1
|
Mathisen AF, Abadpour S, Legøy TA, Paulo JA, Ghila L, Scholz H, Chera S. Global proteomics reveals insulin abundance as a marker of human islet homeostasis alterations. Acta Physiol (Oxf) 2023; 239:e14037. [PMID: 37621186 PMCID: PMC10592125 DOI: 10.1111/apha.14037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
AIM The variation in quality between the human islet samples represents a major problem for research, especially when used as control material. The assays assessing the quality of human islets used in research are non-standardized and limited, with many important parameters not being consistently assessed. High-throughput studies aimed at characterizing the diversity and segregation markers among apparently functionally healthy islet preps are thus a requirement. Here, we designed a pilot study to comprehensively identify the diversity of global proteome signatures and the deviation from normal homeostasis in randomly selected human-isolated islet samples. METHODS By using Tandem Mass Tag 16-plex proteomics, we focused on the recurrently observed disparity in the detected insulin abundance between the samples, used it as a segregating parameter, and analyzed the correlated changes in the proteome signature and homeostasis by pathway analysis. RESULTS In this pilot study, we showed that insulin protein abundance is a predictor of human islet homeostasis and quality. This parameter is independent of other quality predictors within their acceptable range, thus being able to further stratify islets samples of apparent good quality. Human islets with low amounts of insulin displayed changes in their metabolic and signaling profile, especially in regard to energy homeostasis and cell identity maintenance. We further showed that xenotransplantation into diabetic hosts is not expected to improve the pre-transplantation signature, as it has a negative effect on energy balance, antioxidant activity, and islet cell identity. CONCLUSIONS Insulin protein abundance predicts significant changes in human islet homeostasis among random samples of apparently good quality.
Collapse
Affiliation(s)
- Andreas F. Mathisen
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Shadab Abadpour
- Hybrid Technology Hub-Centre of Excellence, Faculty of Medicine, University of Oslo, Norway
- Institute for Surgical Research and Department of Transplant Medicine, Oslo University Hospital, Oslo, Norway
| | - Thomas Aga Legøy
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Luiza Ghila
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Hanne Scholz
- Hybrid Technology Hub-Centre of Excellence, Faculty of Medicine, University of Oslo, Norway
- Institute for Surgical Research and Department of Transplant Medicine, Oslo University Hospital, Oslo, Norway
| | - Simona Chera
- Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| |
Collapse
|
2
|
Ramanadham S, Turk J, Bhatnagar S. Noncanonical Regulation of cAMP-Dependent Insulin Secretion and Its Implications in Type 2 Diabetes. Compr Physiol 2023; 13:5023-5049. [PMID: 37358504 PMCID: PMC10809800 DOI: 10.1002/cphy.c220031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Impaired glucose tolerance (IGT) and β-cell dysfunction in insulin resistance associated with obesity lead to type 2 diabetes (T2D). Glucose-stimulated insulin secretion (GSIS) from β-cells occurs via a canonical pathway that involves glucose metabolism, ATP generation, inactivation of K ATP channels, plasma membrane depolarization, and increases in cytosolic concentrations of [Ca 2+ ] c . However, optimal insulin secretion requires amplification of GSIS by increases in cyclic adenosine monophosphate (cAMP) signaling. The cAMP effectors protein kinase A (PKA) and exchange factor activated by cyclic-AMP (Epac) regulate membrane depolarization, gene expression, and trafficking and fusion of insulin granules to the plasma membrane for amplifying GSIS. The widely recognized lipid signaling generated within β-cells by the β-isoform of Ca 2+ -independent phospholipase A 2 enzyme (iPLA 2 β) participates in cAMP-stimulated insulin secretion (cSIS). Recent work has identified the role of a G-protein coupled receptor (GPCR) activated signaling by the complement 1q like-3 (C1ql3) secreted protein in inhibiting cSIS. In the IGT state, cSIS is attenuated, and the β-cell function is reduced. Interestingly, while β-cell-specific deletion of iPLA 2 β reduces cAMP-mediated amplification of GSIS, the loss of iPLA 2 β in macrophages (MØ) confers protection against the development of glucose intolerance associated with diet-induced obesity (DIO). In this article, we discuss canonical (glucose and cAMP) and novel noncanonical (iPLA 2 β and C1ql3) pathways and how they may affect β-cell (dys)function in the context of impaired glucose intolerance associated with obesity and T2D. In conclusion, we provide a perspective that in IGT states, targeting noncanonical pathways along with canonical pathways could be a more comprehensive approach for restoring β-cell function in T2D. © 2023 American Physiological Society. Compr Physiol 13:5023-5049, 2023.
Collapse
Affiliation(s)
- Sasanka Ramanadham
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Alabama, USA
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Alabama, USA
| | - John Turk
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sushant Bhatnagar
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Alabama, USA
- Department of Medicine, University of Alabama at Birmingham, Alabama, USA
| |
Collapse
|
3
|
Colasante C, Bonilla-Martinez R, Berg T, Windhorst A, Baumgart-Vogt E. Peroxisomes during postnatal development of mouse endocrine and exocrine pancreas display cell-type- and stage-specific protein composition. Cell Tissue Res 2023:10.1007/s00441-023-03766-6. [PMID: 37126142 DOI: 10.1007/s00441-023-03766-6] [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: 12/20/2022] [Accepted: 03/15/2023] [Indexed: 05/02/2023]
Abstract
Peroxisomal dysfunction unhinges cellular metabolism by causing the accumulation of toxic metabolic intermediates (e.g. reactive oxygen species, very -chain fatty acids, phytanic acid or eicosanoids) and the depletion of important lipid products (e.g. plasmalogens, polyunsaturated fatty acids), leading to various proinflammatory and devastating pathophysiological conditions like metabolic syndrome and age-related diseases including diabetes. Because the peroxisomal antioxidative marker enzyme catalase is low abundant in Langerhans islet cells, peroxisomes were considered scarcely present in the endocrine pancreas. Recently, studies demonstrated that the peroxisomal metabolism is relevant for pancreatic cell functionality. During the postnatal period, significant changes occur in the cell structure and the metabolism to trigger the final maturation of the pancreas, including cell proliferation, regulation of energy metabolism, and activation of signalling pathways. Our aim in this study was to (i) morphometrically analyse the density of peroxisomes in mouse endocrine versus exocrine pancreas and (ii) investigate how the distribution and the abundance of peroxisomal proteins involved in biogenesis, antioxidative defence and fatty acid metabolism change during pancreatic maturation in the postnatal period. Our results prove that endocrine and exocrine pancreatic cells contain high amounts of peroxisomes with heterogeneous protein content indicating that distinct endocrine and exocrine cell types require a specific set of peroxisomal proteins depending on their individual physiological functions. We further show that significant postnatal changes occur in the peroxisomal compartment of different pancreatic cells that are most probably relevant for the metabolic maturation and differentiation of the pancreas during the development from birth to adulthood.
Collapse
Affiliation(s)
- Claudia Colasante
- Institute for Anatomy and Cell Biology, Medical Cell Biology, Justus Liebig -University, Aulweg 123, 35392, Giessen, Germany
| | - Rocio Bonilla-Martinez
- Institute for Anatomy and Cell Biology, Medical Cell Biology, Justus Liebig -University, Aulweg 123, 35392, Giessen, Germany
| | - Timm Berg
- Institute for Anatomy and Cell Biology, Medical Cell Biology, Justus Liebig -University, Aulweg 123, 35392, Giessen, Germany
| | - Anita Windhorst
- Institute for Medical Informatic, Justus Liebig University, Rudolf-Buchheim-Str. 6, 35392, Gießen, Germany
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology, Medical Cell Biology, Justus Liebig -University, Aulweg 123, 35392, Giessen, Germany.
| |
Collapse
|
4
|
Proteomic Profiling of Intra-Islet Features Reveals Substructure-Specific Protein Signatures. Mol Cell Proteomics 2022; 21:100426. [PMID: 36244662 PMCID: PMC9706166 DOI: 10.1016/j.mcpro.2022.100426] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 11/11/2022] Open
Abstract
Despite their diminutive size, islets of Langerhans play a large role in maintaining systemic energy balance in the body. New technologies have enabled us to go from studying the whole pancreas to isolated whole islets, to partial islet sections, and now to islet substructures isolated from within the islet. Using a microfluidic nanodroplet-based proteomics platform coupled with laser capture microdissection and field asymmetric waveform ion mobility spectrometry, we present an in-depth investigation of protein profiles specific to features within the islet. These features include the islet-acinar interface vascular tissue, inner islet vasculature, isolated endocrine cells, whole islet with vasculature, and acinar tissue from around the islet. Compared to interface vasculature, unique protein signatures observed in the inner vasculature indicate increased innervation and intra-islet neuron-like crosstalk. We also demonstrate the utility of these data for identifying localized structure-specific drug-target interactions using existing protein/drug binding databases.
Collapse
|
5
|
Yau B, Naghiloo S, Diaz-Vegas A, Carr AV, Van Gerwen J, Needham EJ, Jevon D, Chen SY, Hoehn KL, Brandon AE, Macia L, Cooney GJ, Shortreed MR, Smith LM, Keller MP, Thorn P, Larance M, James DE, Humphrey SJ, Kebede MA. Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet. iScience 2021; 24:103099. [PMID: 34622154 PMCID: PMC8479695 DOI: 10.1016/j.isci.2021.103099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/09/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
Pancreatic islets are essential for maintaining physiological blood glucose levels, and declining islet function is a hallmark of type 2 diabetes. We employ mass spectrometry-based proteomics to systematically analyze islets from 9 genetic or diet-induced mouse models representing a broad cross-section of metabolic health. Quantifying the islet proteome to a depth of >11,500 proteins, this study represents the most detailed analysis of mouse islet proteins to date. Our data highlight that the majority of islet proteins are expressed in all strains and diets, but more than half of the proteins vary in expression levels, principally due to genetics. Associating these varied protein expression levels on an individual animal basis with individual phenotypic measures reveals islet mitochondrial function as a major positive indicator of metabolic health regardless of strain. This compendium of strain-specific and dietary changes to mouse islet proteomes represents a comprehensive resource for basic and translational islet cell biology.
Collapse
Affiliation(s)
- Belinda Yau
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Sheyda Naghiloo
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Alexis Diaz-Vegas
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Austin V. Carr
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Julian Van Gerwen
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Elise J. Needham
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Dillon Jevon
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Sing-Young Chen
- Department of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Kyle L. Hoehn
- Department of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Amanda E. Brandon
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Laurance Macia
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Gregory J. Cooney
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | | | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Peter Thorn
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| | - Mark Larance
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - David E. James
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Sean J. Humphrey
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Melkam A. Kebede
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, University of Sydney, Camperdown 2006, Australia
| |
Collapse
|
6
|
Tabang DN, Cui Y, Tremmel DM, Ford M, Li Z, Sackett SD, Odorico JS, Li L. Analysis of pancreatic extracellular matrix protein post-translational modifications via electrostatic repulsion-hydrophilic interaction chromatography coupled with mass spectrometry. Mol Omics 2021; 17:652-664. [PMID: 34318855 PMCID: PMC8511275 DOI: 10.1039/d1mo00104c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The pancreas is a vital organ with digestive and endocrine roles, and diseases of the pancreas affect millions of people yearly. A better understanding of the pancreas proteome and its dynamic post-translational modifications (PTMs) is necessary to engineer higher fidelity tissue analogues for use in transplantation. The extracellular matrix (ECM) has major roles in binding and signaling essential to the viability of insulin-producing islets of Langerhans. To characterize PTMs in the pancreas, native and decellularized tissues from four donors were analyzed. N-Glycosylated and phosphorylated peptides were simultaneously enriched via electrostatic repulsion-hydrophilic interaction chromatography and analyzed with mass spectrometry, maximizing PTM information from one workflow. A modified surfactant and chaotropic agent assisted sequential extraction/on-pellet digestion was used to maximize solubility of the ECM. The analysis resulted in the confident identification of 3650 proteins, including 517 N-glycoproteins and 148 phosphoproteins. We identified 214 ECM proteins, of which 99 were N-glycosylated, 18 were phosphorylated, and 9 were found to have both modifications. Collagens, a major component of the ECM, were the most highly glycosylated of the ECM proteins and several were also heavily phosphorylated, raising the possibility of structural and thus functional changes resulting from these modifications. To our knowledge, this work represents the first characterization of PTMs in pancreatic ECM proteins. This work provides a basal profile of PTMs in the healthy human pancreatic ECM, laying the foundation for future investigations to determine disease-specific changes such as in diabetes and pancreatic cancer, and potentially helping to guide the development of tissue replacement constructs. Data are available via ProteomeXchange with identifier PXD025048.
Collapse
Affiliation(s)
- Dylan Nicholas Tabang
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Daniel M Tremmel
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Megan Ford
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
| | - Sara Dutton Sackett
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jon S Odorico
- Department of Surgery, Division of Transplantation, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI, 53706, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| |
Collapse
|
7
|
Alam CM, Baghestani S, Pajari A, Omary MB, Toivola DM. Keratin 7 Is a Constituent of the Keratin Network in Mouse Pancreatic Islets and Is Upregulated in Experimental Diabetes. Int J Mol Sci 2021; 22:ijms22157784. [PMID: 34360548 PMCID: PMC8346022 DOI: 10.3390/ijms22157784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
Keratin (K) 7 is an intermediate filament protein expressed in ducts and glands of simple epithelial organs and in urothelial tissues. In the pancreas, K7 is expressed in exocrine ducts, and apico-laterally in acinar cells. Here, we report K7 expression with K8 and K18 in the endocrine islets of Langerhans in mice. K7 filament formation in islet and MIN6 β-cells is dependent on the presence and levels of K18. K18-knockout (K18‒/‒) mice have undetectable islet K7 and K8 proteins, while K7 and K18 are downregulated in K8‒/‒ islets. K7, akin to F-actin, is concentrated at the apical vertex of β-cells in wild-type mice and along the lateral membrane, in addition to forming a fine cytoplasmic network. In K8‒/‒ β-cells, apical K7 remains, but lateral keratin bundles are displaced and cytoplasmic filaments are scarce. Islet K7, rather than K8, is increased in K18 over-expressing mice and the K18-R90C mutation disrupts K7 filaments in mouse β-cells and in MIN6 cells. Notably, islet K7 filament networks significantly increase and expand in the perinuclear regions when examined in the streptozotocin diabetes model. Hence, K7 represents a significant component of the murine islet keratin network and becomes markedly upregulated during experimental diabetes.
Collapse
Affiliation(s)
- Catharina M. Alam
- Department of Biosciences, Cell Biology, Åbo Akademi University, Tykistökatu 6A, BioCity 2nd Floor, FIN-20520 Turku, Finland; (S.B.); (A.P.)
- Correspondence: (C.M.A.); (D.M.T.)
| | - Sarah Baghestani
- Department of Biosciences, Cell Biology, Åbo Akademi University, Tykistökatu 6A, BioCity 2nd Floor, FIN-20520 Turku, Finland; (S.B.); (A.P.)
| | - Ada Pajari
- Department of Biosciences, Cell Biology, Åbo Akademi University, Tykistökatu 6A, BioCity 2nd Floor, FIN-20520 Turku, Finland; (S.B.); (A.P.)
| | - M. Bishr Omary
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA;
| | - Diana M. Toivola
- Department of Biosciences, Cell Biology, Åbo Akademi University, Tykistökatu 6A, BioCity 2nd Floor, FIN-20520 Turku, Finland; (S.B.); (A.P.)
- Turku Center for Disease Modeling, University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland
- Correspondence: (C.M.A.); (D.M.T.)
| |
Collapse
|
8
|
Smets T, Waelkens E, De Moor B. Prioritization of m/z-Values in Mass Spectrometry Imaging Profiles Obtained Using Uniform Manifold Approximation and Projection for Dimensionality Reduction. Anal Chem 2020; 92:5240-5248. [DOI: 10.1021/acs.analchem.9b05764] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Tina Smets
- STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, 3001 Leuven, Belgium
| | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, KU Leuven, 3001 Leuven, Belgium
| | - Bart De Moor
- STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, 3001 Leuven, Belgium
| |
Collapse
|
9
|
Prentice BM, Hart NJ, Phillips N, Haliyur R, Judd A, Armandala R, Spraggins JM, Lowe CL, Boyd KL, Stein RW, Wright CV, Norris JL, Powers AC, Brissova M, Caprioli RM. Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue. Diabetologia 2019; 62:1036-1047. [PMID: 30955045 PMCID: PMC6553460 DOI: 10.1007/s00125-019-4855-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 02/20/2019] [Indexed: 12/20/2022]
Abstract
AIMS/HYPOTHESIS The molecular response and function of pancreatic islet cells during metabolic stress is a complex process. The anatomical location and small size of pancreatic islets coupled with current methodological limitations have prevented the achievement of a complete, coherent picture of the role that lipids and proteins play in cellular processes under normal conditions and in diseased states. Herein, we describe the development of untargeted tissue imaging mass spectrometry (IMS) technologies for the study of in situ protein and, more specifically, lipid distributions in murine and human pancreases. METHODS We developed matrix-assisted laser desorption/ionisation (MALDI) IMS protocols to study metabolite, lipid and protein distributions in mouse (wild-type and ob/ob mouse models) and human pancreases. IMS allows for the facile discrimination of chemically similar lipid and metabolite isoforms that cannot be distinguished using standard immunohistochemical techniques. Co-registration of MS images with immunofluorescence images acquired from serial tissue sections allowed accurate cross-registration of cell types. By acquiring immunofluorescence images first, this serial section approach guides targeted high spatial resolution IMS analyses (down to 15 μm) of regions of interest and leads to reduced time requirements for data acquisition. RESULTS MALDI IMS enabled the molecular identification of specific phospholipid and glycolipid isoforms in pancreatic islets with intra-islet spatial resolution. This technology shows that subtle differences in the chemical structure of phospholipids can dramatically affect their distribution patterns and, presumably, cellular function within the islet and exocrine compartments of the pancreas (e.g. 18:1 vs 18:2 fatty acyl groups in phosphatidylcholine lipids). We also observed the localisation of specific GM3 ganglioside lipids [GM3(d34:1), GM3(d36:1), GM3(d38:1) and GM3(d40:1)] within murine islet cells that were correlated with a higher level of GM3 synthase as verified by immunostaining. However, in human pancreas, GM3 gangliosides were equally distributed in both the endocrine and exocrine tissue, with only one GM3 isoform showing islet-specific localisation. CONCLUSIONS/INTERPRETATION The development of more complete molecular profiles of pancreatic tissue will provide important insight into the molecular state of the pancreas during islet development, normal function, and diseased states. For example, this study demonstrates that these results can provide novel insight into the potential signalling mechanisms involving phospholipids and glycolipids that would be difficult to detect by targeted methods, and can help raise new hypotheses about the types of physiological control exerted on endocrine hormone-producing cells in islets. Importantly, the in situ measurements afforded by IMS do not require a priori knowledge of molecules of interest and are not susceptible to the limitations of immunohistochemistry, providing the opportunity for novel biomarker discovery. Notably, the presence of multiple GM3 isoforms in mouse islets and the differential localisation of lipids in human tissue underscore the important role these molecules play in regulating insulin modulation and suggest species, organ, and cell specificity. This approach demonstrates the importance of both high spatial resolution and high molecular specificity to accurately survey the molecular composition of complex, multi-functional tissues such as the pancreas.
Collapse
Affiliation(s)
- Boone M Prentice
- 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Nathaniel J Hart
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Neil Phillips
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rachana Haliyur
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Audra Judd
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Radhika Armandala
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey M Spraggins
- 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Cindy L Lowe
- Translational Pathology Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kelli L Boyd
- Translational Pathology Shared Resource, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Roland W Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Christopher V Wright
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Jeremy L Norris
- 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Alvin C Powers
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Marcela Brissova
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Richard M Caprioli
- 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Pharmacology and Medicine, Vanderbilt University, Nashville, TN, USA.
| |
Collapse
|
10
|
Miraee-Nedjad S, Sims PFG, Schwartz JM, Doig AJ. Effect of IAPP on the proteome of cultured Rin-5F cells. BMC BIOCHEMISTRY 2018; 19:9. [PMID: 30419808 PMCID: PMC6233276 DOI: 10.1186/s12858-018-0099-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/22/2018] [Indexed: 11/12/2022]
Abstract
Background Islet amyloid polypeptide (IAPP) or amylin deposits can be found in the islets of type 2 diabetes patients. The peptide is suggested to be involved in the etiology of the disease through formation of amyloid deposits and destruction of β islet cells, though the underlying molecular events leading from IAPP deposition to β cell death are still largely unknown. Results We used OFFGEL™ proteomics to study how IAPP exposure affects the proteome of rat pancreatic insulinoma Rin-5F cells. The OFFGEL™ methodology is highly effective at generating quantitative data on hundreds of proteins affected by IAPP, with its accuracy confirmed by In Cell Western and Quantitative Real Time PCR results. Combining data on individual proteins identifies pathways and protein complexes affected by IAPP. IAPP disrupts protein synthesis and degradation, and induces oxidative stress. It causes decreases in protein transport and localization. IAPP disrupts the regulation of ubiquitin-dependent protein degradation and increases catabolic processes. IAPP causes decreases in protein transport and localization, and affects the cytoskeleton, DNA repair and oxidative stress. Conclusions Results are consistent with a model where IAPP aggregates overwhelm the ability of a cell to degrade proteins via the ubiquitin system. Ultimately this leads to apoptosis. IAPP aggregates may be also toxic to the cell by causing oxidative stress, leading to DNA damage or by decreasing protein transport. The reversal of any of these effects, perhaps by targeting proteins which alter in response to IAPP, may be beneficial for type II diabetes. Electronic supplementary material The online version of this article (10.1186/s12858-018-0099-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Samaneh Miraee-Nedjad
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Paul F G Sims
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jean-Marc Schwartz
- Division of Evolution & Genomic Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK.
| |
Collapse
|
11
|
Lobanov AV, Heaphy SM, Turanov AA, Gerashchenko MV, Pucciarelli S, Devaraj RR, Xie F, Petyuk VA, Smith RD, Klobutcher LA, Atkins JF, Miceli C, Hatfield DL, Baranov PV, Gladyshev VN. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation. Nat Struct Mol Biol 2017; 24:61-68. [PMID: 27870834 PMCID: PMC5295771 DOI: 10.1038/nsmb.3330] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 10/31/2016] [Indexed: 11/09/2022]
Abstract
The ribosome can change its reading frame during translation in a process known as programmed ribosomal frameshifting. These rare events are supported by complex mRNA signals. However, we found that the ciliates Euplotes crassus and Euplotes focardii exhibit widespread frameshifting at stop codons. 47 different codons preceding stop signals resulted in either +1 or +2 frameshifts, and +1 frameshifting at AAA was the most frequent. The frameshifts showed unusual plasticity and rapid evolution, and had little influence on translation rates. The proximity of a stop codon to the 3' mRNA end, rather than its occurrence or sequence context, appeared to designate termination. Thus, a 'stop codon' is not a sufficient signal for translation termination, and the default function of stop codons in Euplotes is frameshifting, whereas termination is specific to certain mRNA positions and probably requires additional factors.
Collapse
Affiliation(s)
- Alexei V. Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| | - Stephen M. Heaphy
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Anton A. Turanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| | - Maxim V. Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| | - Sandra Pucciarelli
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Raghul R. Devaraj
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Fang Xie
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Richard D. Smith
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lawrence A. Klobutcher
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Cristina Miceli
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Dolph L. Hatfield
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| |
Collapse
|
12
|
Villafuerte BC, Barati MT, Rane MJ, Isaacs S, Li M, Wilkey DW, Merchant ML. Over-expression of insulin-response element binding protein-1 (IRE-BP1) in mouse pancreatic islets increases expression of RACK1 and TCTP: Beta cell markers of high glucose sensitivity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:186-194. [PMID: 27816562 DOI: 10.1016/j.bbapap.2016.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/16/2016] [Accepted: 10/31/2016] [Indexed: 12/29/2022]
Abstract
BACKGROUND A targeted analysis of the 50kDa C-terminal fragment of insulin-response element binding protein-1 (IRE-BP1) activation of target genes through the insulin receptor substrate receptor/PI-3 kinase/Akt pathway has been demonstrated for the insulin growth factor-1 receptor. The broader effects of 50kDa C-terminal IRE-BP1 fragment over-expression on protein abundance in pancreatic islet beta cells have not been determined. RESULTS Liquid-chromatography coupled to tandem mass spectrometry (LC-MS/MS) analyses of replicate lysates of pancreatic islets isolated from background strain animals and transgenic animals, overexpressing IRE-BP1 in pancreatic islet beta cells, demonstrated statistically significant increases in the expression of proteins involved in protein synthesis, endoplasmic reticulum (ER) stress and scaffolding proteins important for protein kinase C signaling; some of which were confirmed by immunoblot analyses. Bioinformatic analysis of protein expression network patterns suggested IRE-BP1 over-expression leads to protein expression patterns indicative of activation of functional protein networks utilized for protein post-translational modification, protein folding, and protein synthesis. Co-immunoprecipitation experiments demonstrate a novel interaction between two differentially regulated proteins receptor for activated protein kinase C (RACK1) and translationally controlled tumor protein (TCTP). CONCLUSIONS Proteomic analysis of IRE-BP1 over-expression in pancreatic islet beta cells suggest IRE-BP1 (a) directly or indirectly through establishing hyperglycemia results in increased expression of ribosomal proteins and markers of ER stress and (b) leads to the enhanced and previously un-described interaction of RACK1 and TCTP. SIGNIFICANCE This study identified C-terminal 50kDa domain of IRE-BP1 over-expression results in increased markers of ER-stress and a novel interaction between the scaffolding proteins RACK1 and TCTP.
Collapse
Affiliation(s)
- Betty C Villafuerte
- Department of Medicine, University of Louisville, Louisville, KY, United States
| | - Michelle T Barati
- Department of Medicine, University of Louisville, Louisville, KY, United States
| | - Madhavi J Rane
- Department of Medicine, University of Louisville, Louisville, KY, United States
| | - Susan Isaacs
- Department of Medicine, University of Louisville, Louisville, KY, United States; Core Proteomics Laboratory, University of Louisville, Louisville, KY, United States
| | - Ming Li
- Department of Medicine, University of Louisville, Louisville, KY, United States; Core Proteomics Laboratory, University of Louisville, Louisville, KY, United States
| | - Daniel W Wilkey
- Department of Medicine, University of Louisville, Louisville, KY, United States; Core Proteomics Laboratory, University of Louisville, Louisville, KY, United States
| | - Michael L Merchant
- Department of Medicine, University of Louisville, Louisville, KY, United States; Core Proteomics Laboratory, University of Louisville, Louisville, KY, United States.
| |
Collapse
|
13
|
Yang H, Yang L. Targeting cAMP/PKA pathway for glycemic control and type 2 diabetes therapy. J Mol Endocrinol 2016; 57:R93-R108. [PMID: 27194812 DOI: 10.1530/jme-15-0316] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/18/2016] [Indexed: 12/11/2022]
Abstract
In mammals, cyclic adenosine monophosphate (cAMP) is an intracellular second messenger that is usually elicited by binding of hormones and neurotransmitters to G protein-coupled receptors (GPCRs). cAMP exerts many of its physiological effects by activating cAMP-dependent protein kinase (PKA), which in turn phosphorylates and regulates the functions of downstream protein targets including ion channels, enzymes, and transcription factors. cAMP/PKA signaling pathway regulates glucose homeostasis at multiple levels including insulin and glucagon secretion, glucose uptake, glycogen synthesis and breakdown, gluconeogenesis, and neural control of glucose homeostasis. This review summarizes recent genetic and pharmacological studies concerning the regulation of glucose homeostasis by cAMP/PKA in pancreas, liver, skeletal muscle, adipose tissues, and brain. We also discuss the strategies for targeting cAMP/PKA pathway for research and potential therapeutic treatment of type 2 diabetes mellitus (T2D).
Collapse
Affiliation(s)
- Haihua Yang
- Division of EndocrinologyZhengzhou Children's Hospital, Zhengzhou, Henan, China
| | - Linghai Yang
- Department of PharmacologyUniversity of Washington, Seattle, Washington, USA
| |
Collapse
|
14
|
A new dimethyl labeling-based SID-MRM-MS method and its application to three proteases involved in insulin maturation. BIOPHYSICS REPORTS 2015; 1:71-80. [PMID: 26942221 PMCID: PMC4762191 DOI: 10.1007/s41048-015-0012-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 04/13/2015] [Indexed: 11/04/2022] Open
Abstract
The absolute quantification of target proteins in proteomics involves stable isotope dilution coupled with multiple reactions monitoring mass spectrometry (SID-MRM-MS). The successful preparation of stable isotope-labeled internal standard peptides is an important prerequisite for the SID-MRM absolute quantification methods. Dimethyl labeling has been widely used in relative quantitative proteomics and it is fast, simple, reliable, cost-effective, and applicable to any protein sample, making it an ideal candidate method for the preparation of stable isotope-labeled internal standards. MRM mass spectrometry is of high sensitivity, specificity, and throughput characteristics and can quantify multiple proteins simultaneously, including low-abundance proteins in precious samples such as pancreatic islets. In this study, a new method for the absolute quantification of three proteases involved in insulin maturation, namely PC1/3, PC2 and CPE, was developed by coupling a stable isotope dimethyl labeling strategy for internal standard peptide preparation with SID-MRM-MS quantitative technology. This method offers a new and effective approach for deep understanding of the functional status of pancreatic β cells and pathogenesis in diabetes.
Collapse
|
15
|
Yoshimatsu G, Sakata N, Tsuchiya H, Minowa T, Takemura T, Morita H, Hata T, Fukase M, Aoki T, Ishida M, Motoi F, Naitoh T, Katayose Y, Egawa S, Unno M. The co-transplantation of bone marrow derived mesenchymal stem cells reduced inflammation in intramuscular islet transplantation. PLoS One 2015; 10:e0117561. [PMID: 25679812 PMCID: PMC4332659 DOI: 10.1371/journal.pone.0117561] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/27/2014] [Indexed: 12/12/2022] Open
Abstract
Aims/Hypothesis Although the muscle is one of the preferable transplant sites in islet transplantation, its transplant efficacy is poor. Here we attempted to determine whether an intramuscular co-transplantation of mesenchymal stem cells (MSCs) could improve the outcome. Methods We co-cultured murine islets with MSCs and then analyzed the morphological changes, viability, insulin-releasing function (represented by the stimulation index), and gene expression of the islets. We also transplanted 500 islets intramuscularly with or without 5 × 105 MSCs to diabetic mice and measured their blood glucose level, the glucose changes in an intraperitoneal glucose tolerance test, and the plasma IL-6 level. Inflammation, apoptosis, and neovascularization in the transplantation site were evaluated histologically. Results The destruction of islets tended to be prevented by co-culture with MSCs. The stimulation index was significantly higher in islets co-cultured with MSCs (1.78 ± 0.59 vs. 7.08 ± 2.53; p = 0.0025). In terms of gene expression, Sult1c2, Gstm1, and Rab37 were significantly upregulated in islets co-cultured with MSCs. Although MSCs were effective in the in vitro assays, they were only partially effective in facilitating intramuscular islet transplantation. Co-transplanted MSCs prevented an early inflammatory reaction from the islets (plasma IL-6; p = 0.0002, neutrophil infiltration; p = 0.016 inflammatory area; p = 0.021), but could not promote neovascularization in the muscle, resulting in the failure of many intramuscular transplanted islets to engraft. Conclusions In conclusion, co-culturing and co-transplanting MSCs is potentially useful in islet transplantation, especially in terms of anti-inflammation, but further augmentation for an anti-apoptosis effect and neovascularization is necessary.
Collapse
Affiliation(s)
- Gumpei Yoshimatsu
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoaki Sakata
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Haruyuki Tsuchiya
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Minowa
- Nanotechnology Innovation Station, National Institute for Materials Science, Tsukuba, Japan
| | - Taro Takemura
- Nanotechnology Innovation Station, National Institute for Materials Science, Tsukuba, Japan
| | - Hiromi Morita
- Nanotechnology Innovation Station, National Institute for Materials Science, Tsukuba, Japan
| | - Tatsuo Hata
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masahiko Fukase
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takeshi Aoki
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masaharu Ishida
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fuyuhiko Motoi
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takeshi Naitoh
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yu Katayose
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan; Division of Integrated Surgery and Oncology, Tohoku University Hospital, Sendai, Japan
| | - Shinichi Egawa
- Division of International Cooperation for Disaster Medicine, Tohoku University, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| |
Collapse
|
16
|
Nayak DK, Calderon B, Vomund AN, Unanue ER. ZnT8-reactive T cells are weakly pathogenic in NOD mice but can participate in diabetes under inflammatory conditions. Diabetes 2014; 63:3438-48. [PMID: 24812429 PMCID: PMC4171664 DOI: 10.2337/db13-1882] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Autoantibodies to the islet-specific Zn transporter ZnT8 (Slc30a8), as well as CD4 T cells, have been identified in patients with type 1 diabetes. Here we examined for CD4 T-cell reactivity to ZnT8 epitopes in the NOD mouse. Immunization with a cytoplasmic domain of the protein or with peptides predicted to bind to I-A(g7) resulted in a CD4 T-cell response, indicating a lack of deletional tolerance. However, presentation by intraislet antigen-presenting cells (APC) to the T cells was not detectable in prediabetic mice. Presentation by islet APC was found only in islets of mice with active diabetes. In accordance, a culture assay indicated the weak transfer of ZnT8 reactivity from insulinomas or primary β-cells to APC for presentation to T cells. A T cell directed to one peptide (345-359) resulted in the transfer of diabetes, but only in conditions in which the recipient NOD mice or NOD.Rag1(-/-) mice were subjected to light irradiation. In late diabetic NOD mice, CD4 T cells were found as well as a weak antibody response. We conclude that in NOD mice, ZnT8 is a minor diabetogenic antigen that can participate in diabetes in conditions in which the islet is first made receptive to immunological insults.
Collapse
Affiliation(s)
- Deepak K Nayak
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Boris Calderon
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Anthony N Vomund
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Emil R Unanue
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| |
Collapse
|
17
|
Cao Z, Robinson RAS. Proteome characterization of splenocytes from an A
βpp/ps-
1 Alzheimer's disease model. Proteomics 2014; 14:291-7. [DOI: 10.1002/pmic.201300130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 10/22/2013] [Accepted: 11/21/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Zhiyun Cao
- Department of Chemistry; University of Pittsburgh; Pittsburgh PA USA
| | | |
Collapse
|
18
|
Zhou Y, Waanders LF, Holmseth S, Guo C, Berger UV, Li Y, Lehre AC, Lehre KP, Danbolt NC. Proteome analysis and conditional deletion of the EAAT2 glutamate transporter provide evidence against a role of EAAT2 in pancreatic insulin secretion in mice. J Biol Chem 2013; 289:1329-44. [PMID: 24280215 DOI: 10.1074/jbc.m113.529065] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Islet function is incompletely understood in part because key steps in glutamate handling remain undetermined. The glutamate (excitatory amino acid) transporter 2 (EAAT2; Slc1a2) has been hypothesized to (a) provide islet cells with glutamate, (b) protect islet cells against high extracellular glutamate concentrations, (c) mediate glutamate release, or (d) control the pH inside insulin secretory granules. Here we floxed the EAAT2 gene to produce the first conditional EAAT2 knock-out mice. Crossing with Nestin-cyclization recombinase (Cre) eliminated EAAT2 from the brain, resulting in epilepsy and premature death, confirming the importance of EAAT2 for brain function and validating the genetic construction. Crossing with insulin-Cre lines (RIP-Cre and IPF1-Cre) to obtain pancreas-selective deletion did not appear to affect survival, growth, glucose tolerance, or β-cell number. We found (using TaqMan RT-PCR, immunoblotting, immunocytochemistry, and proteome analysis) that the EAAT2 levels were too low to support any of the four hypothesized functions. The proteome analysis detected more than 7,000 islet proteins of which more than 100 were transporters. Although mitochondrial glutamate transporters and transporters for neutral amino acids were present at high levels, all other transporters with known ability to transport glutamate were strikingly absent. Glutamate-metabolizing enzymes were abundant. The level of glutamine synthetase was 2 orders of magnitude higher than that of glutaminase. Taken together this suggests that the uptake of glutamate by islets from the extracellular fluid is insignificant and that glutamate is intracellularly produced. Glutamine synthetase may be more important for islets than assumed previously.
Collapse
Affiliation(s)
- Yun Zhou
- From The Neurotransporter Group, Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Mitchell HD, Eisfeld AJ, Sims AC, McDermott JE, Matzke MM, Webb-Robertson BJM, Tilton SC, Tchitchek N, Josset L, Li C, Ellis AL, Chang JH, Heegel RA, Luna ML, Schepmoes AA, Shukla AK, Metz TO, Neumann G, Benecke AG, Smith RD, Baric RS, Kawaoka Y, Katze MG, Waters KM. A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses. PLoS One 2013; 8:e69374. [PMID: 23935999 PMCID: PMC3723910 DOI: 10.1371/journal.pone.0069374] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 06/07/2013] [Indexed: 12/02/2022] Open
Abstract
Respiratory infections stemming from influenza viruses and the Severe Acute Respiratory Syndrome corona virus (SARS-CoV) represent a serious public health threat as emerging pandemics. Despite efforts to identify the critical interactions of these viruses with host machinery, the key regulatory events that lead to disease pathology remain poorly targeted with therapeutics. Here we implement an integrated network interrogation approach, in which proteome and transcriptome datasets from infection of both viruses in human lung epithelial cells are utilized to predict regulatory genes involved in the host response. We take advantage of a novel “crowd-based” approach to identify and combine ranking metrics that isolate genes/proteins likely related to the pathogenicity of SARS-CoV and influenza virus. Subsequently, a multivariate regression model is used to compare predicted lung epithelial regulatory influences with data derived from other respiratory virus infection models. We predicted a small set of regulatory factors with conserved behavior for consideration as important components of viral pathogenesis that might also serve as therapeutic targets for intervention. Our results demonstrate the utility of integrating diverse ‘omic datasets to predict and prioritize regulatory features conserved across multiple pathogen infection models.
Collapse
Affiliation(s)
- Hugh D. Mitchell
- Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| | - Amie J. Eisfeld
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Amy C. Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jason E. McDermott
- Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Melissa M. Matzke
- Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Bobbi-Jo M. Webb-Robertson
- Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Susan C. Tilton
- Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Nicolas Tchitchek
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Laurence Josset
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Chengjun Li
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Amy L. Ellis
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jean H. Chang
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Robert A. Heegel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Maria L. Luna
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Athena A. Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Anil K. Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Arndt G. Benecke
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Université Pierre et Marie Curie, Centre National de la Recherche Scientifique UMR7224, Paris, France
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- ERATO Infection-Induced Host Responses Project, Saitama, Japan
| | - Michael G. Katze
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
| | - Katrina M. Waters
- Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| |
Collapse
|
20
|
Ljubicic S, Bezzi P, Brajkovic S, Nesca V, Guay C, Ohbayashi N, Fukuda M, Abderrhamani A, Regazzi R. The GTPase Rab37 Participates in the Control of Insulin Exocytosis. PLoS One 2013; 8:e68255. [PMID: 23826383 PMCID: PMC3694898 DOI: 10.1371/journal.pone.0068255] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 05/27/2013] [Indexed: 01/04/2023] Open
Abstract
Rab37 belongs to a subclass of Rab GTPases regulating exocytosis, including also Rab3a and Rab27a. Proteomic studies indicate that Rab37 is associated with insulin-containing large dense core granules of pancreatic β-cells. In agreement with these observations, we detected Rab37 in extracts of β-cell lines and human pancreatic islets and confirmed by confocal microscopy the localization of the GTPase on insulin-containing secretory granules. We found that, as is the case for Rab3a and Rab27a, reduction of Rab37 levels by RNA interference leads to impairment in glucose-induced insulin secretion and to a decrease in the number of granules in close apposition to the plasma membrane. Pull-down experiments revealed that, despite similar functional effects, Rab37 does not interact with known Rab3a or Rab27a effectors and is likely to operate through a different mechanism. Exposure of insulin-secreting cells to proinflammatory cytokines, fatty acids or oxidized low-density lipoproteins, mimicking physiopathological conditions that favor the development of diabetes, resulted in a decrease in Rab37 expression. Our data identify Rab37 as an additional component of the machinery governing exocytosis of β-cells and suggest that impaired expression of this GTPase may contribute to defective insulin release in pre-diabetic and diabetic conditions.
Collapse
Affiliation(s)
- Sanda Ljubicic
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Paola Bezzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Saska Brajkovic
- EGID FR 3508, INSERM U859, Université de Lille 2, Lille, France
| | - Valeria Nesca
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Norihiko Ohbayashi
- Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
- * E-mail:
| |
Collapse
|
21
|
Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. J Virol 2013; 87:3885-902. [PMID: 23365422 DOI: 10.1128/jvi.02520-12] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus accessory protein ORF6 antagonizes interferon signaling by blocking karyopherin-mediated nuclear import processes. Viral nuclear import antagonists, expressed by several highly pathogenic RNA viruses, likely mediate pleiotropic effects on host gene expression, presumably interfering with transcription factors, cytokines, hormones, and/or signaling cascades that occur in response to infection. By bioinformatic and systems biology approaches, we evaluated the impact of nuclear import antagonism on host expression networks by using human lung epithelial cells infected with either wild-type virus or a mutant that does not express ORF6 protein. Microarray analysis revealed significant changes in differential gene expression, with approximately twice as many upregulated genes in the mutant virus samples by 48 h postinfection, despite identical viral titers. Our data demonstrated that ORF6 protein expression attenuates the activity of numerous karyopherin-dependent host transcription factors (VDR, CREB1, SMAD4, p53, EpasI, and Oct3/4) that are critical for establishing antiviral responses and regulating key host responses during virus infection. Results were confirmed by proteomic and chromatin immunoprecipitation assay analyses and in parallel microarray studies using infected primary human airway epithelial cell cultures. The data strongly support the hypothesis that viral antagonists of nuclear import actively manipulate host responses in specific hierarchical patterns, contributing to the viral pathogenic potential in vivo. Importantly, these studies and modeling approaches not only provide templates for evaluating virus antagonism of nuclear import processes but also can reveal candidate cellular genes and pathways that may significantly influence disease outcomes following severe acute respiratory syndrome coronavirus infection in vivo.
Collapse
|
22
|
A travel guide to Cytoscape plugins. Nat Methods 2012; 9:1069-76. [PMID: 23132118 DOI: 10.1038/nmeth.2212] [Citation(s) in RCA: 1036] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 09/27/2012] [Indexed: 01/04/2023]
Abstract
Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set of tools. We present a travel guide to the world of plugins, covering the 152 publicly available plugins for Cytoscape 2.5-2.8. We also describe ongoing efforts to distribute, organize and maintain the quality of the collection.
Collapse
|
23
|
Abstract
The incidence of type 2 diabetes mellitus (T2DM) is rapidly increasing worldwide with significant consequences on individual quality of life as well as economic burden on states' healthcare costs. While origins of the pathogenesis of T2DM are poorly understood, an early defect in glucose-stimulated insulin secretion (GSIS) from pancreatic β-cells is considered a hallmark of T2DM. Upon a glucose stimulus, insulin is secreted in a biphasic manner with an early first-phase burst of insulin, which is followed by a second, more sustained phase of insulin output. First phase insulin secretion is diminished early in T2DM as well is in subjects who are at risk of developing T2DM. An effective treatment of T2DM with incretin hormone glucagon-like peptide-1 (GLP-1) or its long acting peptide analogue exendin-4 (E4), restores first-phase and augments second-phase glucose stimulated insulin secretion. This effect of incretin action occurs within minutes of GLP-1/E4 infusion in T2DM humans. An additional important consideration is that incretin hormones augment GSIS only above a certain glucose threshold, which is slightly above the normal glucose range. This ensures that incretin hormones stimulate GSIS only when glucose levels are high, while they are ineffective when insulin levels are below a certain threshold. Activation of the GLP-1 receptor, which is highly expressed on pancreatic β-cells, stimulates 2 -distinct intracellular signaling pathways: a) the cAMP-protein kinase A branch and b) the cAMP-EPAC2 (EPAC=exchange protein activated by cAMP) branch. While the EPAC2 branch is considered to mediate GLP-1 effects on first-phase GSIS, the PKA branch is necessary for the former branch to be active. However, how these 2 branches interplay and converge and how their effects on insulin secretion and insulin vesicle exocytosis are coordinated is poorly understood.Thus, at the outset of our studies we have a poorly understood intracellular interplay of cAMP-dependent signaling pathways, which - when stimulated - restore glucose-dependent first phase and augment second phase insulin secretion in the ailing β-cells of T2DM.
Collapse
Affiliation(s)
- M A Hussain
- Department of Pediatrics, Medicine and Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | | | | |
Collapse
|
24
|
Zhou JY, Dann GP, Liew CW, Smith RD, Kulkarni RN, Qian WJ. Unraveling pancreatic islet biology by quantitative proteomics. Expert Rev Proteomics 2012; 8:495-504. [PMID: 21819304 DOI: 10.1586/epr.11.39] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The pancreatic islets of Langerhans play a critical role in maintaining blood glucose homeostasis by secreting insulin and several other important peptide hormones. Impaired insulin secretion due to islet dysfunction is linked to the pathogenesis underlying both Type 1 and Type 2 diabetes. Over the past 5 years, emerging proteomic technologies have been applied to dissect the signaling pathways that regulate islet functions and gain an understanding of the mechanisms of islet dysfunction relevant to diabetes. Herein, we briefly review some of the recent quantitative proteomic studies involving pancreatic islets geared towards gaining a better understanding of islet biology relevant to metabolic diseases.
Collapse
Affiliation(s)
- Jian-Ying Zhou
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | | | | | | | | |
Collapse
|
25
|
Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO. Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics. J Proteome Res 2012; 11:3520-32. [PMID: 22578083 DOI: 10.1021/pr3002996] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The prevalence of diabetes mellitus is increasing dramatically throughout the world, and the disease has become a major public health issue. The most common form of the disease, type 2 diabetes, is characterized by insulin resistance and insufficient insulin production from the pancreatic beta-cell. Since glucose is the most potent regulator of beta-cell function under physiological conditions, identification of the insulin secretory defect underlying type 2 diabetes requires a better understanding of glucose regulation of human beta-cell function. To this aim, a bottom-up LC-MS/MS-based proteomics approach was used to profile pooled islets from multiple donors under basal (5 mM) or high (15 mM) glucose conditions. Our analysis discovered 256 differentially abundant proteins (∼p < 0.05) after 24 h of high glucose exposure from more than 4500 identified in total. Several novel glucose-regulated proteins were elevated under high glucose conditions, including regulators of mRNA splicing (pleiotropic regulator 1), processing (retinoblastoma binding protein 6), and function (nuclear RNA export factor 1), in addition to neuron navigator 1 and plasminogen activator inhibitor 1. Proteins whose abundances markedly decreased during incubation at 15 mM glucose included Bax inhibitor 1 and synaptotagmin-17. Up-regulation of dicer 1 and SLC27A2 and down-regulation of phospholipase Cβ4 were confirmed by Western blots. Many proteins found to be differentially abundant after high glucose stimulation are annotated as uncharacterized or hypothetical. These findings expand our knowledge of glucose regulation of the human islet proteome and suggest many hitherto unknown responses to glucose that require additional studies to explore novel functional roles.
Collapse
|
26
|
Song WJ, Seshadri M, Ashraf U, Mdluli T, Mondal P, Keil M, Azevedo M, Kirschner LS, Stratakis CA, Hussain MA. Snapin mediates incretin action and augments glucose-dependent insulin secretion. Cell Metab 2011; 13:308-19. [PMID: 21356520 PMCID: PMC3053597 DOI: 10.1016/j.cmet.2011.02.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/06/2010] [Accepted: 01/28/2011] [Indexed: 01/16/2023]
Abstract
Impaired insulin secretion contributes to the pathogenesis of type 2 diabetes mellitus (T2DM). Treatment with the incretin hormone glucagon-like peptide-1 (GLP-1) potentiates insulin secretion and improves metabolic control in humans with T2DM. GLP-1 receptor-mediated signaling leading to insulin secretion occurs via cyclic AMP stimulated protein kinase A (PKA)- as well as guanine nucleotide exchange factor-mediated pathways. However, how these two pathways integrate and coordinate insulin secretion remains poorly understood. Here we show that these incretin-stimulated pathways converge at the level of snapin, and that PKA-dependent phosphorylation of snapin increases interaction among insulin secretory vesicle-associated proteins, thereby potentiating glucose-stimulated insulin secretion (GSIS). In diabetic islets with impaired GSIS, snapin phosphorylation is reduced, and expression of a snapin mutant, which mimics site-specific phosphorylation, restores GSIS. Thus, snapin is a critical node in GSIS regulation and provides a potential therapeutic target to improve β cell function in T2DM.
Collapse
Affiliation(s)
- Woo-Jin Song
- Department of Pediatrics, Metabolism Division, Johns Hopkins University, Baltimore, MD 21287, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Schoenherr RM, Kelly-Spratt KS, Lin C, Whiteaker JR, Liu T, Holzman T, Coleman I, Feng LC, Lorentzen TD, Krasnoselsky AL, Wang P, Liu Y, Gurley KE, Amon LM, Schepmoes AA, Moore RJ, Camp DG, Chodosh LA, Smith RD, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG. Proteome and transcriptome profiles of a Her2/Neu-driven mouse model of breast cancer. Proteomics Clin Appl 2011; 5:179-88. [PMID: 21448875 DOI: 10.1002/prca.201000037] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 08/31/2010] [Accepted: 10/14/2010] [Indexed: 11/08/2022]
Abstract
PURPOSE We generated extensive transcriptional and proteomic profiles from a Her2-driven mouse model of breast cancer that closely recapitulates human breast cancer. This report makes these data publicly available in raw and processed forms, as a resource to the community. Importantly, we previously made biospecimens from this same mouse model freely available through a sample repository, so researchers can obtain samples to test biological hypotheses without the need of breeding animals and collecting biospecimens. EXPERIMENTAL DESIGN Twelve datasets are available, encompassing 841 LC-MS/MS experiments (plasma and tissues) and 255 microarray analyses of multiple tissues (thymus, spleen, liver, blood cells, and breast). Cases and controls were rigorously paired to avoid bias. RESULTS In total, 18,880 unique peptides were identified (PeptideProphet peptide error rate ≤1%), with 3884 and 1659 non-redundant protein groups identified in plasma and tissue datasets, respectively. Sixty-one of these protein groups overlapped between cancer plasma and cancer tissue. CONCLUSIONS AND CLINICAL RELEVANCE These data are of use for advancing our understanding of cancer biology, for software and quality control tool development, investigations of analytical variation in MS/MS data, and selection of proteotypic peptides for multiple reaction monitoring-MS. The availability of these datasets will contribute positively to clinical proteomics.
Collapse
|
28
|
Guo X, Zhang P, Qi Y, Chen W, Chen X, Zhou Z, Sha J. Proteomic analysis of male 4C germ cell proteins involved in mouse meiosis. Proteomics 2010; 11:298-308. [PMID: 21204256 DOI: 10.1002/pmic.200900726] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 09/30/2010] [Accepted: 10/20/2010] [Indexed: 11/07/2022]
Abstract
Male meiosis is a specialized type of cell division that gives rise to sperm. Errors in this process can result in the generation of aneuploid gametes, which are associated with birth defects and infertility in humans. Until now, there has been a lack of a large-scale identification of proteins involved in male meiosis in mammals. In this study, we report the high-confidence identification of 3625 proteins in mouse male germ cells with 4C DNA content undergoing meiosis I. Of these, 397 were found to be testis specific. Bioinformatics analysis of the proteome led to the identification of 28 proteins known to be essential for male meiosis in mice. We also found 172 proteins that had yeast orthologs known to be essential for meiosis. Chromosome distribution analysis of the proteome showed underrepresentation of the identified proteins on the X chromosome, which may be due to meiotic sex chromosome inactivation. Characterization of the proteome of 4C germ cells from mouse testis provides an inventory of proteins, which is useful for understanding meiosis and the mechanisms of male infertility.
Collapse
Affiliation(s)
- Xuejiang Guo
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, P R China
| | | | | | | | | | | | | |
Collapse
|
29
|
Hansson SF, Henriksson Å, Johansson L, Korsgren O, Eriksson JW, Tornqvist H, Davidsson P. Membrane Protein Profiling of Human Islets of Langerhans Using Several Extraction Methods. Clin Proteomics 2010. [DOI: 10.1007/s12014-010-9060-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Abstract
Introduction
Proteomic characterization of the human pancreatic islets, containing the insulin producing beta-cells, is likely to be of great importance for improved treatment and understanding of the pathophysiology of diabetes mellitus.
Objective
The focus of this study was to characterize the human islet membrane proteome.
Methods
In order to identify as many membrane proteins as possible, five different extraction procedures were used, i.e., phase separation using Triton X-114, a plasma membrane protein kit, cell surface protein biotinylation, total protein extraction, and lipid-based protein immobilization flow cell. Digested protein extracts were analyzed by nanoflow liquid chromatography tandem mass spectrometry. Then the identified proteins were categorized according to cellular location using their gene ontology annotation and by prediction of transmembrane helices in the sequence. This information was used to estimate the amount of membrane proteins identified.
Results
By combining the results from all extraction procedures, the total number of membrane proteins identified from the human islets was increased, accentuating that a combination of methods usually gives a higher coverage of the proteome. A total of 1,700 proteins were identified (≥2 unique peptides), and 735 of these proteins were annotated as membrane proteins while 360 proteins had at least one predicted transmembrane helix. The extraction method using phase separation with Triton X-114 yielded both the highest number and the highest proportion of membrane proteins.
Conclusion
This study gave an enhanced characterization of the human islet membrane proteome which may contribute to a better understanding of islet biology.
Collapse
|
30
|
Abstract
The mammalian oocyte possesses powerful reprogramming factors, which can reprogram terminally differentiated germ cells (sperm) or somatic cells within a few cell cycles. Although it has been suggested that use of oocyte-derived transcripts may enhance the generation of induced pluripotent stem cells, the reprogramming factors in oocytes are undetermined, and even the identified proteins composition of oocytes is very limited. In the present study, 7,000 mouse oocytes at different developmental stages, including the germinal vesicle stage, the metaphase II (MII) stage, and the fertilized oocytes (zygotes), were collected. We successfully identified 2,781 proteins present in germinal vesicle oocytes, 2,973 proteins in MII oocytes, and 2,082 proteins in zygotes through semiquantitative MS analysis. Furthermore, the results of the bioinformatics analysis indicated that different protein compositions are correlated with oocyte characteristics at different developmental stages. For example, specific transcription factors and chromatin remodeling factors are more abundant in MII oocytes, which may be crucial for the epigenetic reprogramming of sperm or somatic nuclei. These results provided important knowledge to better understand the molecular mechanisms in early development and may improve the generation of induced pluripotent stem cells.
Collapse
|
31
|
Abstract
The complementary disciplines of genomics and proteomics offer better insights into the molecular mechanisms of diseases. While genomics hunts for defining our static genetic substrate, proteomics explores the structure and function of proteins expressed by a cell or tissue type under specified conditions. In the past decade, proteomics has been revolutionized by the application of techniques such as two-dimensional gel electrophoresis (2DGE), mass spectrometry (MS), and protein arrays. These techniques have tremendous potential for biomarker development, target validation, diagnosis, prognosis, and optimization of treatment in medical care, especially in the field of islet and diabetes research. This chapter will highlight the contributions of proteomic technologies toward the dissection of complex network of signaling molecules regulating islet function, the identification of potential biomarkers, and the understanding of mechanisms involved in the pathogenesis of diabetes.
Collapse
|
32
|
Kislinger T, Gramolini AO. Proteome analysis of mouse model systems: A tool to model human disease and for the investigation of tissue-specific biology. J Proteomics 2010; 73:2205-18. [PMID: 20478424 DOI: 10.1016/j.jprot.2010.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 05/05/2010] [Accepted: 05/10/2010] [Indexed: 12/14/2022]
Abstract
The molecular dissections of the mechanistic pathways involved in human disease have always relied on the use of model organisms. Among the higher mammalian organisms, the laboratory mouse (Mus musculus) is the most widely used model. A large number of commercially-available, inbred strains are available to the community, including an ever growing collection of transgenic, knock-out, and disease models. Coupled to availability is the fact that animal colonies can be kept under standardized housing condition at most major universities and research institutes, with relative ease and cost efficiency (compared to larger vertebrates). As such, mouse models to study human biology and disease remains extremely attractive. In the current review we will provide an historic overview of the use of mouse models in proteome research with a focus on general tissue and organelle biology, comparative proteomics of human and mouse and the use of mouse models to study cardiac disease.
Collapse
Affiliation(s)
- Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
| | | |
Collapse
|
33
|
Zhang X, Monroe ME, Chen B, Chin MH, Heibeck TH, Schepmoes AA, Yang F, Petritis BO, Camp DG, Pounds JG, Jacobs JM, Smith DJ, Bigelow DJ, Smith RD, Qian WJ. Endogenous 3,4-dihydroxyphenylalanine and dopaquinone modifications on protein tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical. Mol Cell Proteomics 2010; 9:1199-208. [PMID: 20124354 DOI: 10.1074/mcp.m900321-mcp200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Oxidative modifications of protein tyrosines have been implicated in multiple human diseases. Among these modifications, elevations in levels of 3,4-dihydroxyphenylalanine (DOPA), a major product of hydroxyl radical addition to tyrosine, has been observed in a number of pathologies. Here we report the first proteome survey of endogenous site-specific modifications, i.e. DOPA and its further oxidation product dopaquinone in mouse brain and heart tissues. Results from LC-MS/MS analyses included 50 and 14 DOPA-modified tyrosine sites identified from brain and heart, respectively, whereas only a few nitrotyrosine-containing peptides, a more commonly studied marker of oxidative stress, were detectable, suggesting the much higher abundance for DOPA modification as compared with tyrosine nitration. Moreover, 20 and 12 dopaquinone-modified peptides were observed from brain and heart, respectively; nearly one-fourth of these peptides were also observed with DOPA modification on the same sites. For both tissues, these modifications are preferentially found in mitochondrial proteins with metal binding properties, consistent with metal-catalyzed hydroxyl radical formation from mitochondrial superoxide and hydrogen peroxide. These modifications also link to a number of mitochondrially associated and other signaling pathways. Furthermore, many of the modification sites were common sites of previously reported tyrosine phosphorylation, suggesting potential disruption of signaling pathways. Collectively, the results suggest that these modifications are linked with mitochondrially derived oxidative stress and may serve as sensitive markers for disease pathologies.
Collapse
Affiliation(s)
- Xu Zhang
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Li F, Li P, Xu W, Peng Y, Bo X, Wang S. PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks. Bioinformatics 2009; 26:275-7. [PMID: 19914922 DOI: 10.1093/bioinformatics/btp634] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED The propagation of perturbations in protein concentration through a protein interaction network (PIN) can shed light on network dynamics and function. In order to facilitate this type of study, PerturbationAnalyzer, which is an open source plugin for Cytoscape, has been developed. PerturbationAnalyzer can be used in manual mode for simulating user-defined perturbations, as well as in batch mode for evaluating network robustness and identifying significant proteins that cause large propagation effects in the PINs when their concentrations are perturbed. Results from PerturbationAnalyzer can be represented in an intuitive and customizable way and can also be exported for further exploration. PerturbationAnalyzer has great potential in mining the design principles of protein networks, and may be a useful tool for identifying drug targets. AVAILABILITY PerturbationAnalyzer can be accessed from the Cytoscape web site http://www.cytoscape.org/plugins/index.php or http://biotech.bmi.ac.cn/PerturbationAnalyzer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Fei Li
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China
| | | | | | | | | | | |
Collapse
|
35
|
Abstract
Islet protein profiling is defined as generation of extended protein expression data sets from islets or islet cells. Islets from rodent control and animal models of type 1 and type 2 diabetes mellitus and healthy humans and insulin- and glucagon-producing cell lines have been used. Protein profiling entails separation, differential expression determination, identification and expression analysis. Protein/peptide separation is either gel-based or by chromatography. Differential expression is based on comparison of visualized spots/proteins between gels or by sample labelling in gel-free systems. Identification of proteins is made by tryptic fragmentation of proteins, fragment mass determination and mass comparison with protein databases. Analysis of expression data sets interprets the complex protein changes into cellular mechanisms to generate hypotheses. The importance of such protein expression sets to elucidate islet cellular events is evidenced by the observation that only about 50% of the differentially expressed proteins and transcripts showed concordance when measured in parallel. Using protein profiling, different areas related to islet dysfunction in type 1 and type 2 diabetes mellitus have been addressed, including dysfunction induced by elevated levels of glucose and fatty acids and cytokines. Because islets from individuals with type 1 or type 2 diabetes mellitus have not yet been protein profiled, islets from rat (BB-DP) and mouse (NOD, ob/ob, MKR) models of the disease have been used, and mechanisms responsible for islet dysfunction delineated offering avenues of intervention.
Collapse
Affiliation(s)
- P Bergsten
- Department of Medical Cell Biology, Uppsala University, Sweden.
| |
Collapse
|
36
|
Abstract
Technological developments make mass spectrometry (MS)-based proteomics a central pillar of biochemical research. MS has been very successful in cell culture systems, where sample amounts are not limiting. To extend its capabilities to extremely small, physiologically distinct cell types isolated from tissue, we developed a high sensitivity chromatographic system that measures nanogram protein mixtures for 8 h with very high resolution. This technology is based on splitting gradient effluents into a capture capillary and provides an inherent technical replicate. In a single analysis, this allowed us to characterize kidney glomeruli isolated by laser capture microdissection to a depth of more than 2,400 proteins. From pooled pancreatic islets of Langerhans, another type of "miniorgan," we obtained an in-depth proteome of 6,873 proteins, many of them involved in diabetes. We quantitatively compared the proteome of single islets, containing 2,000-4,000 cells, treated with high or low glucose levels, and covered most of the characteristic functions of beta cells. Our ultrasensitive analysis recapitulated known hyperglycemic changes but we also find components up-regulated such as the mitochondrial stress regulator Park7. Direct proteomic analysis of functionally distinct cellular structures opens up perspectives in physiology and pathology.
Collapse
|
37
|
Zhang P, Ni X, Guo Y, Guo X, Wang Y, Zhou Z, Huo R, Sha J. Proteomic-based identification of maternal proteins in mature mouse oocytes. BMC Genomics 2009; 10:348. [PMID: 19646285 PMCID: PMC2730056 DOI: 10.1186/1471-2164-10-348] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 08/03/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mature mouse oocyte contains the full complement of maternal proteins required for fertilization, reprogramming, zygotic gene activation (ZGA), and the early stages of embryogenesis. However, due to limitations of traditional proteomics strategies, only a few abundantly expressed proteins have yet been identified. Our laboratory applied a more effective strategy: one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D SDS-PAGE) and reverse-phase liquid chromatography tandem mass spectrometry (RP-LC-MS/MS) were employed to analyze the mature oocyte proteome in depth. RESULTS Using this high-performance proteomic approach, we successfully identified 625 different proteins from 2700 mature mouse oocytes lacking zona pellucidae. This is the largest catalog of mature mouse oocyte proteins compiled to date. According to their pattern of expression, we screened 76 maternal proteins with high levels of mRNA expression both in oocytes and fertilized eggs. Many well-known maternal effect proteins were included in this subset, including MATER and NPM2. In addition, our mouse oocyte proteome was compared with a recently published mouse embryonic stem cell (ESC) proteome and 371 overlapping proteins were identified. CONCLUSION This proteomics analysis will be a valuable resource to aid in the characterization of important maternal proteins involved in oogenesis, fertilization, early embryonic development and in revealing their mechanisms of action.
Collapse
Affiliation(s)
- Ping Zhang
- Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, PR China.
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Leib RD, Flick TG, Williams ER. Direct quantitation of peptide mixtures without standards using clusters formed by electrospray ionization mass spectrometry. Anal Chem 2009; 81:3965-72. [PMID: 19354265 DOI: 10.1021/ac900294r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In electrospray ionization mass spectrometry, ion abundances depend on a number of different factors, including analyte surface activity, competition between analytes for charge, analyte concentration, as well as instrumental factors, including mass-dependent ion transmission and detection. Here, a novel method for obtaining quantitative information about solution-phase concentrations of peptide mixtures is described and demonstrated for five different peptide mixtures with relative concentrations ranging from 0.05% to 50%. In this method, the abundances of large clusters containing anywhere from 0 to 13 impurity molecules are measured and directly related to the relative solution-phase concentration of the peptides. For clusters containing approximately 15 or more peptides, the composition of the clusters approaches the statistical value indicating that these clusters are formed nonspecifically and that any differences in ion detection or ionization efficiency are negligible at these large cluster sizes. This method is accurate to within approximately 20% or better, even when the relative ion intensities of the protonated monomers can differ by over an order of magnitude compared to their solution-phase concentrations. Although less accurate than other quantitation methods that employ internal standards, this method does have the key advantages of speed, simplicity, and the ability to quantitate components in solution even when the identities of the components are unknown.
Collapse
Affiliation(s)
- Ryan D Leib
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
| | | | | |
Collapse
|
39
|
Abstract
Type 1 and type 2 diabetes mellitus together are predicted to affect over 300 million people worldwide by the year 2020. A relative or absolute paucity of functional β-cells is a central feature of both types of disease, and identifying the pathways that mediate the embryonic origin of new β-cells and mechanisms that underlie the proliferation of existing β-cells are major efforts in the fields of developmental and islet biology. A poor secretory response of existing β-cells to nutrients and hormones and the defects in hormone processing also contribute to the hyperglycemia observed in type 2 diabetes and has prompted studies aimed at enhancing β-cell function. The factors that contribute to a greater susceptibility in aging individuals to develop diabetes is currently unclear and may be linked to a poor turnover of β-cells and/or enhanced susceptibility of β-cells to apoptosis. This review is an update on the recent work in the areas of islet/β-cell regeneration and hormone processing that are relevant to the pathophysiology of the endocrine pancreas in type 1, type 2 and obesity-associated diabetes.
Collapse
Affiliation(s)
- Anke Assmann
- Research Division, Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | | | | |
Collapse
|