexed: 01/28/2023]
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34
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Matlock MK, Holehouse AS, Naegle KM. ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. Nucleic Acids Res 2014; 43:D521-30. [PMID: 25414335 PMCID: PMC4383955 DOI: 10.1093/nar/gku1154] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
ProteomeScout (https://proteomescout.wustl.edu) is a resource for the study of proteins and their post-translational modifications (PTMs) consisting of a database of PTMs, a repository for experimental data, an analysis suite for PTM experiments, and a tool for visualizing the relationships between complex protein annotations. The PTM database is a compendium of public PTM data, coupled with user-uploaded experimental data. ProteomeScout provides analysis tools for experimental datasets, including summary views and subset selection, which can identify relationships within subsets of data by testing for statistically significant enrichment of protein annotations. Protein annotations are incorporated in the ProteomeScout database from external resources and include terms such as Gene Ontology annotations, domains, secondary structure and non-synonymous polymorphisms. These annotations are available in the database download, in the analysis tools and in the protein viewer. The protein viewer allows for the simultaneous visualization of annotations in an interactive web graphic, which can be exported in Scalable Vector Graphics (SVG) format. Finally, quantitative data measurements associated with public experiments are also easily viewable within protein records, allowing researchers to see how PTMs change across different contexts. ProteomeScout should prove useful for protein researchers and should benefit the proteomics community by providing a stable repository for PTM experiments.
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Affiliation(s)
- Matthew K Matlock
- Department of Biomedical Engineering and the Center for Biological Systems Engineering, Washington University, St Louis, MO 63130, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering and the Center for Biological Systems Engineering, Washington University, St Louis, MO 63130, USA
| | - Kristen M Naegle
- Department of Biomedical Engineering and the Center for Biological Systems Engineering, Washington University, St Louis, MO 63130, USA
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Kettenbach AN, Sano H, Keller SR, Lienhard GE, Gerber SA. SPECHT - single-stage phosphopeptide enrichment and stable-isotope chemical tagging: quantitative phosphoproteomics of insulin action in muscle. J Proteomics 2014; 114:48-60. [PMID: 25463755 DOI: 10.1016/j.jprot.2014.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 10/20/2014] [Accepted: 11/03/2014] [Indexed: 02/04/2023]
Abstract
UNLABELLED The study of cellular signaling remains a significant challenge for translational and clinical research. In particular, robust and accurate methods for quantitative phosphoproteomics in tissues and tumors represent significant hurdles for such efforts. In the present work, we design, implement and validate a method for single-stage phosphopeptide enrichment and stable isotope chemical tagging, or SPECHT, that enables the use of iTRAQ, TMT and/or reductive dimethyl-labeling strategies to be applied to phosphoproteomics experiments performed on primary tissue. We develop and validate our approach using reductive dimethyl-labeling and HeLa cells in culture, and find these results indistinguishable from data generated from more traditional SILAC-labeled HeLa cells mixed at the cell level. We apply the SPECHT approach to the quantitative analysis of insulin signaling in a murine myotube cell line and muscle tissue, identify known as well as new phosphorylation events, and validate these phosphorylation sites using phospho-specific antibodies. Taken together, our work validates chemical tagging post-single-stage phosphoenrichment as a general strategy for studying cellular signaling in primary tissues. BIOLOGICAL SIGNIFICANCE Through the use of a quantitatively reproducible, proteome-wide phosphopeptide enrichment strategy, we demonstrated the feasibility of post-phosphopeptide purification chemical labeling and tagging as an enabling approach for quantitative phosphoproteomics of primary tissues. Using reductive dimethyl labeling as a generalized chemical tagging strategy, we compared the performance of post-phosphopeptide purification chemical tagging to the well established community standard, SILAC, in insulin-stimulated tissue culture cells. We then extended our method to the analysis of low-dose insulin signaling in murine muscle tissue, and report on the analytical and biological significance of our results.
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Affiliation(s)
- Arminja N Kettenbach
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Lebanon, NH 03756, USA.
| | - Hiroyuki Sano
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Susanna R Keller
- Department of Medicine, Division of Endocrinology, University of Virginia, Charlottesville, VA 22903, USA
| | - Gustav E Lienhard
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Scott A Gerber
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Lebanon, NH 03756, USA; Department of Genetics, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA.
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36
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Ramalingam L, Yoder SM, Oh E, Thurmond DC. Munc18c: a controversial regulator of peripheral insulin action. Trends Endocrinol Metab 2014; 25:601-8. [PMID: 25028245 PMCID: PMC4253632 DOI: 10.1016/j.tem.2014.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/12/2014] [Accepted: 06/20/2014] [Indexed: 12/19/2022]
Abstract
Insulin resistance, a hallmark of impaired glucose tolerance and type 2 diabetes (T2D), arises from dysfunction of insulin action and subsequent glucose uptake by peripheral tissues, predominantly skeletal muscle and fat. Exocytosis of glucose transporter (GLUT4)-containing vesicles facilitated by soluble NSF (N-ethylmaleimide-sensitive factor) attachment receptor (SNARE) protein isoforms, and Munc18c (mammalian homolog of Unc-18c) mediates this glucose uptake. Emerging evidences, including recent human clinical studies, point to pivotal roles for Munc18c in peripheral insulin action in adipose and skeletal muscle. Intriguing new advances are also initiating debates regarding the molecular mechanism(s) controlling Munc18c action. The objective of this review is therefore to present a balanced perspective of new continuities and controversies surrounding the regulation and requirement for Munc18c in the regulation of peripheral insulin action.
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Affiliation(s)
- Latha Ramalingam
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Stephanie M Yoder
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Eunjin Oh
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Debbie C Thurmond
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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37
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Kioumourtzoglou D, Sadler JBA, Black HL, Berends R, Wellburn C, Bryant NJ, Gould GW. Studies of the regulated assembly of SNARE complexes in adipocytes. Biochem Soc Trans 2014; 42:1396-400. [PMID: 25233421 DOI: 10.1042/bst20140114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2024]
Abstract
Insulin plays a fundamental role in whole-body glucose homeostasis. Central to this is the hormone's ability to rapidly stimulate the rate of glucose transport into adipocytes and muscle cells [1]. Upon binding its receptor, insulin stimulates an intracellular signalling cascade that culminates in redistribution of glucose transporter proteins, specifically the GLUT4 isoform, from intracellular stores to the plasma membrane, a process termed 'translocation' [1,2]. This is an example of regulated membrane trafficking [3], a process that also underpins other aspects of physiology in a number of specialized cell types, for example neurotransmission in brain/neurons and release of hormone-containing vesicles from specialized secretory cells such as those found in pancreatic islets. These processes invoke a number of intriguing biological questions as follows. How is the machinery involved in these membrane trafficking events mobilized in response to a stimulus? How do the signalling pathways that detect the external stimulus interface with the trafficking machinery? Recent studies of insulin-stimulated GLUT4 translocation offer insight into such questions. In the present paper, we have reviewed these studies and draw parallels with other regulated trafficking systems.
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Affiliation(s)
- Dimitrios Kioumourtzoglou
- *Henry Wellcome Laboratory of Cell Biology, Institute for Molecular, Cell and Systems Biology, Davidson Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Jessica B A Sadler
- *Henry Wellcome Laboratory of Cell Biology, Institute for Molecular, Cell and Systems Biology, Davidson Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Hannah L Black
- †Department of Biology, University of York, Heslington, York YO10 5DD, U.K
| | - Rebecca Berends
- *Henry Wellcome Laboratory of Cell Biology, Institute for Molecular, Cell and Systems Biology, Davidson Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Cassie Wellburn
- *Henry Wellcome Laboratory of Cell Biology, Institute for Molecular, Cell and Systems Biology, Davidson Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Nia J Bryant
- †Department of Biology, University of York, Heslington, York YO10 5DD, U.K
| | - Gwyn W Gould
- *Henry Wellcome Laboratory of Cell Biology, Institute for Molecular, Cell and Systems Biology, Davidson Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, U.K
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38
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Ramalingam L, Oh E, Thurmond DC. Doc2b enrichment enhances glucose homeostasis in mice via potentiation of insulin secretion and peripheral insulin sensitivity. Diabetologia 2014; 57:1476-84. [PMID: 24705606 PMCID: PMC4055500 DOI: 10.1007/s00125-014-3227-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 03/11/2014] [Indexed: 01/08/2023]
Abstract
AIMS/HYPOTHESIS Insulin secretion from pancreatic beta cells and insulin-stimulated glucose uptake into skeletal muscle are processes regulated by similar isoforms of the soluble N-ethylmaleimide-sensitive factor-attachment protein receptor (SNARE) and mammalian homologue of unc-18 (Munc18) protein families. Double C2 domain β (Doc2b), a SNARE- and Munc18-interacting protein, is implicated as a crucial effector of glycaemic control. However, whether Doc2b is naturally limiting for these processes, and whether Doc2b enrichment might exert a beneficial effect upon glycaemia in vivo, remains undetermined. METHODS Tetracycline-repressible transgenic (Tg) mice engineered to overexpress Doc2b simultaneously in the pancreas, skeletal muscle and adipose tissues were compared with wild-type (Wt) littermate mice regarding glucose and insulin tolerance, islet function in vivo and ex vivo, and skeletal muscle GLUT4 accumulation in transverse tubule/sarcolemmal surface membranes. SNARE complex formation was further assessed using Doc2b overexpressing L6-GLUT4-myc myoblasts to derive mechanisms relatable to physiological in vivo analyses. RESULTS Doc2b Tg mice cleared glucose substantially faster than Wt mice, correlated with enhancements in both phases of insulin secretion and peripheral insulin sensitivity. Heightened peripheral insulin sensitivity correlated with elevated insulin-stimulated GLUT4 vesicle accumulation in cell surface membranes of Doc2b Tg mouse skeletal muscle. Mechanistic studies demonstrated Doc2b enrichment to enhance syntaxin-4-SNARE complex formation in skeletal muscle cells. CONCLUSIONS/INTERPRETATION Doc2b is a limiting factor in SNARE exocytosis events pertinent to glycaemic regulation in vivo. Doc2b enrichment may provide a novel means to simultaneously boost islet and skeletal muscle function in vivo in the treatment and/or prevention of diabetes.
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Affiliation(s)
- Latha Ramalingam
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
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39
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Kheterpal I, Scherp P, Kelley L, Wang Z, Johnson W, Ribnicky D, Cefalu WT. Bioactives from Artemisia dracunculus L. enhance insulin sensitivity via modulation of skeletal muscle protein phosphorylation. Nutrition 2014; 30:S43-51. [PMID: 24985106 DOI: 10.1016/j.nut.2014.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVES A botanical extract from Artemisia dracunculus L., termed PMI 5011, has been shown to improve insulin sensitivity by increasing cellular insulin signaling in in vitro and in vivo studies. These studies suggest that PMI 5011 effects changes in phosphorylation levels of proteins involved in insulin signaling. The aim of this study was to explore the effects of this promising botanical extract on the human skeletal muscle phosphoproteome, by evaluating changes in site-specific protein phosphorylation levels in primary skeletal muscle cultures from obese, insulin-resistant individuals stimulated with and without insulin. METHODS Insulin resistance is a condition in which a normal or elevated insulin level results in an abnormal biologic response, e.g., glucose uptake. Using isobaric tagging for relative and absolute quantification (iTRAQ™) followed by phosphopeptide enrichment and liquid chromatography-tandem mass spectrometry, 125 unique phosphopeptides and 159 unique phosphorylation sites from 80 unique proteins were identified and quantified. RESULTS Insulin stimulation of primary cultured muscle cells from insulin-resistant individuals resulted in minimal increase in phosphorylation, demonstrating impaired insulin action in this condition. Treatment with PMI 5011 resulted in significant up-regulation of 35 phosphopeptides that were mapped to proteins participating in the regulation of transcription, translation, actin cytoskeleton signaling, caveolae translocation, and translocation of glucose transporter 4. These data further showed that PMI 5011 increased phosphorylation levels of specific amino acids in proteins in the insulin-resistant state that are normally phosphorylated by insulin (thus, increasing cellular insulin signaling) and PMI 5011 also increased the abundance of phosphorylation sites of proteins regulating anti-apoptotic effects. CONCLUSION This phosphoproteomics analysis demonstrated conclusively that PMI 5011 effects changes in phosphorylation levels of proteins and identified novel pathways by which PMI 5011 exerts its insulin-sensitizing effects in skeletal muscle.
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Affiliation(s)
- Indu Kheterpal
- Protein Structural Biology and Proteomics and Metabolomics Core Facility, Pennington Biomedical Research Center, Louisiana State University System, Louisiana, USA
| | - Peter Scherp
- Protein Structural Biology and Proteomics and Metabolomics Core Facility, Pennington Biomedical Research Center, Louisiana State University System, Louisiana, USA
| | - Lauren Kelley
- Protein Structural Biology and Proteomics and Metabolomics Core Facility, Pennington Biomedical Research Center, Louisiana State University System, Louisiana, USA
| | - Zhong Wang
- Diabetes and Nutrition Laboratory, Pennington Biomedical Research Center, Louisiana State University System, Louisiana, USA
| | - William Johnson
- Biostatistics and Data Management, Pennington Biomedical Research Center, Louisiana State University System, Louisiana, USA
| | - David Ribnicky
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - William T Cefalu
- Diabetes and Nutrition Laboratory, Pennington Biomedical Research Center, Louisiana State University System, Louisiana, USA.
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40
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Landis J, Shaw LM. Insulin receptor substrate 2-mediated phosphatidylinositol 3-kinase signaling selectively inhibits glycogen synthase kinase 3β to regulate aerobic glycolysis. J Biol Chem 2014; 289:18603-13. [PMID: 24811175 DOI: 10.1074/jbc.m114.564070] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Insulin receptor substrate 1 (IRS-1) and IRS-2 are cytoplasmic adaptor proteins that mediate the activation of signaling pathways in response to ligand stimulation of upstream cell surface receptors. Despite sharing a high level of homology and the ability to activate PI3K, only Irs-2 positively regulates aerobic glycolysis in mammary tumor cells. To determine the contribution of Irs-2-dependent PI3K signaling to this selective regulation, we generated an Irs-2 mutant deficient in the recruitment of PI3K. We identified four tyrosine residues (Tyr-649, Tyr-671, Tyr-734, and Tyr-814) that are essential for the association of PI3K with Irs-2 and demonstrate that combined mutation of these tyrosines inhibits glucose uptake and lactate production, two measures of aerobic glycolysis. Irs-2-dependent activation of PI3K regulates the phosphorylation of specific Akt substrates, most notably glycogen synthase kinase 3β (Gsk-3β). Inhibition of Gsk-3β by Irs-2-dependent PI3K signaling promotes glucose uptake and aerobic glycolysis. The regulation of unique subsets of Akt substrates by Irs-1 and Irs-2 may explain their non-redundant roles in mammary tumor biology. Taken together, our study reveals a novel mechanism by which Irs-2 signaling preferentially regulates tumor cell metabolism and adds to our understanding of how this adaptor protein contributes to breast cancer progression.
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Affiliation(s)
- Justine Landis
- From the Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Leslie M Shaw
- From the Department of Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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41
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Huang D, Li Y, Liu N, Zhang Z, Peng Z, Duan C, Tang X, Tan G, Yan G, Tang F. Identification of novel signaling components in N,N'-dinitrosopiperazine-mediated metastasis of nasopharyngeal carcinoma by quantitative phosphoproteomics. BMC Cancer 2014; 14:243. [PMID: 24708550 PMCID: PMC4101831 DOI: 10.1186/1471-2407-14-243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/25/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is a highly invasive and metastatic cancer. N,N'-dinitrosopiperazine (DNP), a carcinogen with specificity for nasopharyngeal epithelium, facilitates NPC metastasis. However, the underlying mechanism is not known. METHODS Quantitative phosphoproteomics, using stable isotope labeling of amino acids in cell cultures, was employed to identify phosphoproteins associated with NPC metastasis mediated by DNP. NPC cell line 6-10B, which is relatively less metastatic, was used to investigate DNP-mediated metastasis. Boyden chamber invasion assay was used to measure DNP-induced motility and invasion, and nude mice were used to verify DNP-mediated metastasis in vivo. Several different phosphoproteins detected by proteomics analysis were verified by immunoblotting. DNP-mediated metastasis facilitated by lysine-rich CEACAM1 co-isolated protein (LYRIC) phosphorylation at serine 568 was confirmed using mutations targeting the phosphorylation site of LYRIC. DNP-mediated metastasis through LYRIC phosphorylation was confirmed in the NPC cell line CNE1. DNP-mediated LYRIC phosphorylation at serine 568 was also verified in metastatic tumors of BABL/c nude mice. RESULTS Boyden chamber invasion assay indicated that DNP mediated cell motility and invasion of NPC cell 6-10B in vitro, and experiments with nude mice indicated that DNP increased 6-10B metastasis in vivo. In the phosphoproteomics analysis, we detected 216 phosphorylation sites on 130 proteins; among these, 48 phosphorylation sites on 30 unique phosphopeptides were modulated by DNP by at least 1.5-fold. DNP mediated the expression of phosphorylated GTPase, ferritin, LYRIC, and RNA polymerase, and it decreased the expression of phosphorylated torsin-1A protein 1. Furthermore, DNP induced LYRIC phosphorylation at serine 568 to facilitate cell motility and invasion, whereas DNP-mediated motility and invasion was decreased when serine 568 in LYRIC was mutated. In another NPC cell line, CNE1, DNP also mediated cell motility and invasion followed by enhanced phosphorylation of LYRIC at serine 568. Finally, phosphorylated-LYRIC expression at serine 568 was significantly increased in metastatic tumors induced by DNP. CONCLUSION DNP regulates multiple signaling pathways through protein phosphorylation, including the phosphorylation of LYRIC at serine 568, and mediates NPC metastasis. These findings provide insights on the complexity and dynamics of DNP-facilitated metastasis, and may help to gain a better understanding of the mechanisms by clarifying NPC-induced metastasis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Faqing Tang
- Medical Research Center and Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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42
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Insulin stimulates syntaxin4 SNARE complex assembly via a novel regulatory mechanism. Mol Cell Biol 2014; 34:1271-9. [PMID: 24469400 DOI: 10.1128/mcb.01203-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Insulin stimulates glucose transport into fat and muscle cells by increasing the exocytic trafficking rate of the GLUT4 facilitative glucose transporter from intracellular stores to the plasma membrane. Delivery of GLUT4 to the plasma membrane is mediated by formation of functional SNARE complexes containing syntaxin4, SNAP23, and VAMP2. Here we have used an in situ proximity ligation assay to integrate these two observations by demonstrating for the first time that insulin stimulation causes an increase in syntaxin4-containing SNARE complex formation in adipocytes. Furthermore, we demonstrate that insulin brings about this increase in SNARE complex formation by mobilizing a pool of syntaxin4 held in an inactive state under basal conditions. Finally, we have identified phosphorylation of the regulatory protein Munc18c, a direct target of the insulin receptor, as a molecular switch to coordinate this process. Hence, this report provides molecular detail of how the cell alters membrane traffic in response to an external stimulus, in this case, insulin.
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Ding SJ, Qian WJ, Smith RD. Quantitative proteomic approaches for studying phosphotyrosine signaling. Expert Rev Proteomics 2014; 4:13-23. [PMID: 17288512 DOI: 10.1586/14789450.4.1.13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein tyrosine phosphorylation is a fundamental mechanism for controlling many aspects of cellular processes, as well as aspects of human health and diseases. Compared with phosphoserine and phosphothreonine, phosphotyrosine signaling is more tightly regulated, but often more challenging to characterize, due to significantly lower levels of tyrosine phosphorylation (i.e., a relative abundance of 1800:200:1 was estimated for phosphoserine/phosphothreonine/phosphotyrosine in vertebrate cells). In this review, we outline recent advances in analytical methodologies for enrichment, identification and accurate quantitation of tyrosine-phosphorylated proteins and peptides. Advances in antibody-based technologies, capillary liquid chromatography coupled with mass spectrometry, and various stable isotope labeling strategies are discussed, as well as non-mass spectrometry-based methods, such as those using protein/peptide arrays. As a result of these advances, powerful tools now have the power to crack signal transduction codes at the system level, and provide a basis for discovering novel drug targets for human diseases.
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Affiliation(s)
- Shi-Jian Ding
- Pacific Northwest National Laboratory, Biological Science Division & Environmental Molecular Sciences Laboratory, Richland, WA 99352, USA.
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Abstract
GLUT4 is regulated by its intracellular localization. In the absence of insulin, GLUT4 is efficiently retained intracellularly within storage compartments in muscle and fat cells. Upon insulin stimulation (and contraction in muscle), GLUT4 translocates from these compartments to the cell surface where it transports glucose from the extracellular milieu into the cell. Its implication in insulin-regulated glucose uptake makes GLUT4 not only a key player in normal glucose homeostasis but also an important element in insulin resistance and type 2 diabetes. Nevertheless, how GLUT4 is retained intracellularly and how insulin acts on this retention mechanism is largely unclear. In this review, the current knowledge regarding the various molecular processes that govern GLUT4 physiology is discussed as well as the questions that remain.
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Engholm-Keller K, Larsen MR. Technologies and challenges in large-scale phosphoproteomics. Proteomics 2013; 13:910-31. [PMID: 23404676 DOI: 10.1002/pmic.201200484] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/18/2013] [Accepted: 01/31/2013] [Indexed: 12/23/2022]
Abstract
Phosphorylation, the reversible addition of a phosphate group to amino acid side chains of proteins, is a fundamental regulator of protein activity, stability, and molecular interactions. Most cellular processes, such as inter- and intracellular signaling, protein synthesis, degradation, and apoptosis, rely on phosphorylation. This PTM is thus involved in many diseases, rendering localization and assessment of extent of phosphorylation of major scientific interest. MS-based phosphoproteomics, which aims at describing all phosphorylation sites in a specific type of cell, tissue, or organism, has become the main technique for discovery and characterization of phosphoproteins in a nonhypothesis driven fashion. In this review, we describe methods for state-of-the-art MS-based analysis of protein phosphorylation as well as the strategies employed in large-scale phosphoproteomic experiments with focus on the various challenges and limitations this field currently faces.
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Affiliation(s)
- Kasper Engholm-Keller
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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Kweon HK, Andrews PC. Quantitative analysis of global phosphorylation changes with high-resolution tandem mass spectrometry and stable isotopic labeling. Methods 2013; 61:251-9. [PMID: 23611819 PMCID: PMC3700606 DOI: 10.1016/j.ymeth.2013.04.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 03/05/2013] [Accepted: 04/13/2013] [Indexed: 11/23/2022] Open
Abstract
Quantitative measurement of specific protein phosphorylation sites is a primary interest of biologists, as site-specific phosphorylation information provides insights into cell signaling networks and cellular dynamics at a system level. Over the last decade, selective phosphopeptide enrichment methods including IMAC and metal oxides (TiO₂ and ZrO₂) have been developed and greatly facilitate large scale phosphoproteome analysis of various cells, tissues and living organisms, in combination with modern mass spectrometers featuring high mass accuracy and high mass resolution. Various quantification strategies have been applied to detecting relative changes in expression of proteins, peptides, and specific modifications between samples. The combination of mass spectrometry-based phosphoproteome analysis with quantification strategies provides a straightforward and unbiased method to identify and quantify site-specific phosphorylation. We describe common strategies for mass spectrometric analysis of stable isotope labeled samples, as well as two widely applied phosphopeptide enrichment methods based on IMAC(NTA-Fe³⁺) and metal oxide (ZrO₂). Instrumental configurations for on-line LC-tandem mass spectrometric analysis and parameters of conventional bioinformatic analysis of large data sets are also considered for confident identification, localization, and reliable quantification of site-specific phosphorylation.
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Affiliation(s)
- Hye Kyong Kweon
- Department of Biological Chemistry, University of Michigan, USA.
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Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013; 138:333-408. [PMID: 23384594 PMCID: PMC3647006 DOI: 10.1016/j.pharmthera.2013.01.016] [Citation(s) in RCA: 512] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 02/02/2023]
Abstract
Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network description and analysis not only give a systems-level understanding of drug action and disease complexity, but can also help to improve the efficiency of drug design. We give a comprehensive assessment of the analytical tools of network topology and dynamics. The state-of-the-art use of chemical similarity, protein structure, protein-protein interaction, signaling, genetic interaction and metabolic networks in the discovery of drug targets is summarized. We propose that network targeting follows two basic strategies. The "central hit strategy" selectively targets central nodes/edges of the flexible networks of infectious agents or cancer cells to kill them. The "network influence strategy" works against other diseases, where an efficient reconfiguration of rigid networks needs to be achieved by targeting the neighbors of central nodes/edges. It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates. We review the recent boom in network methods helping hit identification, lead selection optimizing drug efficacy, as well as minimizing side-effects and drug toxicity. Successful network-based drug development strategies are shown through the examples of infections, cancer, metabolic diseases, neurodegenerative diseases and aging. Summarizing >1200 references we suggest an optimized protocol of network-aided drug development, and provide a list of systems-level hallmarks of drug quality. Finally, we highlight network-related drug development trends helping to achieve these hallmarks by a cohesive, global approach.
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Affiliation(s)
- Peter Csermely
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary.
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Garrido-Sanchez L, Escote X, Coin-Aragüez L, Fernandez-Garcia JC, El Bekay R, Vendrell J, Garcia-Fuentes E, Tinahones FJ. Munc18c in adipose tissue is downregulated in obesity and is associated with insulin. PLoS One 2013; 8:e63937. [PMID: 23700440 PMCID: PMC3659121 DOI: 10.1371/journal.pone.0063937] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/09/2013] [Indexed: 02/07/2023] Open
Abstract
Objective Munc18c is associated with glucose metabolism and could play a relevant role in obesity. However, little is known about the regulation of Munc18c expression. We analyzed Munc18c gene expression in human visceral (VAT) and subcutaneous (SAT) adipose tissue and its relationship with obesity and insulin. Materials and Methods We evaluated 70 subjects distributed in 12 non-obese lean subjects, 23 overweight subjects, 12 obese subjects and 23 nondiabetic morbidly obese patients (11 with low insulin resistance and 12 with high insulin resistance). Results The lean, overweight and obese persons had a greater Munc18c gene expression in adipose tissue than the morbidly obese patients (p<0.001). VAT Munc18c gene expression was predicted by the body mass index (B = −0.001, p = 0.009). In SAT, no associations were found by different multiple regression analysis models. SAT Munc18c gene expression was the main determinant of the improvement in the HOMA-IR index 15 days after bariatric surgery (B = −2148.4, p = 0.038). SAT explant cultures showed that insulin produced a significant down-regulation of Munc18c gene expression (p = 0.048). This decrease was also obtained when explants were incubated with liver X receptor alpha (LXRα) agonist, either without (p = 0.038) or with insulin (p = 0.050). However, Munc18c gene expression was not affected when explants were incubated with insulin plus a sterol regulatory element-binding protein-1c (SREBP-1c) inhibitor (p = 0.504). Conclusions Munc18c gene expression in human adipose tissue is down-regulated in morbid obesity. Insulin may have an effect on the Munc18c expression, probably through LXRα and SREBP-1c.
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Affiliation(s)
- Lourdes Garrido-Sanchez
- Endocrinology and Diabetes Unit, Joan XXIII University Hospital, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Tarragona, Spain
| | - Xavier Escote
- Endocrinology and Diabetes Unit, Joan XXIII University Hospital, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Tarragona, Spain
| | - Leticia Coin-Aragüez
- Servicio de Endocrinología y Nutrición, Hospital Clínico Virgen de la Victoria, Malaga, Spain
- Ciber Fisiopatología Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Málaga, Spain
| | | | - Rajaa El Bekay
- Servicio de Endocrinología y Nutrición, Hospital Clínico Virgen de la Victoria, Malaga, Spain
- Ciber Fisiopatología Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Málaga, Spain
- Instituto de Investigaciones Biomédicas de Málaga (IBIMA), Málaga, Spain
| | - Joan Vendrell
- Endocrinology and Diabetes Unit, Joan XXIII University Hospital, IISPV, Universitat Rovira i Virgili, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Tarragona, Spain
| | - Eduardo Garcia-Fuentes
- Ciber Fisiopatología Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Málaga, Spain
- Instituto de Investigaciones Biomédicas de Málaga (IBIMA), Málaga, Spain
- Servicio de Endocrinología y Nutrición, Hospital Regional Universitario Carlos Haya, Malaga, Spain
- * E-mail: (EGF); (FT)
| | - Francisco J. Tinahones
- Servicio de Endocrinología y Nutrición, Hospital Clínico Virgen de la Victoria, Malaga, Spain
- Ciber Fisiopatología Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Málaga, Spain
- * E-mail: (EGF); (FT)
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Miraldi ER, Sharfi H, Friedline RH, Johnson H, Zhang T, Lau KS, Ko HJ, Curran TG, Haigis KM, Yaffe MB, Bonneau R, Lauffenburger DA, Kahn BB, Kim JK, Neel BG, Saghatelian A, White FM. Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice. Integr Biol (Camb) 2013; 5:940-63. [PMID: 23685806 DOI: 10.1039/c3ib40013a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Metabolic syndrome describes a set of obesity-related disorders that increase diabetes, cardiovascular, and mortality risk. Studies of liver-specific protein-tyrosine phosphatase 1b (PTP1b) deletion mice (L-PTP1b(-/-)) suggest that hepatic PTP1b inhibition would mitigate metabolic-syndrome through amelioration of hepatic insulin resistance, endoplasmic-reticulum stress, and whole-body lipid metabolism. However, the altered molecular-network states underlying these phenotypes are poorly understood. We used mass spectrometry to quantify protein-phosphotyrosine network changes in L-PTP1b(-/-) mouse livers relative to control mice on normal and high-fat diets. We applied a phosphosite-set-enrichment analysis to identify known and novel pathways exhibiting PTP1b- and diet-dependent phosphotyrosine regulation. Detection of a PTP1b-dependent, but functionally uncharacterized, set of phosphosites on lipid-metabolic proteins motivated global lipidomic analyses that revealed altered polyunsaturated-fatty-acid (PUFA) and triglyceride metabolism in L-PTP1b(-/-) mice. To connect phosphosites and lipid measurements in a unified model, we developed a multivariate-regression framework, which accounts for measurement noise and systematically missing proteomics data. This analysis resulted in quantitative models that predict roles for phosphoproteins involved in oxidation-reduction in altered PUFA and triglyceride metabolism.
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Affiliation(s)
- Emily R Miraldi
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Renes J, Mariman E. Application of proteomics technology in adipocyte biology. MOLECULAR BIOSYSTEMS 2013; 9:1076-91. [PMID: 23629546 DOI: 10.1039/c3mb25596d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Obesity and its associated complications have reached epidemic proportions in Western-type societies. Concomitantly, the obesity incidence in developing countries is increasing. One hallmark of obesity is the differentiation of pre-adipocytes into mature triglyceride-loaded adipocytes present in subcutaneous and visceral adipose tissue depots. This may ultimately lead to dysfunctional adipose tissue together with detrimental changes in the profiles of (pre-)adipocyte-secreted proteins, known as adipokines. Obesity-induced alterations in adipokine profiles contribute to the development of obesity-associated disorders. Consequently, the interest in the molecular events responsible for adipose tissue modifications during weight gain and weight loss as well as in the aetiology of obesity-associated disorders is growing. Molecular mechanisms involved in pre-adipocyte differentiation and alterations in adipokine profiles have been examined at the gene and protein level by high-throughput technologies. Independent proteomics studies have contributed significantly to further insight into adipocyte biology, particularly with respect to adipokine profiling. In this review novel findings obtained with adipo-proteomics studies are highlighted and the relevance of proteomics technologies to further understand molecular aspects of adipocyte biology is discussed.
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Affiliation(s)
- Johan Renes
- Department of Human Biology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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