1
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Fiametti LO, Correa CN, Castro LMD. Peptide Profile of Zebrafish Brain in a 6-OHDA-Induced Parkinson Model. Zebrafish 2021; 18:55-65. [PMID: 33570475 DOI: 10.1089/zeb.2020.1945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease (PD) is a chronic neurodegenerative disorder mainly attributed to the progressive loss of dopaminergic neurons in the substantia nigra, which leads to uncontrolled voluntary movements causing tremors, postural instability, joint stiffness, and speech and locomotion difficulties, among other symptoms. Previous studies have shown the participation of specific peptides in neurodegenerative diseases. In this context, the present work analyzed changes in the peptide profile in zebrafish brain induced to parkinsonian conditions with 6-hydroxydopamine, using isotopic labeling techniques plus mass spectrometry. These analyses allowed the relative quantitation and identification of 118 peptides. Of these, nine peptides showed significant changes, one peptide was increased and eight decreased. The most altered sequences were fragment of cytosolic and extracellular proteins related to lipid metabolism and dynamic cytoskeleton. These results open new perspectives of study about the function of peptides in PD.
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Affiliation(s)
| | - Claudia Neves Correa
- Bioscience Institute, Sao Paulo State University (UNESP), Sao Vicente, Brazil.,Biodiversity of Coastal Environments Postgraduate Program, Bioscience Institute, Sao Paulo State University (UNESP), Sao Vicente, Brazil
| | - Leandro Mantovani de Castro
- Bioscience Institute, Sao Paulo State University (UNESP), Sao Vicente, Brazil.,Biodiversity of Coastal Environments Postgraduate Program, Bioscience Institute, Sao Paulo State University (UNESP), Sao Vicente, Brazil
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2
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Furlan S, Campione M, Murgia M, Mosole S, Argenton F, Volpe P, Nori A. Calsequestrins New Calcium Store Markers of Adult Zebrafish Cerebellum and Optic Tectum. Front Neuroanat 2020; 14:15. [PMID: 32372920 PMCID: PMC7188384 DOI: 10.3389/fnana.2020.00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/18/2020] [Indexed: 12/26/2022] Open
Abstract
Calcium stores in neurons are heterogeneous in compartmentalization and molecular composition. Danio rerio (zebrafish) is an animal model with a simply folded cerebellum similar in cellular organization to that of mammals. The aim of the study was to identify new endoplasmic reticulum (ER) calcium store markers in zebrafish adult brain with emphasis on cerebellum and optic tectum. By quantitative polymerase chain reaction, we found three RNA transcripts coding for the intra-ER calcium binding protein calsequestrin: casq1a, casq1b, and casq2. In brain homogenates, two isoforms were detected by mass spectrometry and western blotting. Fractionation experiments of whole brain revealed that Casq1a and Casq2 were enriched in a heavy fraction containing ER microsomes and synaptic membranes. By in situ hybridization, we found the heterogeneous expression of casq1a and casq2 mRNA to be compatible with the cellular localization of calsequestrins investigated by immunofluorescence. Casq1 was expressed in neurogenic differentiation 1 expressing the granule cells of the cerebellum and the periventricular zone of the optic tectum. Casq2 was concentrated in parvalbumin expressing Purkinje cells. At a subcellular level, Casq1 was restricted to granular cell bodies, and Casq2 was localized in cell bodies, dendrites, and axons. Data are discussed in relation to the differential cellular and subcellular distribution of other cerebellum calcium store markers and are evaluated with respect to the putative relevance of calsequestrins in the neuron-specific functional activity.
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Affiliation(s)
- Sandra Furlan
- Consiglio Nazionale delle Ricerche, Institute of Neuroscience, Padova, Italy
| | - Marina Campione
- Consiglio Nazionale delle Ricerche, Institute of Neuroscience, Padova, Italy
| | - Marta Murgia
- Department of Biomedical Sciences, University of Padova, Istituto Interuniversitario di Miologia, Padova, Italy.,Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Simone Mosole
- Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | | | - Pompeo Volpe
- Department of Biomedical Sciences, University of Padova, Istituto Interuniversitario di Miologia, Padova, Italy
| | - Alessandra Nori
- Department of Biomedical Sciences, University of Padova, Istituto Interuniversitario di Miologia, Padova, Italy
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3
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Brandt C, Nolte H, Henschke S, Engström Ruud L, Awazawa M, Morgan DA, Gabel P, Sprenger HG, Hess ME, Günther S, Langer T, Rahmouni K, Fenselau H, Krüger M, Brüning JC. Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation. Cell 2019; 175:1321-1335.e20. [PMID: 30445039 DOI: 10.1016/j.cell.2018.10.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/10/2018] [Accepted: 10/02/2018] [Indexed: 12/17/2022]
Abstract
Adaptation of liver to the postprandial state requires coordinated regulation of protein synthesis and folding aligned with changes in lipid metabolism. Here we demonstrate that sensory food perception is sufficient to elicit early activation of hepatic mTOR signaling, Xbp1 splicing, increased expression of ER-stress genes, and phosphatidylcholine synthesis, which translate into a rapid morphological ER remodeling. These responses overlap with those activated during refeeding, where they are maintained and constantly increased upon nutrient supply. Sensory food perception activates POMC neurons in the hypothalamus, optogenetic activation of POMC neurons activates hepatic mTOR signaling and Xbp1 splicing, whereas lack of MC4R expression attenuates these responses to sensory food perception. Chemogenetic POMC-neuron activation promotes sympathetic nerve activity (SNA) subserving the liver, and norepinephrine evokes the same responses in hepatocytes in vitro and in liver in vivo as observed upon sensory food perception. Collectively, our experiments unravel that sensory food perception coordinately primes postprandial liver ER adaption through a melanocortin-SNA-mTOR-Xbp1s axis. VIDEO ABSTRACT.
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Affiliation(s)
- Claus Brandt
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Hendrik Nolte
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, Cologne 50931, Germany
| | - Sinika Henschke
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Linda Engström Ruud
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Motoharu Awazawa
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Donald A Morgan
- Department of Pharmacology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 3181 MERF, 375 Newton Rd., Iowa City, IA 52242, USA
| | - Paula Gabel
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | | | - Martin E Hess
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, Parkstr. 1, 61231 Bad Nauheim, Germany
| | - Thomas Langer
- Institute for Genetics, University of Cologne, Cologne 50931, Germany; Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Kamal Rahmouni
- Department of Pharmacology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 3181 MERF, 375 Newton Rd., Iowa City, IA 52242, USA
| | - Henning Fenselau
- Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Synaptic Transmission in Energy Homeostasis Group, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany
| | - Marcus Krüger
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, Cologne 50931, Germany
| | - Jens C Brüning
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; National Center for Diabetes Research (DZD), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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4
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Ruud J, Alber J, Tokarska A, Engström Ruud L, Nolte H, Biglari N, Lippert R, Lautenschlager Ä, Cieślak PE, Szumiec Ł, Hess ME, Brönneke HS, Krüger M, Nissbrandt H, Korotkova T, Silberberg G, Rodriguez Parkitna J, Brüning JC. The Fat Mass and Obesity-Associated Protein (FTO) Regulates Locomotor Responses to Novelty via D2R Medium Spiny Neurons. Cell Rep 2019; 27:3182-3198.e9. [DOI: 10.1016/j.celrep.2019.05.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 12/14/2018] [Accepted: 05/09/2019] [Indexed: 12/17/2022] Open
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5
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aPKC controls endothelial growth by modulating c-Myc via FoxO1 DNA-binding ability. Nat Commun 2018; 9:5357. [PMID: 30559384 PMCID: PMC6297234 DOI: 10.1038/s41467-018-07739-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
Strict regulation of proliferation is vital for development, whereas unregulated cell proliferation is a fundamental characteristic of cancer. The polarity protein atypical protein kinase C lambda/iota (aPKCλ) is associated with cell proliferation through unknown mechanisms. In endothelial cells, suppression of aPKCλ impairs proliferation despite hyperactivated mitogenic signaling. Here we show that aPKCλ phosphorylates the DNA binding domain of forkhead box O1 (FoxO1) transcription factor, a gatekeeper of endothelial growth. Although mitogenic signaling excludes FoxO1 from the nucleus, consequently increasing c-Myc abundance and proliferation, aPKCλ controls c-Myc expression via FoxO1/miR-34c signaling without affecting its localization. We find this pathway is strongly activated in the malignant vascular sarcoma, angiosarcoma, and aPKC inhibition reduces c-Myc expression and proliferation of angiosarcoma cells. Moreover, FoxO1 phosphorylation at Ser218 and aPKC expression correlates with poor patient prognosis. Our findings may provide a potential therapeutic strategy for treatment of malignant cancers, like angiosarcoma. The cell polarity regulator aPKC is associated with cell proliferation but the precise mechanism are unknown. Here, the authors find that aPKC lambda phosphorylates the FoxO1 transcription factor, a gatekeeper of endothelial growth, during both angiogenesis and angiosarcomas.
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6
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Sialana FJ, Schneebauer G, Paunkov A, Pelster B, Lubec G. Proteomic Studies on the Swim Bladder of the European Eel (Anguilla anguilla). Proteomics 2018; 18:e1700445. [PMID: 29469228 DOI: 10.1002/pmic.201700445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/08/2018] [Indexed: 01/07/2023]
Abstract
The swim bladder of a fish is a vital organ that with gas gland cells in the swim bladder wall enables key physiological functions including buoyancy regulation in the face of different hydrostatic pressures. Specific gas gland cells produce and secrete acidic metabolites into the blood in order to reduce the physical solubility of gases and blood gas transport capacity for regulating the volume of the swim bladder. Transcriptomic analyses have provided evidence at the RNA level but no specific studies at the protein level have been carried out so far. Herein, it was the aim of the study to show swim bladder proteins of the yellow stage European eel by label-free LCMS (Q-Exactive Plus) that resulted in the identification of 6223 protein groups. Neurotransmitter receptors and transporters were enriched in the membrane fraction and enzymes for acid production were observed. The list of identified proteins may represent a useful tool for further proteomics experiments on this organ. All MS proteomics data are available at the PRIDE repository with the dataset identifier PXD007850.
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Affiliation(s)
- Fernando J Sialana
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Gabriel Schneebauer
- Institute of Zoology, University of Innsbruck, Innsbruck, Austria.,Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Ana Paunkov
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Bernd Pelster
- Institute of Zoology, University of Innsbruck, Innsbruck, Austria.,Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Gert Lubec
- Paracelsus Private Medical University, Salzburg, Austria
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7
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Neurovascular EGFL7 regulates adult neurogenesis in the subventricular zone and thereby affects olfactory perception. Nat Commun 2017; 8:15922. [PMID: 28656980 PMCID: PMC5493759 DOI: 10.1038/ncomms15922] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/11/2017] [Indexed: 01/19/2023] Open
Abstract
Adult neural stem cells reside in a specialized niche in the subventricular zone (SVZ). Throughout life they give rise to adult-born neurons in the olfactory bulb (OB), thus contributing to neural plasticity and pattern discrimination. Here, we show that the neurovascular protein EGFL7 is secreted by endothelial cells and neural stem cells (NSCs) of the SVZ to shape the vascular stem-cell niche. Loss of EGFL7 causes an accumulation of activated NSCs, which display enhanced activity and re-entry into the cell cycle. EGFL7 pushes activated NSCs towards quiescence and neuronal progeny towards differentiation. This is achieved by promoting Dll4-induced Notch signalling at the blood vessel-stem cell interface. Fewer inhibitory neurons form in the OB of EGFL7-knockout mice, which increases the absolute signal conducted from the mitral cell layer of the OB but decreases neuronal network synchronicity. Consequently, EGFL7-knockout mice display severe physiological defects in olfactory behaviour and perception. The vascular stem cell niche regulates the proliferation and differentiation of neural stem cells (NSCs) in the adult subventricular zone. Here the authors identify EGFL7 as a neurovascular regulator of NSCs in vivo; EGFL7-knockout mice show reduced neurogenesis, and exhibit impaired olfactory perception and behaviour.
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8
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Bayés À, Collins MO, Reig-Viader R, Gou G, Goulding D, Izquierdo A, Choudhary JS, Emes RD, Grant SGN. Evolution of complexity in the zebrafish synapse proteome. Nat Commun 2017; 8:14613. [PMID: 28252024 PMCID: PMC5337974 DOI: 10.1038/ncomms14613] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/15/2017] [Indexed: 11/09/2022] Open
Abstract
The proteome of human brain synapses is highly complex and is mutated in over 130 diseases. This complexity arose from two whole-genome duplications early in the vertebrate lineage. Zebrafish are used in modelling human diseases; however, its synapse proteome is uncharacterized, and whether the teleost-specific genome duplication (TSGD) influenced complexity is unknown. We report the characterization of the proteomes and ultrastructure of central synapses in zebrafish and analyse the importance of the TSGD. While the TSGD increases overall synapse proteome complexity, the postsynaptic density (PSD) proteome of zebrafish has lower complexity than mammals. A highly conserved set of ∼1,000 proteins is shared across vertebrates. PSD ultrastructural features are also conserved. Lineage-specific proteome differences indicate that vertebrate species evolved distinct synapse types and functions. The data sets are a resource for a wide range of studies and have important implications for the use of zebrafish in modelling human synaptic diseases.
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Affiliation(s)
- Àlex Bayés
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Maria Claret 167, 08025 Barcelona, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Bellaterra, Spain
| | - Mark O. Collins
- Department of Biomedical Science, The Centre for Membrane Interactions and Dynamics, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Rita Reig-Viader
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Maria Claret 167, 08025 Barcelona, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Bellaterra, Spain
| | - Gemma Gou
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Maria Claret 167, 08025 Barcelona, Spain
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Bellaterra, Spain
| | - David Goulding
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Abril Izquierdo
- School of Veterinary Medicine and Science, University of Nottingham. Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Jyoti S. Choudhary
- Proteomic Mass Spectrometry, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Richard D. Emes
- School of Veterinary Medicine and Science, University of Nottingham. Sutton Bonington Campus, Leicestershire LE12 5RD, UK
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Seth G. N. Grant
- Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh EH16 4SB, UK
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9
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Lehmann WD. A timeline of stable isotopes and mass spectrometry in the life sciences. MASS SPECTROMETRY REVIEWS 2017; 36:58-85. [PMID: 26919394 DOI: 10.1002/mas.21497] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
This review retraces the role of stable isotopes and mass spectrometry in the life sciences. The timeline is divided into four segments covering the years 1920-1950, 1950-1980, 1980-2000, and 2000 until today. For each period methodic progress and typical applications are discussed. Application of stable isotopes is driven by improvements of mass spectrometry, chromatography, and related fields in sensitivity, mass accuracy, structural specificity, complex sample handling ability, data output, and data evaluation. We currently experience the vision of omics-type analyses, that is, the comprehensive identification and quantification of a complete compound class within one or a few analytical runs. This development is driven by stable isotopes without competition by radioisotopes. In metabolic studies as classic field of isotopic tracer experiments, stable isotopes and radioisotopes were competing solutions, with stable isotopes as the long-term junior partner. Since the 1990s the number of metabolic studies with radioisotopes decreases, whereas stable isotope studies retain their slow but stable upward tendency. Unique fields of stable isotopes are metabolic tests in newborns, metabolic experiments in healthy controls, newborn screening for inborn errors, quantification of drugs and drug metabolites in doping control, natural isotope fractionation in geology, ecology, food authentication, or doping control, and more recently the field of quantitative omics-type analyses. There, cells or whole organisms are systematically labeled with stable isotopes to study proteomic differences or specific responses to stimuli or genetic manipulation. The duo of stable isotopes and mass spectrometry will probably continue to grow in the life sciences, since it delivers reference-quality quantitative data with molecular specificity, often combined with informative isotope effects. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:58-85, 2017.
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Affiliation(s)
- Wolf D Lehmann
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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10
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Wai T, Saita S, Nolte H, Müller S, König T, Richter-Dennerlein R, Sprenger HG, Madrenas J, Mühlmeister M, Brandt U, Krüger M, Langer T. The membrane scaffold SLP2 anchors a proteolytic hub in mitochondria containing PARL and the i-AAA protease YME1L. EMBO Rep 2016; 17:1844-1856. [PMID: 27737933 DOI: 10.15252/embr.201642698] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 02/05/2023] Open
Abstract
The SPFH (stomatin, prohibitin, flotillin, HflC/K) superfamily is composed of scaffold proteins that form ring-like structures and locally specify the protein-lipid composition in a variety of cellular membranes. Stomatin-like protein 2 (SLP2) is a member of this superfamily that localizes to the mitochondrial inner membrane (IM) where it acts as a membrane organizer. Here, we report that SLP2 anchors a large protease complex composed of the rhomboid protease PARL and the i-AAA protease YME1L, which we term the SPY complex (for SLP2-PARL-YME1L). Association with SLP2 in the SPY complex regulates PARL-mediated processing of PTEN-induced kinase PINK1 and the phosphatase PGAM5 in mitochondria. Moreover, SLP2 inhibits the stress-activated peptidase OMA1, which can bind to SLP2 and cleaves PGAM5 in depolarized mitochondria. SLP2 restricts OMA1-mediated processing of the dynamin-like GTPase OPA1 allowing stress-induced mitochondrial hyperfusion under starvation conditions. Together, our results reveal an important role of SLP2 membrane scaffolds for the spatial organization of IM proteases regulating mitochondrial dynamics, quality control, and cell survival.
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Affiliation(s)
- Timothy Wai
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Shotaro Saita
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Hendrik Nolte
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Sebastian Müller
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Tim König
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Ricarda Richter-Dennerlein
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Hans-Georg Sprenger
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Joaquin Madrenas
- Microbiome and Disease Tolerance Centre, Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Mareike Mühlmeister
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ulrich Brandt
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marcus Krüger
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany
| | - Thomas Langer
- Institute for Genetics Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), and University of Cologne, Cologne, Germany .,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
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11
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Smidak R, Aradska J, Kirchberger S, Distel M, Sialana FJ, Wackerlig J, Mechtcheriakova D, Lubec G. A detailed proteomic profiling of plasma membrane from zebrafish brain. Proteomics Clin Appl 2016; 10:1264-1268. [PMID: 27459904 DOI: 10.1002/prca.201600081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/29/2016] [Accepted: 07/21/2016] [Indexed: 12/11/2022]
Abstract
Zebrafish (Danio rerio) is a well-established model organism in developmental biology and disease modeling. In recent years, an increasing amount of studies used zebrafish to analyze the genetic changes underlying various neurological disorders. The brain plasma membrane proteome represents the major subsets of signaling proteins and promising drug targets, but is often understudied due to traditional experimental difficulties including problems with solubility, detergent removal, or low abundance. Here, we report a comprehensive dataset of the proteins identified in the enriched plasma membrane of the zebrafish brain by applying sequential trypsin/chymotrypsin digestion with multidimensional LC-MS/MS. A total number of 97 017 peptide groups corresponding to 9201 proteins were identified. These were annotated in various molecular functions or neurological disorders. The dataset of the current study provides a useful data source for further utilizing zebrafish in basic and clinical neuroscience.
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Affiliation(s)
- Roman Smidak
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Jana Aradska
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Stefanie Kirchberger
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Innovative Cancer Models, Vienna, Austria
| | - Martin Distel
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Innovative Cancer Models, Vienna, Austria
| | | | - Judith Wackerlig
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Diana Mechtcheriakova
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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12
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Williamson JC, Edwards AVG, Verano-Braga T, Schwämmle V, Kjeldsen F, Jensen ON, Larsen MR. High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis: Observations and implications. Proteomics 2016; 16:907-14. [PMID: 26791339 DOI: 10.1002/pmic.201400545] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/19/2015] [Accepted: 01/12/2016] [Indexed: 11/05/2022]
Abstract
We present basic workups and quantitative comparisons for two current generation Orbitrap mass spectrometers, the Q Exactive Plus and Orbitrap Fusion Tribrid, which are widely considered two of the highest performing instruments on the market. We assessed the performance of two quantitative methods on both instruments, namely label-free quantitation and stable isotope labeling using isobaric tags, for studying the heat shock response in Escherichia coli. We investigated the recently reported MS3 method on the Fusion instrument and the potential of MS3-based reporter ion isolation Synchronous Precursor Selection (SPS) and its impact on quantitative accuracy. We confirm that the label-free approach offers a more linear response with a wider dynamic range than MS/MS-based isobaric tag quantitation and that the MS3/SPS approach alleviates but does not eliminate dynamic range compression. We observed, however, that the choice of quantitative approach had little impact on the ability to statistically evaluate the E. coli heat shock response. We conclude that in the experimental conditions tested, MS/MS-based reporter ion quantitation provides reliable biological insight despite the issue of compressed dynamic range, an observation that significantly impacts the choice of instrument.
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Affiliation(s)
- James C Williamson
- Protein Research Group, VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Alistair V G Edwards
- Protein Research Group, VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Thiago Verano-Braga
- Protein Research Group, VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.,Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Veit Schwämmle
- Protein Research Group, VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Frank Kjeldsen
- Protein Research Group, VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ole N Jensen
- Protein Research Group, VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R Larsen
- Protein Research Group, VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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Nolte H, Hölper S, Housley MP, Islam S, Piller T, Konzer A, Stainier DYR, Braun T, Krüger M. Dynamics of zebrafish fin regeneration using a pulsed SILAC approach. Proteomics 2015; 15:739-51. [PMID: 25504979 DOI: 10.1002/pmic.201400316] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 01/03/2023]
Abstract
The zebrafish owns remarkable regenerative capacities allowing regeneration of several tissues, including the heart, liver, and brain. To identify protein dynamics during fin regeneration we used a pulsed SILAC approach that enabled us to detect the incorporation of (13) C6 -lysine (Lys6) into newly synthesized proteins. Samples were taken at four different time points from noninjured and regrowing fins and incorporation rates were monitored using a combination of single-shot 4-h gradients and high-resolution tandem MS. We identified more than 5000 labeled proteins during the first 3 weeks of fin regeneration and were able to monitor proteins that are responsible for initializing and restoring the shape of these appendages. The comparison of Lys6 incorporation rates between noninjured and regrowing fins enabled us to identify proteins that are directly involved in regeneration. For example, we observed increased incorporation rates of two actinodin family members at the actinotrichia, which is a hairlike fiber structure at the tip of regrowing fins. Moreover, we used quantitative real-time RNA measurements of several candidate genes, including osteoglycin, si:ch211-288h17.3, and prostaglandin reductase 1 to correlate the mRNA expression to Lys6 incorporation data. This novel pulsed SILAC methodology in fish can be used as a versatile tool to monitor newly synthesized proteins and will help to characterize protein dynamics during regenerative processes in zebrafish beyond fin regeneration.
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Affiliation(s)
- Hendrik Nolte
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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14
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Czopka T. Insights into mechanisms of central nervous system myelination using zebrafish. Glia 2015; 64:333-49. [PMID: 26250418 DOI: 10.1002/glia.22897] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 12/12/2022]
Abstract
Myelin is the multi-layered membrane that surrounds most axons and is produced by oligodendrocytes in the central nervous system (CNS). In addition to its important role in enabling rapid nerve conduction, it has become clear in recent years that myelin plays additional vital roles in CNS function. Myelinating oligodendrocytes provide metabolic support to axons and active myelination is even involved in regulating forms of learning and memory formation. However, there are still large gaps in our understanding of how myelination by oligodendrocytes is regulated. The small tropical zebrafish has become an increasingly popular model organism to investigate many aspects of nervous system formation, function, and regeneration. This is mainly due to two approaches for which the zebrafish is an ideally suited vertebrate model--(1) in vivo live cell imaging using vital dyes and genetically encoded reporters, and (2) gene and target discovery using unbiased screens. This review summarizes how the use of zebrafish has helped understand mechanisms of oligodendrocyte behavior and myelination in vivo and discusses the potential use of zebrafish to shed light on important future questions relating to myelination in the context of CNS development, function and repair.
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Affiliation(s)
- Tim Czopka
- Institute of Neuronal Cell Biology, Technische Universität München, Munich, Germany
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15
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Radev Z, Hermel JM, Elipot Y, Bretaud S, Arnould S, Duchateau P, Ruggiero F, Joly JS, Sohm F. A TALEN-Exon Skipping Design for a Bethlem Myopathy Model in Zebrafish. PLoS One 2015. [PMID: 26221953 PMCID: PMC4519248 DOI: 10.1371/journal.pone.0133986] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Presently, human collagen VI-related diseases such as Ullrich congenital muscular dystrophy (UCMD) and Bethlem myopathy (BM) remain incurable, emphasizing the need to unravel their etiology and improve their treatments. In UCMD, symptom onset occurs early, and both diseases aggravate with ageing. In zebrafish fry, morpholinos reproduced early UCMD and BM symptoms but did not allow to study the late phenotype. Here, we produced the first zebrafish line with the human mutation frequently found in collagen VI-related disorders such as UCMD and BM. We used a transcription activator-like effector nuclease (TALEN) to design the col6a1ama605003-line with a mutation within an essential splice donor site, in intron 14 of the col6a1 gene, which provoke an in-frame skipping of exon 14 in the processed mRNA. This mutation at a splice donor site is the first example of a template-independent modification of splicing induced in zebrafish using a targetable nuclease. This technique is readily expandable to other organisms and can be instrumental in other disease studies. Histological and ultrastructural analyzes of homozygous and heterozygous mutant fry and 3 months post-fertilization (mpf) fish revealed co-dominantly inherited abnormal myofibers with disorganized myofibrils, enlarged sarcoplasmic reticulum, altered mitochondria and misaligned sarcomeres. Locomotion analyzes showed hypoxia-response behavior in 9 mpf col6a1 mutant unseen in 3 mpf fish. These symptoms worsened with ageing as described in patients with collagen VI deficiency. Thus, the col6a1ama605003-line is the first adult zebrafish model of collagen VI-related diseases; it will be instrumental both for basic research and drug discovery assays focusing on this type of disorders.
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Affiliation(s)
- Zlatko Radev
- UMS 1374, AMAGEN, INRA, Jouy en Josas, Domaine de Vilvert, France
- UMS 3504, AMAGEN, CNRS, Gif-sur-Yvette, France
| | - Jean-Michel Hermel
- UMR 9197, INRA-CASBAH team, NEURO-Psi, CNRS, Gif sur Yvette, France
- * E-mail: (FS); (JMH)
| | - Yannick Elipot
- UMR 9197, DECA team, NEURO-Psi, CNRS, Gif sur Yvette, France
| | - Sandrine Bretaud
- UMR 5242, Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Lyon, France
| | | | | | - Florence Ruggiero
- UMR 5242, Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Lyon, France
| | | | - Frédéric Sohm
- UMS 1374, AMAGEN, INRA, Jouy en Josas, Domaine de Vilvert, France
- UMS 3504, AMAGEN, CNRS, Gif-sur-Yvette, France
- * E-mail: (FS); (JMH)
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16
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Rossi A, Kontarakis Z, Gerri C, Nolte H, Hölper S, Krüger M, Stainier DYR. Genetic compensation induced by deleterious mutations but not gene knockdowns. Nature 2015; 524:230-3. [PMID: 26168398 DOI: 10.1038/nature14580] [Citation(s) in RCA: 853] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 05/22/2015] [Indexed: 01/04/2023]
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17
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Alli Shaik A, Wee S, Li RHX, Li Z, Carney TJ, Mathavan S, Gunaratne J. Functional Mapping of the Zebrafish Early Embryo Proteome and Transcriptome. J Proteome Res 2014; 13:5536-50. [DOI: 10.1021/pr5005136] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Asfa Alli Shaik
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Sheena Wee
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Rachel Hai Xia Li
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Zhen Li
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, 138672, Singapore
| | - Tom J. Carney
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
- Lee
Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang
Avenue, 639798, Singapore
| | - Sinnakaruppan Mathavan
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, 138672, Singapore
| | - Jayantha Gunaratne
- Institute
of Molecular and Cell Biology, Agency for Science, Technology and Research, 61 Biopolis Drive, 138673, Singapore
- Lee
Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang
Avenue, 639798, Singapore
- Department
of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, 117597, Singapore
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18
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Hustoft HK, Vehus T, Brandtzaeg OK, Krauss S, Greibrokk T, Wilson SR, Lundanes E. Open tubular lab-on-column/mass spectrometry for targeted proteomics of nanogram sample amounts. PLoS One 2014; 9:e106881. [PMID: 25222838 PMCID: PMC4164520 DOI: 10.1371/journal.pone.0106881] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/09/2014] [Indexed: 12/28/2022] Open
Abstract
A novel open tubular nanoproteomic platform featuring accelerated on-line protein digestion and high-resolution nano liquid chromatography mass spectrometry (LC-MS) has been developed. The platform features very narrow open tubular columns, and is hence particularly suited for limited sample amounts. For enzymatic digestion of proteins, samples are passed through a 20 µm inner diameter (ID) trypsin + endoproteinase Lys-C immobilized open tubular enzyme reactor (OTER). Resulting peptides are subsequently trapped on a monolithic pre-column and transferred on-line to a 10 µm ID porous layer open tubular (PLOT) liquid chromatography LC separation column. Wnt/ß-catenein signaling pathway (Wnt-pathway) proteins of potentially diagnostic value were digested+detected in targeted-MS/MS mode in small cell samples and tumor tissues within 120 minutes. For example, a potential biomarker Axin1 was identifiable in just 10 ng of sample (protein extract of ∼1,000 HCT15 colon cancer cells). In comprehensive mode, the current OTER-PLOT set-up could be used to identify approximately 1500 proteins in HCT15 cells using a relatively short digestion+detection cycle (240 minutes), outperforming previously reported on-line digestion/separation systems. The platform is fully automated utilizing common commercial instrumentation and parts, while the reactor and columns are simple to produce and have low carry-over. These initial results point to automated solutions for fast and very sensitive MS based proteomics, especially for samples of limited size.
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Affiliation(s)
| | - Tore Vehus
- Department of Chemistry, University of Oslo, Oslo, Norway
| | | | - Stefan Krauss
- Unit for Cell Signaling, Cancer Stem Cell Innovation Center, Oslo University Hospital, Oslo, Norway
| | - Tyge Greibrokk
- Department of Chemistry, University of Oslo, Oslo, Norway
| | | | - Elsa Lundanes
- Department of Chemistry, University of Oslo, Oslo, Norway
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19
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Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS, Subbannayya T, Selvan LDN, Wang CH, Datta KK, Woo S, Dwivedi SB, Renuse S, Getnet D, Huang TC, Kim MS, Pinto SM, Mitchell CJ, Madugundu AK, Kumar P, Sharma J, Advani J, Dey G, Balakrishnan L, Syed N, Nanjappa V, Subbannayya Y, Goel R, Prasad TSK, Bafna V, Sirdeshmukh R, Gowda H, Wang C, Leach SD, Pandey A. Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Mol Cell Proteomics 2014; 13:3184-98. [PMID: 25060758 DOI: 10.1074/mcp.m114.038299] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Accurate annotation of protein-coding genes is one of the primary tasks upon the completion of whole genome sequencing of any organism. In this study, we used an integrated transcriptomic and proteomic strategy to validate and improve the existing zebrafish genome annotation. We undertook high-resolution mass-spectrometry-based proteomic profiling of 10 adult organs, whole adult fish body, and two developmental stages of zebrafish (SAT line), in addition to transcriptomic profiling of six organs. More than 7,000 proteins were identified from proteomic analyses, and ∼ 69,000 high-confidence transcripts were assembled from the RNA sequencing data. Approximately 15% of the transcripts mapped to intergenic regions, the majority of which are likely long non-coding RNAs. These high-quality transcriptomic and proteomic data were used to manually reannotate the zebrafish genome. We report the identification of 157 novel protein-coding genes. In addition, our data led to modification of existing gene structures including novel exons, changes in exon coordinates, changes in frame of translation, translation in annotated UTRs, and joining of genes. Finally, we discovered four instances of genome assembly errors that were supported by both proteomic and transcriptomic data. Our study shows how an integrative analysis of the transcriptome and the proteome can extend our understanding of even well-annotated genomes.
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Affiliation(s)
- Dhanashree S Kelkar
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Elayne Provost
- §Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205
| | - Raghothama Chaerkady
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Babylakshmi Muthusamy
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Srikanth S Manda
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Tejaswini Subbannayya
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Lakshmi Dhevi N Selvan
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Chieh-Huei Wang
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Keshava K Datta
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡‡School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Sunghee Woo
- §§Department of Computer Science, University of California, San Diego, California 92093
| | - Sutopa B Dwivedi
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Santosh Renuse
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Derese Getnet
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Tai-Chung Huang
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Min-Sik Kim
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Sneha M Pinto
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Christopher J Mitchell
- ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205
| | - Anil K Madugundu
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Praveen Kumar
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Jyoti Sharma
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Jayshree Advani
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Gourav Dey
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Lavanya Balakrishnan
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‖‖Department of Biotechnology, Kuvempu University, Shimoga 577 451, India
| | - Nazia Syed
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Vishalakshi Nanjappa
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India
| | - Yashwanth Subbannayya
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Renu Goel
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - T S Keshava Prasad
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ‡Amrita School of Biotechnology, Amrita University, Kollam 690 525, India; ‖Centre of Excellence in Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India; ¶¶Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India
| | - Vineet Bafna
- §§Department of Computer Science, University of California, San Diego, California 92093
| | - Ravi Sirdeshmukh
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Harsha Gowda
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Charles Wang
- The Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350;
| | - Steven D Leach
- §Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21205; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205;
| | - Akhilesh Pandey
- From the *Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India; ¶McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205; **Departments of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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