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Dupree EJ, Manzoor Z, Alwine S, Crimmins BS, Holsen TM, Darie CC. Proteomic analysis of the lake trout (Salvelinus namaycush) heart and blood: The beginning of a comprehensive lake trout protein database. Proteomics 2021; 22:e2100146. [PMID: 34676671 DOI: 10.1002/pmic.202100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022]
Abstract
Lake trout (Salvelinus namaycush) are a top-predator species in the Laurentian Great Lakes that are often used as bioindicators of chemical stressors in the ecosystem. Although many studies are done using these fish to determine concentrations of stressors like legacy persistent, bioaccumulative and toxic chemicals, there are currently no proteomic studies on the biological effects these stressors have on the ecosystem. This lack of proteomic studies on Great Lakes lake trout is because there is currently no complete, comprehensive protein database for this species. Here, we employed proteomics approaches to develop a lake trout protein database that could aid in future research on this fish, in particular exposomics and adductomics. The current study utilized heart tissue and blood from two lake trout. Our previous work using lake trout liver revealed 4194 potential protein hits in the NCBI databases and 3811 potential protein hits in the UniProtKB databases. In the current study, using the NCBI databases we identified 838 proteins for the heart and 580 proteins for the blood tissues in the biological replicate 1 (BR1) and 1180 potential protein hits for the heart and 561 potential protein hits for the blood in BR2. Similar results were obtained using the UniProtKB databases. This study builds on our previous work by continuing to build the first comprehensive lake trout protein database and provides insight into protein homology through evolutionary relationships. This data is available via the PRIDE partner repository with the dataset identifier PXD023970.
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Affiliation(s)
- Emmalyn J Dupree
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
| | - Zaen Manzoor
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
| | - Shelby Alwine
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
| | - Bernard S Crimmins
- Department of Civil and Environmental Engineering, Clarkson University, Potsdam, New York, USA
- AEACS, LLC, New Kensington, Pennsylvania, USA
| | - Thomas M Holsen
- Department of Civil and Environmental Engineering, Clarkson University, Potsdam, New York, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York, USA
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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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Dupree EJ, Crimmins BS, Holsen TM, Darie CC. Proteomic Analysis of the Lake Trout (Salvelinus namaycush) Liver Identifies Proteins from Evolutionarily Close and -Distant Fish Relatives. Proteomics 2019; 19:e1800429. [PMID: 31578773 DOI: 10.1002/pmic.201800429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 09/12/2019] [Indexed: 12/20/2022]
Abstract
Lake trout are used as bioindicators for toxics exposure in the Great Lakes ecosystem. Here the first lake trout (Salvelinus namaycush) liver proteomics study is performed and searched against specific databases: (NCBI and UniProtKB) Salvelinus, Salmonidae, Actinopterygii, and Oncorhynchus mykiss, and the more distant relative, Danio rerio. In the biological replicate 1 (BR1), technical replicate 1 (TR1), (BR1TR1), a large number of lake trout liver proteins are not in the Salvelinus protein database, suggesting that lake trout liver proteins have homology to some proteins from the Salmonidae family and Actinopterygii class, and to Oncorhynchus mykiss and Danio rerio, two more highly studied fish. In the NCBI search, 4194 proteins are identified: 3069 proteins in Actinopterygii, 1617 in Salmonidae, 68 in Salvelinus, 568 in Oncorhynchus mykiss, and 946 in Danio rerio protein databases. Similar results are observed in the UniProtKB searches of BR1RT1, as well as in a technical replicate (BR1TR2), and then in a second biological replicate experiment, with two technical replicates (BR2TR1 and BR2TR2). This study opens the possibility of identifying evolutionary relationships (i.e., adaptive mutations) between various groups (i.e., zebrafish, rainbow trout, Salmonidae, Salvelinus and lake trout) through evolutionary proteomics. Data are available via the PRIDE Q2 (PXD011924).
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Affiliation(s)
- Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA
| | - Bernard S Crimmins
- Department of Environmental Engineering, Clarkson University, Potsdam, NY, 13699-5708, USA.,AEACS, LLC, New Kensington, PA, 15068, USA
| | - Thomas M Holsen
- Department of Environmental Engineering, Clarkson University, Potsdam, NY, 13699-5708, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA
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Developing Well-Annotated Species-Specific Protein Databases Using Comparative Proteogenomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:389-400. [PMID: 31347060 DOI: 10.1007/978-3-030-15950-4_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proteomics is a mass spectrometry-based discipline that aims to analyze proteomes and their functions. Many proteomic studies require well-developed protein databases for reference. However, most proteomes are not well-annotated, aside from model organisms. Techniques like six-frame translation, ab initio gene prediction, and EST databases can aid in maximizing the amount of proteins identified in proteomics experiments, however, each of these has its downfalls. Proteogenomics is a term used to describe the union of proteomics, genomics and transcriptomics to assist in the identification of peptides which would help build better annotated proteome databases. Here, current proteomic and proteogenomic methods will be reviewed, and an example of a comparative proteomics method using lake trout liver samples will be described.
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Haq N, Schmidt-Hieber C, Sialana FJ, Ciani L, Heller JP, Stewart M, Bentley L, Wells S, Rodenburg RJ, Nolan PM, Forsythe E, Wu MC, Lubec G, Salinas P, Häusser M, Beales PL, Christou-Savina S. Loss of Bardet-Biedl syndrome proteins causes synaptic aberrations in principal neurons. PLoS Biol 2019; 17:e3000414. [PMID: 31479441 PMCID: PMC6743795 DOI: 10.1371/journal.pbio.3000414] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 09/13/2019] [Accepted: 08/19/2019] [Indexed: 02/07/2023] Open
Abstract
Bardet-Biedl syndrome (BBS), a ciliopathy, is a rare genetic condition characterised by retinal degeneration, obesity, kidney failure, and cognitive impairment. In spite of progress made in our general understanding of BBS aetiology, the molecular and cellular mechanisms underlying cognitive impairment in BBS remain elusive. Here, we report that the loss of BBS proteins causes synaptic dysfunction in principal neurons, providing a possible explanation for the cognitive impairment phenotype observed in BBS patients. Using synaptosomal proteomics and immunocytochemistry, we demonstrate the presence of Bbs proteins in the postsynaptic density (PSD) of hippocampal neurons. Loss of Bbs results in a significant reduction of dendritic spines in principal neurons of Bbs mouse models. Furthermore, we show that spine deficiency correlates with events that destabilise spine architecture, such as impaired spine membrane receptor signalling, known to be involved in the maintenance of dendritic spines. Our findings suggest a role for BBS proteins in dendritic spine homeostasis that may be linked to the cognitive phenotype observed in BBS.
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Affiliation(s)
- Naila Haq
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Christoph Schmidt-Hieber
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Fernando J. Sialana
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Lorenza Ciani
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Janosch P. Heller
- Institute of Neurology, University College London, London, United Kingdom
| | - Michelle Stewart
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Liz Bentley
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Sara Wells
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Richard J. Rodenburg
- Radboud Center for Mitochondrial Medicine, Translational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Patrick M. Nolan
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Elizabeth Forsythe
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Michael C. Wu
- Neurodigitech, LLC, San Diego, California, United States of America
| | - Gert Lubec
- Programme in Proteomics, Paracelsus Private Medical University, Salzburg, Austria
| | - P. Salinas
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Michael Häusser
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Philip L. Beales
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sofia Christou-Savina
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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Facchin F, Alviano F, Canaider S, Bianconi E, Rossi M, Bonsi L, Casadei R, Biava PM, Ventura C. Early Developmental Zebrafish Embryo Extract to Modulate Senescence in Multisource Human Mesenchymal Stem Cells. Int J Mol Sci 2019; 20:ijms20112646. [PMID: 31146388 PMCID: PMC6600478 DOI: 10.3390/ijms20112646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/24/2019] [Accepted: 05/25/2019] [Indexed: 12/14/2022] Open
Abstract
Stem cells undergo senescence both in vivo, contributing to the progressive decline in self-healing mechanisms, and in vitro during prolonged expansion. Here, we show that an early developmental zebrafish embryo extract (ZF1) could act as a modulator of senescence in human mesenchymal stem cells (hMSCs) isolated from both adult tissues, including adipose tissue (hASCs), bone marrow (hBM-MSCs), dental pulp (hDP-MSCs), and a perinatal tissue such as the Wharton’s Jelly (hWJ-MSCs). In all the investigated hMSCs, ZF1 decreased senescence-associated β-galactosidase (SA β-gal) activity and enhanced the transcription of TERT, encoding the catalytic telomerase core. In addition, it was associated, only in hASCs, with a transcriptional induction of BMI1, a pleiotropic repressor of senescence. In hBM-MSCs, hDP-MSCs, and hWJ-MSCs, TERT over-expression was concomitant with a down-regulation of two repressors of TERT, TP53 (p53), and CDKN1A (p21). Furthermore, ZF1 increased the natural ability of hASCs to perform adipogenesis. These results indicate the chance of using ZF1 to modulate stem cell senescence in a source-related manner, to be potentially used as a tool to affect stem cell senescence in vitro. In addition, its anti-senescence action could also set the basis for future in vivo approaches promoting tissue rejuvenation bypassing stem cell transplantation.
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Affiliation(s)
- Federica Facchin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
- National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)-Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy.
| | - Francesco Alviano
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
| | - Silvia Canaider
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
- National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)-Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy.
| | - Eva Bianconi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
- National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)-Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy.
| | - Martina Rossi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
| | - Laura Bonsi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
| | - Raffaella Casadei
- Department for Life Quality Studies (QuVi), University of Bologna, Corso D'Augusto 237, 47921 Rimini, Italy.
| | - Pier Mario Biava
- Scientific Institute of Research and Care Multimedica, Via Milanese 300, 20099 Sesto San Giovanni (Milano), Italy.
| | - Carlo Ventura
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
- National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)-Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy.
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Smidak R, Sialana FJ, Kristofova M, Stojanovic T, Rajcic D, Malikovic J, Feyissa DD, Korz V, Hoeger H, Wackerlig J, Mechtcheriakova D, Lubec G. Reduced Levels of the Synaptic Functional Regulator FMRP in Dentate Gyrus of the Aging Sprague-Dawley Rat. Front Aging Neurosci 2017; 9:384. [PMID: 29218006 PMCID: PMC5703695 DOI: 10.3389/fnagi.2017.00384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/09/2017] [Indexed: 11/15/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) encoded by Fragile X mental retardation 1 (FMR1) gene is a RNA-binding regulator of mRNA translation, transport and stability with multiple targets responsible for proper synaptic function. Epigenetic silencing of FMR1 gene expression leads to the development of Fragile X syndrome (FXS) that is characterized by intellectual disability and other behavioral problems including autism. In the rat FXS model, the lack of FMRP caused a deficit in hippocampal-dependent memory. However, the hippocampal changes of FMRP in aging rats are not fully elucidated. The current study addresses the changes in FMRP levels in dentate gyrus (DG) from young (17 weeks) and aging (22 months) Sprague – Dawley rats. The aging animal group showed significant decline in spatial reference memory. Protein samples from five rats per each group were analyzed by quantitative proteomic analysis resulting in 153 significantly changed proteins. FMRP showed significant reduction in aging animals which was confirmed by immunoblotting and immunofluorescence microscopy. Furthermore, bioinformatic analysis of the differential protein dataset revealed several functionally related protein groups with individual interactions with FMRP. These include high representation of the RNA translation and processing machinery connected to FMRP and other RNA-binding regulators including CAPRIN1, the members of Pumilio (PUM) and CUG-BP, Elav-like (CELF) family, and YTH N(6)-methyladenosine RNA-binding proteins (YTHDF). The results of the current study point to the important role of FMRP and regulation of RNA processing in the rat DG and memory decline during the aging process.
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Affiliation(s)
- Roman Smidak
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Fernando J Sialana
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Martina Kristofova
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Tamara Stojanovic
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Dragana Rajcic
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Jovana Malikovic
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Daniel D Feyissa
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Volker Korz
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Vienna, Austria
| | - Harald Hoeger
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Vienna, Austria
| | - Judit 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.,Neuroproteomics, Paracelsus Private Medical University, Salzburg, Austria
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