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Lu G, Tran VNH, Wu W, Ma M, Li L. Neuropeptidomics of the American Lobster Homarus americanus. J Proteome Res 2024; 23:1757-1767. [PMID: 38644788 PMCID: PMC11118981 DOI: 10.1021/acs.jproteome.3c00925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The American lobster, Homarus americanus, is not only of considerable economic importance but has also emerged as a premier model organism in neuroscience research. Neuropeptides, an important class of cell-to-cell signaling molecules, play crucial roles in a wide array of physiological and psychological processes. Leveraging the recently sequenced high-quality draft genome of the American lobster, our study sought to profile the neuropeptidome of this model organism. Employing advanced mass spectrometry techniques, we identified 24 neuropeptide precursors and 101 unique mature neuropeptides in Homarus americanus. Intriguingly, 67 of these neuropeptides were discovered for the first time. Our findings provide a comprehensive overview of the peptidomic attributes of the lobster's nervous system and highlight the tissue-specific distribution of these neuropeptides. Collectively, this research not only enriches our understanding of the neuronal complexities of the American lobster but also lays a foundation for future investigations into the functional roles that these peptides play in crustacean species. The mass spectrometry data have been deposited in the PRIDE repository with the identifier PXD047230.
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Affiliation(s)
- Gaoyuan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Vu Ngoc Huong Tran
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States
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2
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Wiggenhorn AL, Abuzaid HZ, Coassolo L, Li VL, Tanzo JT, Wei W, Lyu X, Svensson KJ, Long JZ. A class of secreted mammalian peptides with potential to expand cell-cell communication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543503. [PMID: 37333131 PMCID: PMC10274650 DOI: 10.1101/2023.06.02.543503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Peptide hormones and neuropeptides are fundamental signaling molecules that control diverse aspects of mammalian homeostasis and physiology. Here we demonstrate the endogenous presence of a sequence diverse class of orphan, blood-borne peptides that we call "capped peptides." Capped peptides are fragments of secreted proteins and defined by the presence of two post-translational modifications - N-terminal pyroglutamylation and C-terminal amidation - which function as chemical "caps" of the intervening sequence. Capped peptides share many regulatory characteristics in common with that of other signaling peptides, including dynamic regulation in blood plasma by diverse environmental and physiologic stimuli. One capped peptide, CAP-TAC1, is a tachykinin neuropeptide-like molecule and a nanomolar agonist of multiple mammalian tachykinin receptors. A second capped peptide, CAP-GDF15, is a 12-mer peptide that reduces food intake and body weight. Capped peptides therefore define a largely unexplored class of circulating molecules with potential to regulate cell-cell communication in mammalian physiology.
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Affiliation(s)
- Amanda L. Wiggenhorn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Hind Z. Abuzaid
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Laetitia Coassolo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Veronica L. Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Julia T. Tanzo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Katrin J. Svensson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Jonathan Z. Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
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3
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Dang X, Coimbra R, Mao L, Podvin S, Li X, Yu H, Costantini TW, Zeng X, Larocca D, Eliceiri BP, Baird A. Open reading frame mining identifies a TLR4 binding domain in the primary sequence of ECRG4. Cell Mol Life Sci 2019; 76:5027-5039. [PMID: 31190084 PMCID: PMC11105628 DOI: 10.1007/s00018-019-03159-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/29/2019] [Accepted: 05/22/2019] [Indexed: 01/22/2023]
Abstract
The embedding of small peptide ligands within large inactive pre-pro-precursor proteins encoded by orphan open reading frames (ORFs) makes them difficult to identify and study. To address this problem, we generated oligonucleotide (< 100-400 base pair) combinatorial libraries from either the epidermal growth factor (EGF) ORF that encodes the > 1200 amino acid EGF precursor protein or the orphan ECRG4 ORF, that encodes a 148 amino acid Esophageal Cancer Related Gene 4 (ECRG4), a putative cytokine precursor protein of up to eight ligands. After phage display and 3-4 rounds of biopanning for phage internalization into prostate cancer epithelial cells, sequencing identified the 53-amino acid EGF ligand encoded by the 5' region of the EGF ORF and three distinct domains within the primary sequence of ECRG4: its membrane targeting hydrophobic signal peptide, an unanticipated amino terminus domain at ECRG437-63 and a C-terminus ECRG4133-148 domain. Using HEK-blue cells transfected with the innate immunity receptor complex, we show that both ECRG437-63 and ECRG4133-148 enter cells by interaction with the TLR4 immune complex but neither stimulate NFkB. Taken together, the results help establish that phage display can be used to identify cryptic domains within ORFs of the human secretome and identify a novel TLR4-targeted internalization domain in the amino terminus of ECRG4 that may contribute to its effects on cell migration, immune cell activation and tumor suppression.
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Affiliation(s)
- Xitong Dang
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | - Raul Coimbra
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
| | - Liang Mao
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | - Sonia Podvin
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
| | - Xue Li
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | - Hua Yu
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | - Todd W Costantini
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
| | - Xiaorong Zeng
- The Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, China
| | | | - Brian P Eliceiri
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA
| | - Andrew Baird
- Department of Surgery, University of California San Diego, San Diego, CA, 92103, USA.
- Department of Surgery, University of California San Diego, La Jolla, San Diego, CA, 98896, USA.
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4
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Hayakawa E, Watanabe H, Menschaert G, Holstein TW, Baggerman G, Schoofs L. A combined strategy of neuropeptide prediction and tandem mass spectrometry identifies evolutionarily conserved ancient neuropeptides in the sea anemone Nematostella vectensis. PLoS One 2019; 14:e0215185. [PMID: 31545805 PMCID: PMC6756747 DOI: 10.1371/journal.pone.0215185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/29/2019] [Indexed: 11/19/2022] Open
Abstract
Neuropeptides are a class of bioactive peptides shown to be involved in various physiological processes, including metabolism, development, and reproduction. Although neuropeptide candidates have been predicted from genomic and transcriptomic data, comprehensive characterization of neuropeptide repertoires remains a challenge owing to their small size and variable sequences. De novo prediction of neuropeptides from genome or transcriptome data is difficult and usually only efficient for those peptides that have identified orthologs in other animal species. Recent peptidomics technology has enabled systematic structural identification of neuropeptides by using the combination of liquid chromatography and tandem mass spectrometry. However, reliable identification of naturally occurring peptides using a conventional tandem mass spectrometry approach, scanning spectra against a protein database, remains difficult because a large search space must be scanned due to the absence of a cleavage enzyme specification. We developed a pipeline consisting of in silico prediction of candidate neuropeptides followed by peptide-spectrum matching. This approach enables highly sensitive and reliable neuropeptide identification, as the search space for peptide-spectrum matching is highly reduced. Nematostella vectensis is a basal eumetazoan with one of the most ancient nervous systems. We scanned the Nematostella protein database for sequences displaying structural hallmarks typical of eumetazoan neuropeptide precursors, including amino- and carboxyterminal motifs and associated modifications. Peptide-spectrum matching was performed against a dataset of peptides that are cleaved in silico from these putative peptide precursors. The dozens of newly identified neuropeptides display structural similarities to bilaterian neuropeptides including tachykinin, myoinhibitory peptide, and neuromedin-U/pyrokinin, suggesting these neuropeptides occurred in the eumetazoan ancestor of all animal species.
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Affiliation(s)
- Eisuke Hayakawa
- Research Group of Functional Genomics and Proteomics, KU Leuven, Leuven, Belgium
- Evolutionary Neurobiology Unit, Okinawa Institute of Science & Technology, Okinawa, Japan
- * E-mail:
| | - Hiroshi Watanabe
- Evolutionary Neurobiology Unit, Okinawa Institute of Science & Technology, Okinawa, Japan
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Gerben Menschaert
- Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Thomas W. Holstein
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Geert Baggerman
- CFP/Ceproma, University Antwerpen, Antwerpen, Belgium
- VITO, Applied Bio & molecular Systems (ABS), Mol, Belgium
| | - Liliane Schoofs
- Research Group of Functional Genomics and Proteomics, KU Leuven, Leuven, Belgium
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5
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Michno W, Wehrli PM, Blennow K, Zetterberg H, Hanrieder J. Molecular imaging mass spectrometry for probing protein dynamics in neurodegenerative disease pathology. J Neurochem 2018; 151:488-506. [PMID: 30040875 DOI: 10.1111/jnc.14559] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022]
Abstract
Recent advances in the understanding of basic pathological mechanisms in various neurological diseases depend directly on the development of novel bioanalytical technologies that allow sensitive and specific chemical imaging at high resolution in cells and tissues. Mass spectrometry-based molecular imaging (IMS) has gained increasing popularity in biomedical research for mapping the spatial distribution of molecular species in situ. The technology allows for comprehensive, untargeted delineation of in situ distribution profiles of metabolites, lipids, peptides and proteins. A major advantage of IMS over conventional histochemical techniques is its superior molecular specificity. Imaging mass spectrometry has therefore great potential for probing molecular regulations in CNS-derived tissues and cells for understanding neurodegenerative disease mechanism. The goal of this review is to familiarize the reader with the experimental workflow, instrumental developments and methodological challenges as well as to give a concise overview of the major advances and recent developments and applications of IMS-based protein and peptide profiling with particular focus on neurodegenerative diseases. This article is part of the Special Issue "Proteomics".
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Affiliation(s)
- Wojciech Michno
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Patrick M Wehrli
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, UK.,Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
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6
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Corbière A, Walet-Balieu ML, Chan P, Basille-Dugay M, Hardouin J, Vaudry D. A Peptidomic Approach to Characterize Peptides Involved in Cerebellar Cortex Development Leads to the Identification of the Neurotrophic Effects of Nociceptin. Mol Cell Proteomics 2018; 17:1737-1749. [PMID: 29895708 PMCID: PMC6126386 DOI: 10.1074/mcp.ra117.000184] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/16/2018] [Indexed: 12/20/2022] Open
Abstract
The cerebellum is a brain structure involved in motor and cognitive functions. The development of the cerebellar cortex (the external part of the cerebellum) is under the control of numerous factors. Among these factors, neuropeptides including PACAP or somatostatin modulate the survival, migration and/or differentiation of cerebellar granule cells. Interestingly, such peptides contributing to cerebellar ontogenesis usually exhibit a specific transient expression profile with a low abundance at birth, a high expression level during the developmental processes, which take place within the first two postnatal weeks in rodents, and a gradual decline toward adulthood. Thus, to identify new peptides transiently expressed in the cerebellum during development, rat cerebella were sampled from birth to adulthood, and analyzed by a semi-quantitative peptidomic approach. A total of 33 peptides were found to be expressed in the cerebellum. Among these 33 peptides, 8 had a clear differential expression pattern during development, 4 of them i.e. cerebellin 2, nociceptin, somatostatin and VGF [353-372], exhibiting a high expression level during the first two postnatal weeks followed by a significative decrease at adulthood. A focus by a genomic approach on nociceptin, confirmed that its precursor mRNA is transiently expressed during the first week of life in granule neurons within the internal granule cell layer of the cerebellum, and showed that the nociceptin receptor is also actively expressed between P8 and P16 by the same neurons. Finally, functional studies revealed a new role for nociceptin, acting as a neurotrophic peptide able to promote the survival and differentiation of developing cerebellar granule neurons.
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Affiliation(s)
- Auriane Corbière
- From the ‡Normandie Univ, UNIROUEN, Inserm, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Neuropeptides, Neuronal death and Cell plasticity team, 76000 Rouen, France
| | - Marie-Laure Walet-Balieu
- §Normandie Univ, UNIROUEN, Rouen Proteomic Platform (PISSARO), Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - Philippe Chan
- §Normandie Univ, UNIROUEN, Rouen Proteomic Platform (PISSARO), Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - Magali Basille-Dugay
- From the ‡Normandie Univ, UNIROUEN, Inserm, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Neuropeptides, Neuronal death and Cell plasticity team, 76000 Rouen, France
| | - Julie Hardouin
- §Normandie Univ, UNIROUEN, Rouen Proteomic Platform (PISSARO), Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
| | - David Vaudry
- From the ‡Normandie Univ, UNIROUEN, Inserm, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Neuropeptides, Neuronal death and Cell plasticity team, 76000 Rouen, France;
- §Normandie Univ, UNIROUEN, Rouen Proteomic Platform (PISSARO), Institute for Research and Innovation in Biomedicine (IRIB), 76000 Rouen, France
- ¶Normandie Univ, UNIROUEN, Regional Cell Imaging Platform of Normandy (PRIMACEN), 76000 Rouen, France
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7
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DeAtley KL, Colgrave ML, Cánovas A, Wijffels G, Ashley RL, Silver GA, Rincon G, Medrano JF, Islas-Trejo A, Fortes MRS, Reverter A, Porto-Neto L, Lehnert SA, Thomas MG. Neuropeptidome of the Hypothalamus and Pituitary Gland of Indicine × Taurine Heifers: Evidence of Differential Neuropeptide Processing in the Pituitary Gland before and after Puberty. J Proteome Res 2018; 17:1852-1865. [PMID: 29510626 DOI: 10.1021/acs.jproteome.7b00875] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Puberty in cattle is regulated by an endocrine axis, which includes a complex milieu of neuropeptides in the hypothalamus and pituitary gland. The neuropeptidome of hypothalamic-pituitary gland tissue of pre- (PRE) and postpubertal (POST) Bos indicus-influenced heifers was characterized, followed by quantitative analysis of 51 fertility-related neuropeptides in these tissues. Comparison of peptide abundances with gene expression levels allowed assessment of post-transcriptional peptide processing. On the basis of classical cleavage, 124 mature neuropeptides from 35 precursor proteins were detected in hypothalamus and pituitary gland tissues of three PRE and three POST Brangus heifers. An additional 19 peptides (cerebellins, PEN peptides) previously reported as neuropeptides that did not follow classical cleavage were also identified. In the pre-pubertal hypothalamus, a greater diversity of neuropeptides (25.8%) was identified relative to post-pubertal heifers, while in the pituitary gland, 38.6% more neuropeptides were detected in the post-pubertal heifers. Neuro-tissues of PRE and POST heifers revealed abundance differences ( p < 0.05) in peptides from protein precursors involved in packaging and processing (e.g., the granin family and ProSAAS) or neuron stimulation (PENK, CART, POMC, cerebellins). On their own, the transcriptome data of the precursor genes could not predict the neuropeptide profile in the exact same tissues in several cases. This provides further evidence of the importance of differential processing of the neuropeptide precursors in the pituitary before and after puberty.
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Affiliation(s)
- Kasey L DeAtley
- Department of Animal and Range Sciences , New Mexico State University , Las Cruces , New Mexico 88003 , United States
| | - Michelle L Colgrave
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences , University of Guelph , Guelph , Ontario N1G 2W1 , Canada
| | - Gene Wijffels
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Ryan L Ashley
- Department of Animal and Range Sciences , New Mexico State University , Las Cruces , New Mexico 88003 , United States
| | - Gail A Silver
- Department of Animal and Range Sciences , New Mexico State University , Las Cruces , New Mexico 88003 , United States
| | - Gonzalo Rincon
- Zoetis Animal Health , Kalamazoo , Michigan 49007 , United States
| | - Juan F Medrano
- Department of Animal Science , University of California , Davis , California 95616 , United States
| | - Alma Islas-Trejo
- Department of Animal Science , University of California , Davis , California 95616 , United States
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences , University of Queensland , St. Lucia , Queensland 4042 , Australia
- Queensland Alliance for Agriculture and Food Innovation, St. Lucia , Queensland 4072 , Australia
| | - Antonio Reverter
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Laercio Porto-Neto
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Sigrid A Lehnert
- CSIRO, Agriculture and Food , 306 Carmody Road , St. Lucia , Queensland 4067 , Australia
| | - Milton G Thomas
- Department of Animal Sciences , Colorado State University , Fort Collins , Colorado 80523 , United States
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8
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Hook V, Lietz CB, Podvin S, Cajka T, Fiehn O. Diversity of Neuropeptide Cell-Cell Signaling Molecules Generated by Proteolytic Processing Revealed by Neuropeptidomics Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:807-816. [PMID: 29667161 PMCID: PMC5946320 DOI: 10.1007/s13361-018-1914-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 05/23/2023]
Abstract
Neuropeptides are short peptides in the range of 3-40 residues that are secreted for cell-cell communication in neuroendocrine systems. In the nervous system, neuropeptides comprise the largest group of neurotransmitters. In the endocrine system, neuropeptides function as peptide hormones to coordinate intercellular signaling among target physiological systems. The diversity of neuropeptide functions is defined by their distinct primary sequences, peptide lengths, proteolytic processing of pro-neuropeptide precursors, and covalent modifications. Global, untargeted neuropeptidomics mass spectrometry is advantageous for defining the structural features of the thousands to tens of thousands of neuropeptides present in biological systems. Defining neuropeptide structures is the basis for defining the proteolytic processing pathways that convert pro-neuropeptides into active peptides. Neuropeptidomics has revealed that processing of pro-neuropeptides occurs at paired basic residues sites, and at non-basic residue sites. Processing results in neuropeptides with known functions and generates novel peptides representing intervening peptide domains flanked by dibasic residue processing sites, identified by neuropeptidomics. While very short peptide products of 2-4 residues are predicted from pro-neuropeptide dibasic processing sites, such peptides have not been readily identified; therefore, it will be logical to utilize metabolomics to identify very short peptides with neuropeptidomics in future studies. Proteolytic processing is accompanied by covalent post-translational modifications (PTMs) of neuropeptides comprising C-terminal amidation, N-terminal pyroglutamate, disulfide bonds, phosphorylation, sulfation, acetylation, glycosylation, and others. Neuropeptidomics can define PTM features of neuropeptides. In summary, neuropeptidomics for untargeted, global analyses of neuropeptides is essential for elucidation of proteases that generate diverse neuropeptides for cell-cell signaling. Graphical Abstract ᅟ.
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Affiliation(s)
- Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA.
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Christopher B Lietz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Sonia Podvin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Tomas Cajka
- West Coast Metabolomics Center, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA
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9
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Van Bael S, Zels S, Boonen K, Beets I, Schoofs L, Temmerman L. A Caenorhabditis elegans Mass Spectrometric Resource for Neuropeptidomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:879-889. [PMID: 29299835 DOI: 10.1007/s13361-017-1856-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/13/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Neuropeptides are important signaling molecules used by nervous systems to mediate and fine-tune neuronal communication. They can function as neurotransmitters or neuromodulators in neural circuits, or they can be released as neurohormones to target distant cells and tissues. Neuropeptides are typically cleaved from larger precursor proteins by the action of proteases and can be the subject of post-translational modifications. The short, mature neuropeptide sequences often entail the only evolutionarily reasonably conserved regions in these precursor proteins. Therefore, it is particularly challenging to predict all putative bioactive peptides through in silico mining of neuropeptide precursor sequences. Peptidomics is an approach that allows de novo characterization of peptides extracted from body fluids, cells, tissues, organs, or whole-body preparations. Mass spectrometry, often combined with on-line liquid chromatography, is a hallmark technique used in peptidomics research. Here, we used an acidified methanol extraction procedure and a quadrupole-Orbitrap LC-MS/MS pipeline to analyze the neuropeptidome of Caenorhabditis elegans. We identified an unprecedented number of 203 mature neuropeptides from C. elegans whole-body extracts, including 35 peptides from known, hypothetical, as well as from completely novel neuropeptide precursor proteins that have not been predicted in silico. This set of biochemically verified peptide sequences provides the most elaborate C. elegans reference neurpeptidome so far. To exploit this resource to the fullest, we make our in-house database of known and predicted neuropeptides available to the community as a valuable resource. We are providing these collective data to help the community progress, amongst others, by supporting future differential and/or functional studies. Graphical Abstract ᅟ.
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Affiliation(s)
- Sven Van Bael
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Sven Zels
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Kurt Boonen
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Isabel Beets
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Liliane Schoofs
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Leuven, Belgium.
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10
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Secher A, Kelstrup CD, Conde-Frieboes KW, Pyke C, Raun K, Wulff BS, Olsen JV. Analytic framework for peptidomics applied to large-scale neuropeptide identification. Nat Commun 2016; 7:11436. [PMID: 27142507 PMCID: PMC4857386 DOI: 10.1038/ncomms11436] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 03/24/2016] [Indexed: 01/03/2023] Open
Abstract
Large-scale mass spectrometry-based peptidomics for drug discovery is relatively unexplored because of challenges in peptide degradation and identification following tissue extraction. Here we present a streamlined analytical pipeline for large-scale peptidomics. We developed an optimized sample preparation protocol to achieve fast, reproducible and effective extraction of endogenous peptides from sub-dissected organs such as the brain, while diminishing unspecific protease activity. Each peptidome sample was analysed by high-resolution tandem mass spectrometry and the resulting data set was integrated with publically available databases. We developed and applied an algorithm that reduces the peptide complexity for identification of biologically relevant peptides. The developed pipeline was applied to rat hypothalamus and identifies thousands of neuropeptides and their post-translational modifications, which is combined in a resource format for visualization, qualitative and quantitative analyses. Neuropeptide research is challenged by technical difficulties in identifying new bioactive peptides. Here the authors present an analytical pipeline for large-scale peptidomics applied to the rat hypothalamus, identifying thousands of endogenous neuropeptides and their post-translational modifications.
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Affiliation(s)
- Anna Secher
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.,Histology and Imaging, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Maaloev, Denmark
| | - Christian D Kelstrup
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | | | - Charles Pyke
- Histology and Imaging, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Maaloev, Denmark
| | - Kirsten Raun
- Incretin &Obesity Pharmacology, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Maaloev, Denmark
| | - Birgitte S Wulff
- Incretin &Obesity Research, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Maaloev, Denmark
| | - Jesper V Olsen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
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11
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Hanrieder J, Malmberg P, Ewing AG. Spatial neuroproteomics using imaging mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:718-31. [PMID: 25582083 DOI: 10.1016/j.bbapap.2014.12.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/11/2014] [Accepted: 12/19/2014] [Indexed: 12/12/2022]
Abstract
The nervous system constitutes arguably the most complicated and least understood cellular network in the human body. This consequently manifests itself in the fact that the molecular bases of neurodegenerative diseases remain unknown. The limited understanding of neurobiological mechanisms relates directly to the lack of appropriate bioanalytical technologies that allow highly resolved, sensitive, specific and comprehensive molecular imaging in complex biological matrices. Imaging mass spectrometry (IMS) is an emerging technique for molecular imaging. The technique is characterized by its high chemical specificity allowing comprehensive, spatial protein and peptide profiling in situ. Imaging MS represents therefore a powerful approach for investigation of spatio-temporal protein and peptide regulations in CNS derived tissue and cells. This review aims to provide a concise overview of major developments and applications concerning imaging mass spectrometry based protein and peptide profiling in neurobiological and biomedical research. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Jörg Hanrieder
- National Center for Imaging Mass Spectrometry, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden; Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Institute of Neuroscience and Physiology, Department Psychiatry and Neurochemistry, University of Gothenburg, Sahlgrenska University Hospital Mölndal, Mölndal, Sweden
| | - Per Malmberg
- National Center for Imaging Mass Spectrometry, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden; Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew G Ewing
- National Center for Imaging Mass Spectrometry, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden; Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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12
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Schrader M, Schulz-Knappe P, Fricker LD. Historical perspective of peptidomics. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.02.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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13
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Zhang X, Petruzziello F, Rainer G. Extending the scope of neuropeptidomics in the mammalian brain. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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14
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Stingl C, Söderquist M, Karlsson O, Borén M, Luider TM. Uncovering Effects of Ex Vivo Protease Activity during Proteomics and Peptidomics Sample Extraction in Rat Brain Tissue by Oxygen-18 Labeling. J Proteome Res 2014; 13:2807-17. [DOI: 10.1021/pr401232e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Christoph Stingl
- Department
of Neurology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | | | - Oskar Karlsson
- Department
of Pharmaceutical Biosciences, Uppsala University, 751 05 Uppsala, Sweden
| | | | - Theo M. Luider
- Department
of Neurology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
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15
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Mériaux C, Franck J, Park DB, Quanico J, Kim YH, Chung CK, Park YM, Steinbusch H, Salzet M, Fournier I. Human temporal lobe epilepsy analyses by tissue proteomics. Hippocampus 2014; 24:628-42. [DOI: 10.1002/hipo.22246] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Céline Mériaux
- Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée-EA 4550, Bât SN3, 1 étage; Université de Lille 1; Villeneuve d'Ascq France
- EURON-European Graduate School of Neuroscience, Maastricht University; Maastricht The Netherlands
| | - Julien Franck
- Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée-EA 4550, Bât SN3, 1 étage; Université de Lille 1; Villeneuve d'Ascq France
- EURON-European Graduate School of Neuroscience, Maastricht University; Maastricht The Netherlands
| | - Dan Bi Park
- Division of Mass Spectrometry Research; Korea Basic Science Institute; Ochang Chungbuk Republic of Korea
- Graduate School of Analytical Science and Technology; Chungnam National University; Daejeon Republic of Korea
| | - Jusal Quanico
- Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée-EA 4550, Bât SN3, 1 étage; Université de Lille 1; Villeneuve d'Ascq France
- EURON-European Graduate School of Neuroscience, Maastricht University; Maastricht The Netherlands
| | - Young Hye Kim
- Division of Mass Spectrometry Research; Korea Basic Science Institute; Ochang Chungbuk Republic of Korea
| | - Chun Kee Chung
- Department of Neurosurgery; College of Medicine, Seoul National University; Seoul Republic of Korea
| | - Young Mok Park
- Division of Mass Spectrometry Research; Korea Basic Science Institute; Ochang Chungbuk Republic of Korea
- Graduate School of Analytical Science and Technology; Chungnam National University; Daejeon Republic of Korea
| | - Harry Steinbusch
- EURON-European Graduate School of Neuroscience, Maastricht University; Maastricht The Netherlands
- Department of Translational Neuroscience; Faculty of Health; Medicine & Life Sciences; Maastricht University; Maastricht The Netherlands
| | - Michel Salzet
- Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée-EA 4550, Bât SN3, 1 étage; Université de Lille 1; Villeneuve d'Ascq France
- EURON-European Graduate School of Neuroscience, Maastricht University; Maastricht The Netherlands
| | - Isabelle Fournier
- Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée-EA 4550, Bât SN3, 1 étage; Université de Lille 1; Villeneuve d'Ascq France
- EURON-European Graduate School of Neuroscience, Maastricht University; Maastricht The Netherlands
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16
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Southey BR, Lee JE, Zamdborg L, Atkins N, Mitchell JW, Li M, Gillette MU, Kelleher NL, Sweedler JV. Comparing label-free quantitative peptidomics approaches to characterize diurnal variation of peptides in the rat suprachiasmatic nucleus. Anal Chem 2013; 86:443-52. [PMID: 24313826 PMCID: PMC3886391 DOI: 10.1021/ac4023378] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Mammalian
circadian rhythm is maintained by the suprachiasmatic nucleus (SCN)
via an intricate set of neuropeptides and other signaling molecules.
In this work, peptidomic analyses from two times of day were examined
to characterize variation in SCN peptides using three different label-free
quantitation approaches: spectral count, spectra index and SIEVE.
Of the 448 identified peptides, 207 peptides were analyzed by two
label-free methods, spectral count and spectral index. There were
24 peptides with significant (adjusted p-value <
0.01) differential peptide abundances between daytime and nighttime,
including multiple peptides derived from secretogranin II, cocaine
and amphetamine regulated transcript, and proprotein convertase subtilisin/kexin
type 1 inhibitor. Interestingly, more peptides were analyzable and
had significantly different abundances between the two time points
using the spectral count and spectral index methods than with a prior
analysis using the SIEVE method with the same data. The results of
this study reveal the importance of using the appropriate data analysis
approaches for label-free relative quantitation of peptides. The detection
of significant changes in so rich a set of neuropeptides reflects
the dynamic nature of the SCN and the number of influences such as
feeding behavior on circadian rhythm. Using spectral count and spectral
index, peptide level changes are correlated to time of day, suggesting
their key role in circadian function.
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Affiliation(s)
- Bruce R Southey
- Department of Animal Sciences, ‡Department of Chemistry, §Institute for Genomic Biology, ∥Neuroscience Program, ⊥Department of Cell and Developmental Biology, and ¶Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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17
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Hayakawa E, Menschaert G, De Bock PJ, Luyten W, Gevaert K, Baggerman G, Schoofs L. Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation. J Proteome Res 2013; 12:5410-21. [PMID: 24032530 DOI: 10.1021/pr400446z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Tandem mass spectrometry (MS/MS) combined with bioinformatics tools have enabled fast and systematic protein identification based on peptide-to-spectrum matches. However, it remains challenging to obtain accurate identification of endogenous peptides, such as neuropeptides, peptide hormones, peptide pheromones, venom peptides, and antimicrobial peptides. Since these peptides are processed at sites that are difficult to predict reliably, the search of their MS/MS spectra in sequence databases needs to be done without any protease setting. In addition, many endogenous peptides carry various post-translational modifications, making it essential to take these into account in the database search. These characteristics of endogenous peptides result in a huge search space, frequently leading to poor confidence of the peptide characterizations in peptidomics studies. We have developed a new MS/MS spectrum search tool for highly accurate and confident identification of endogenous peptides by combining two different fragmentation methods. Our approach takes advantage of the combination of two independent fragmentation methods (collision-induced dissociation and electron transfer dissociation). Their peptide spectral matching is carried out separately in both methods, and the final score is built as a combination of the two separate scores. We demonstrate that this approach is very effective in discriminating correct peptide identifications from false hits. We applied this approach to a spectral data set of neuropeptides extracted from mouse pituitary tumor cells. Compared to conventional MS-based identification, i.e., using a single fragmentation method, our approach significantly increased the peptide identification rate. It proved also highly effective for scanning spectra against a very large search space, enabling more accurate genome-wide searches and searches including multiple potential post-translational modifications.
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Affiliation(s)
- Eisuke Hayakawa
- Research Group of Functional Genomics and Proteomics, KU Leuven , Leuven, Belgium
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18
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Jia C, Lietz CB, Ye H, Hui L, Yu Q, Yoo S, Li L. A multi-scale strategy for discovery of novel endogenous neuropeptides in the crustacean nervous system. J Proteomics 2013; 91:1-12. [PMID: 23806756 DOI: 10.1016/j.jprot.2013.06.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/26/2013] [Accepted: 06/16/2013] [Indexed: 12/18/2022]
Abstract
UNLABELLED The conventional mass spectrometry (MS)-based strategy is often inadequate for the comprehensive characterization of various size neuropeptides without the assistance of genomic information. This study evaluated sequence coverage of different size neuropeptides in two crustacean species, blue crab Callinectes sapidus and Jonah crab Cancer borealis using conventional MS methodologies and revealed limitations to mid- and large-size peptide analysis. Herein we attempt to establish a multi-scale strategy for simultaneous and confident sequence elucidation of various sizes of peptides in the crustacean nervous system. Nine novel neuropeptides spanning a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ, the sinus gland of the spiny lobster Panulirus interruptus. These novel neuropeptides included seven allatostatin (A- and B-type) peptides, one crustacean hyperglycemic hormone precursor-related peptide, and one crustacean hyperglycemic hormone. Highly accurate multi-scale characterization of a collection of varied size neuropeptides was achieved by integrating traditional data-dependent tandem MS, improved bottom-up sequencing, multiple fragmentation technique-enabled top-down sequencing, chemical derivatization, and in silico homology search. Collectively, the ability to characterize a neuropeptidome with vastly differing molecule sizes from a neural tissue extract could find great utility in unraveling complex signaling peptide mixtures employed by other biological systems. BIOLOGICAL SIGNIFICANCE Mass spectrometry (MS)-based neuropeptidomics aims to completely characterize the neuropeptides in a target organism as an important first step toward a better understanding of the structure and function of these complex signaling molecules. Although liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) with data-dependent acquisition is a powerful tool in peptidomic research, it often lacks the capability for de novo sequencing of mid-size and large peptides due to inefficient fragmentation of peptides larger than 4kDa. This study describes a multi-scale strategy for complete and confident sequence elucidation of various sizes of neuropeptides in the crustacean nervous system. The aim is to fill a technical gap where the conventional strategy is inefficient for comprehensive characterization of a complex neuropeptidome without assistance of genomic information. Nine novel neuropeptides in a wide range of molecular weights (0.9-8.2kDa) were fully sequenced from a major neuroendocrine organ of the spiny lobster, P. interruptus. The resulting molecular information extracted from such multi-scale peptidomic analysis will greatly accelerate functional studies of these novel neuropeptides.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy, University of Wisconsin-Madison, WI, USA; Department of Chemistry, University of Wisconsin-Madison, WI, USA
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19
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Karlsson O, Kultima K, Wadensten H, Nilsson A, Roman E, Andrén PE, Brittebo EB. Neurotoxin-induced neuropeptide perturbations in striatum of neonatal rats. J Proteome Res 2013; 12:1678-90. [PMID: 23410195 DOI: 10.1021/pr3010265] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The cyanobacterial toxin β-N-methylamino-l-alanine (BMAA) is suggested to play a role in neurodegenerative disease. We have previously shown that although the selective uptake of BMAA in the rodent neonatal striatum does not cause neuronal cell death, exposure during the neonatal development leads to cognitive impairments in adult rats. The aim of the present study was to characterize the changes in the striatal neuropeptide systems of male and female rat pups treated neonatally (postnatal days 9-10) with BMAA (40-460 mg/kg). The label-free quantification of the relative levels of endogenous neuropeptides using mass spectrometry revealed that 25 peptides from 13 neuropeptide precursors were significantly changed in the rat neonatal striatum. The exposure to noncytotoxic doses of BMAA induced a dose-dependent increase of neurosecretory protein VGF-derived peptides, and changes in the relative levels of cholecystokinin, chromogranin, secretogranin, MCH, somatostatin and cortistatin-derived peptides were observed at the highest dose. In addition, the results revealed a sex-dependent increase in the relative level of peptides derived from the proenkephalin-A and protachykinin-1 precursors, including substance P and neurokinin A, in female pups. Because several of these peptides play a critical role in the development and survival of neurons, the observed neuropeptide changes might be possible mediators of BMAA-induced behavioral changes. Moreover, some neuropeptide changes suggest potential sex-related differences in susceptibility toward this neurotoxin. The present study also suggests that neuropeptide profiling might provide a sensitive characterization of the BMAA-induced noncytotoxic effects on the developing brain.
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Affiliation(s)
- Oskar Karlsson
- Department of Pharmaceutical Biosciences, Uppsala University , SE-751 24 Uppsala, Sweden
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20
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Lee JE, Zamdborg L, Southey BR, Atkins N, Mitchell JW, Li M, Gillette MU, Kelleher NL, Sweedler JV. Quantitative peptidomics for discovery of circadian-related peptides from the rat suprachiasmatic nucleus. J Proteome Res 2013; 12:585-93. [PMID: 23256577 DOI: 10.1021/pr300605p] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In mammals the suprachiasmatic nucleus (SCN), the master circadian clock, is sensitive to light input via the optic chiasm and synchronizes many daily biological rhythms. Here we explore variations in the expression levels of neuropeptides present in the SCN of rats using a label-free quantification approach that is based on integrating peak intensities between daytime, Zeitgeber time (ZT) 6, and nighttime, ZT 18. From nine analyses comparing the levels between these two time points, 10 endogenous peptides derived from eight prohormones exhibited significant differences in their expression levels (adjusted p-value <0.05). Of these, seven peptides derived from six prohormones, including GRP, PACAP, and CART, exhibited ≥ 30% increases at ZT 18, and the VGRPEWWMDYQ peptide derived from proenkephalin A showed a >50% increase at nighttime. Several endogenous peptides showing statistically significant changes in this study have not been previously reported to alter their levels as a function of time of day, nor have they been implicated in prior functional SCN studies. This information on peptide expression changes serves as a resource for discovering unknown peptide regulators that affect circadian rhythms in the SCN.
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Affiliation(s)
- Ji Eun Lee
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, USA
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21
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Fouillen L, Petruzziello F, Veit J, Bhattacharyya A, Kretz R, Rainer G, Zhang X. Neuropeptide alterations in the tree shrew hypothalamus during volatile anesthesia. J Proteomics 2012; 80:311-9. [PMID: 23228960 DOI: 10.1016/j.jprot.2012.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/15/2012] [Accepted: 11/04/2012] [Indexed: 12/25/2022]
Abstract
Neuropeptides are critical signaling molecules, involved in the regulation of diverse physiological processes including energy metabolism, pain perception and brain cognitive state. Prolonged general anesthesia has an impact on many of these processes, but the regulation of peptides by general anesthetics is poorly understood. In this study, we present an in-depth characterization of the hypothalamic neuropeptides of the tree shrew during volatile isoflurane/nitrous oxide anesthesia administered accompanying a neurosurgical procedure. Using a predicted-peptide database and hybrid spectral analysis, we first identified 85 peptides from the tree shrew hypothalamus. Differential analysis was then performed between control and experimental group animals. The levels of 12 hypothalamic peptides were up-regulated following prolonged general anesthesia. Our study revealed for the first time that several neuropeptides, including alpha-neoendorphin and somatostatin-14, were altered during general anesthesia. Our study broadens the scope for the involvement of neuropeptides in volatile anesthesia regulation, opening the possibility for investigating the associated regulatory mechanisms.
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Affiliation(s)
- Laetitia Fouillen
- Visual Cognition Laboratory, Department of Medicine, University of Fribourg, Chemin du Musée 5, Fribourg, CH-1700, Switzerland
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22
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Ganesh V, Hettiarachchy NS. Nutriproteomics: A promising tool to link diet and diseases in nutritional research. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1107-17. [DOI: 10.1016/j.bbapap.2012.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 05/25/2012] [Accepted: 06/13/2012] [Indexed: 12/25/2022]
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23
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Menschaert G, Hayakawa E, Schoofs L, Van Criekinge W, Baggerman G. Spectral Clustering in Peptidomics Studies Allows Homology Searching and Modification Profiling: HomClus, a Versatile Tool. J Proteome Res 2012; 11:2774-85. [DOI: 10.1021/pr201114m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gerben Menschaert
- Faculty of Bioscience Engineering,
Laboratory for Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium
- Prometa, Interfaculty Center for Proteomics
and Metabolomics, K.U. Leuven, Leuven,
Belgium
| | - Eisuke Hayakawa
- Prometa, Interfaculty Center for Proteomics
and Metabolomics, K.U. Leuven, Leuven,
Belgium
- Research Group of
Functional Genomics and Proteomics, K.U. Leuven, 3000 Leuven, Belgium
| | - Liliane Schoofs
- Research Group of
Functional Genomics and Proteomics, K.U. Leuven, 3000 Leuven, Belgium
| | - Wim Van Criekinge
- Faculty of Bioscience Engineering,
Laboratory for Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Geert Baggerman
- VITO Nv, 2400 Mol, Belgium
- CFP, Center for Proteomics, 2020 Antwerpen, Belgium
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Hanrieder J, Ljungdahl A, Andersson M. MALDI imaging mass spectrometry of neuropeptides in Parkinson's disease. J Vis Exp 2012:3445. [PMID: 22370902 PMCID: PMC3529518 DOI: 10.3791/3445] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
MALDI imaging mass spectrometry (IMS) is a powerful approach that facilitates the spatial analysis of molecular species in biological tissue samples(2) (Fig.1). A 12 μm thin tissue section is covered with a MALDI matrix, which facilitates desorption and ionization of intact peptides and proteins that can be detected with a mass analyzer, typically using a MALDI TOF/TOF mass spectrometer. Generally hundreds of peaks can be assessed in a single rat brain tissue section. In contrast to commonly used imaging techniques, this approach does not require prior knowledge of the molecules of interest and allows for unsupervised and comprehensive analysis of multiple molecular species while maintaining high molecular specificity and sensitivity(2). Here we describe a MALDI IMS based approach for elucidating region-specific distribution profiles of neuropeptides in the rat brain of an animal model Parkinson's disease (PD). PD is a common neurodegenerative disease with a prevalence of 1% for people over 65 of age(3,4). The most common symptomatic treatment is based on dopamine replacement using L-DOPA(5). However this is accompanied by severe side effects including involuntary abnormal movements, termed L-DOPA-induced dyskinesias (LID)(1,3,6). One of the most prominent molecular change in LID is an upregulation of the opioid precursor prodynorphin mRNA(7). The dynorphin peptides modulate neurotransmission in brain areas that are essentially involved in movement control(7,8). However, to date the exact opioid peptides that originate from processing of the neuropeptide precursor have not been characterized. Therefore, we utilized MALDI IMS in an animal model of experimental Parkinson's disease and L-DOPA induced dyskinesia. MALDI imaging mass spectrometry proved to be particularly advantageous with respect to neuropeptide characterization, since commonly used antibody based approaches targets known peptide sequences and previously observed post-translational modifications. By contrast MALDI IMS can unravel novel peptide processing products and thus reveal new molecular mechanisms of neuropeptide modulation of neuronal transmission. While the absolute amount of neuropeptides cannot be determined by MALDI IMS, the relative abundance of peptide ions can be delineated from the mass spectra, giving insights about changing levels in health and disease. In the examples presented here, the peak intensities of dynorphin B, alpha-neoendorphin and substance P were found to be significantly increased in the dorsolateral, but not the dorsomedial, striatum of animals with severe dyskinesia involving facial, trunk and orolingual muscles (Fig. 5). Furthermore, MALDI IMS revealed a correlation between dyskinesia severity and levels of des-tyrosine alpha-neoendorphin, representing a previously unknown mechanism of functional inactivation of dynorphins in the striatum as the removal of N-terminal tyrosine reduces the dynorphin's opioid-receptor binding capacity(9). This is the first study on neuropeptide characterization in LID using MALDI IMS and the results highlight the potential of the technique for application in all fields of biomedical research.
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Affiliation(s)
- Jörg Hanrieder
- Department of Pharmaceutical Biosciences, Uppsala University
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25
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Ranc V, Petruzziello F, Kretz R, Argandoña EG, Zhang X, Rainer G. Broad characterization of endogenous peptides in the tree shrew visual system. J Proteomics 2012; 75:2526-35. [PMID: 22326962 DOI: 10.1016/j.jprot.2012.01.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/14/2012] [Accepted: 01/23/2012] [Indexed: 12/01/2022]
Abstract
Endogenous neuropeptides, acting as neurotransmitters or hormones in the brain, carry out important functions including neural plasticity, metabolism and angiogenesis. Previous neuropeptide studies have focused on peptide-rich brain regions such as the striatum or hypothalamus. Here we present an investigation of peptides in the visual system, composed of brain regions that are generally less rich in peptides, with the aim of providing the first broad overview of peptides involved in mammalian visual functions. We target three important parts of the visual system: the primary visual cortex (V1), lateral geniculate nucleus (LGN) and superior colliculus (SC). Our study is performed in the tree shrew, a close relative of primates. Using a combination of data dependent acquisition and targeted LC-MS/MS based neuropeptidomics; we identified a total of 52 peptides from the tree shrew visual system. A total of 26 peptides, for example GAV and neuropeptide K were identified in the visual system for the first time. Out of the total 52 peptides, 27 peptides with high signal-to-noise-ratio (>10) in extracted ion chromatograms (EIC) were subjected to label-free quantitation. We observed generally lower abundance of peptides in the LGN compared to V1 and SC. Consistently, a number of individual peptides showed high abundance in V1 (such as neuropeptide Y or somatostatin 28) and in SC (such as somatostatin 28 AA1-12). This study provides the first in-depth characterization of peptides in the mammalian visual system. These findings now permit the investigation of neuropeptide-regulated mechanisms of visual perception.
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Affiliation(s)
- Vaclav Ranc
- University of Fribourg, Department of Medicine, Fribourg, Switzerland
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Kim MH, Vickers E, von Gersdorff H. Patch-clamp capacitance measurements and Ca²⁺ imaging at single nerve terminals in retinal slices. J Vis Exp 2012:3345. [PMID: 22297269 PMCID: PMC3329771 DOI: 10.3791/3345] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Visual stimuli are detected and conveyed over a wide dynamic range of light intensities and frequency changes by specialized neurons in the vertebrate retina. Two classes of retinal neurons, photoreceptors and bipolar cells, accomplish this by using ribbon-type active zones, which enable sustained and high-throughput neurotransmitter release over long time periods. ON-type mixed bipolar cell (Mb) terminals in the goldfish retina, which depolarize to light stimuli and receive mixed rod and cone photoreceptor input, are suitable for the study of ribbon-type synapses both due to their large size (~10-12 μm diameter) and to their numerous lateral and reciprocal synaptic connections with amacrine cell dendrites. Direct access to Mb bipolar cell terminals in goldfish retinal slices with the patch-clamp technique allows the measurement of presynaptic Ca(2+) currents, membrane capacitance changes, and reciprocal synaptic feedback inhibition mediated by GABA(A) and GABA(C) receptors expressed on the terminals. Presynaptic membrane capacitance measurements of exocytosis allow one to study the short-term plasticity of excitatory neurotransmitter release. In addition, short-term and long-term plasticity of inhibitory neurotransmitter release from amacrine cells can also be investigated by recordings of reciprocal feedback inhibition arriving at the Mb terminal. Over short periods of time (e.g. ~10 s), GABAergic reciprocal feedback inhibition from amacrine cells undergoes paired-pulse depression via GABA vesicle pool depletion. The synaptic dynamics of retinal microcircuits in the inner plexiform layer of the retina can thus be directly studied. The brain-slice technique was introduced more than 40 years ago but is still very useful for the investigation of the electrical properties of neurons, both at the single cell soma, single dendrite or axon, and microcircuit synaptic level. Tissues that are too small to be glued directly onto the slicing chamber are often first embedded in agar (or placed onto a filter paper) and then sliced. In this video, we employ the pre-embedding agar technique using goldfish retina. Some of the giant bipolar cell terminals in our slices of goldfish retina are axotomized (axon-cut) during the slicing procedure. This allows us to isolate single presynaptic nerve terminal inputs, because recording from axotomized terminals excludes the signals from the soma-dendritic compartment. Alternatively, one can also record from intact Mb bipolar cells, by recording from terminals attached to axons that have not been cut during the slicing procedure. Overall, use of this experimental protocol will aid in studies of retinal synaptic physiology, microcircuit functional analysis, and synaptic transmission at ribbon synapses.
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Affiliation(s)
- Mean-Hwan Kim
- The Vollum Institute, Oregon Health and Science University, USA
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Petruzziello F, Fouillen L, Wadensten H, Kretz R, Andren PE, Rainer G, Zhang X. Extensive characterization of Tupaia belangeri neuropeptidome using an integrated mass spectrometric approach. J Proteome Res 2011; 11:886-96. [PMID: 22070463 DOI: 10.1021/pr200709j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Neuropeptidomics is used to characterize endogenous peptides in the brain of tree shrews (Tupaia belangeri). Tree shrews are small animals similar to rodents in size but close relatives of primates, and are excellent models for brain research. Currently, tree shrews have no complete proteome information available on which direct database search can be allowed for neuropeptide identification. To increase the capability in the identification of neuropeptides in tree shrews, we developed an integrated mass spectrometry (MS)-based approach that combines methods including data-dependent, directed, and targeted liquid chromatography (LC)-Fourier transform (FT)-tandem MS (MS/MS) analysis, database construction, de novo sequencing, precursor protein search, and homology analysis. Using this integrated approach, we identified 107 endogenous peptides that have sequences identical or similar to those from other mammalian species. High accuracy MS and tandem MS information, with BLAST analysis and chromatographic characteristics were used to confirm the sequences of all the identified peptides. Interestingly, further sequence homology analysis demonstrated that tree shrew peptides have a significantly higher degree of homology to equivalent sequences in humans than those in mice or rats, consistent with the close phylogenetic relationship between tree shrews and primates. Our results provide the first extensive characterization of the peptidome in tree shrews, which now permits characterization of their function in nervous and endocrine system. As the approach developed fully used the conservative properties of neuropeptides in evolution and the advantage of high accuracy MS, it can be portable for identification of neuropeptides in other species for which the fully sequenced genomes or proteomes are not available.
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Affiliation(s)
- Filomena Petruzziello
- Visual Cognition Laboratory, Department of Medicine, University of Fribourg , Chemin de Musee 5, Fribourg, CH-1700, Switzerland
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Nilsson A, Stroth N, Zhang X, Qi H, Fälth M, Sköld K, Hoyer D, Andrén PE, Svenningsson P. Neuropeptidomics of mouse hypothalamus after imipramine treatment reveal somatostatin as a potential mediator of antidepressant effects. Neuropharmacology 2011; 62:347-57. [PMID: 21856315 DOI: 10.1016/j.neuropharm.2011.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 07/15/2011] [Accepted: 08/02/2011] [Indexed: 12/24/2022]
Abstract
Excessive activation of the hypothalamic-pituitary-adrenal (HPA) axis has been associated with numerous diseases, including depression, and the tricyclic antidepressant imipramine has been shown to suppress activity of the HPA axis. Central hypothalamic control of the HPA axis is complex and involves a number of neuropeptides released from multiple hypothalamic subnuclei. The present study was therefore designed to determine the effects of imipramine administration on the mouse hypothalamus using a peptidomics approach. Among the factors found to be downregulated after acute (one day) or chronic (21 days) imipramine administration were peptides derived from secretogranin 1 (chromogranin B) as well as peptides derived from cerebellin precursors. In contrast, peptides SRIF-14 and SRIF-28 (1-11) derived from somatostatin (SRIF, somatotropin release inhibiting factor) were significantly upregulated by imipramine in the hypothalamus. Because diminished SRIF levels have long been known to occur in depression, a second part of the study investigated the roles of individual SRIF receptors in mediating potential antidepressant effects. SRA880, an antagonist of the somatostatin-1 autoreceptor (sst1) which positively modulates release of endogenous SRIF, was found to synergize with imipramine in causing antidepressant-like effects in the tail suspension test. Furthermore, chronic co-administration of SRA880 and imipramine synergistically increased BDNF mRNA expression in the cerebral cortex. Application of SRIF or L054264, an sst2 receptor agonist, but not L803807, an sst4 receptor agonist, increased phosphorylation of CaMKII and GluR1 in cerebrocortical slices. Our present experiments thus provide evidence for antidepressant-induced upregulation of SRIF in the brain, and strengthen the notion that augmented SRIF expression and signaling may counter depressive-like symptoms. This article is part of a Special Issue entitled 'Anxiety and Depression'.
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Affiliation(s)
- Anna Nilsson
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, BMC, P.O. Box 591, SE-751 24 Uppsala, Sweden
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Van Dijck A, Hayakawa E, Landuyt B, Baggerman G, Van Dam D, Luyten W, Schoofs L, De Deyn PP. Comparison of extraction methods for peptidomics analysis of mouse brain tissue. J Neurosci Methods 2011; 197:231-7. [DOI: 10.1016/j.jneumeth.2011.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 02/23/2011] [Indexed: 10/18/2022]
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Colgrave ML, Xi L, Lehnert SA, Flatscher-Bader T, Wadensten H, Nilsson A, Andren PE, Wijffels G. Neuropeptide profiling of the bovine hypothalamus: thermal stabilization is an effective tool in inhibiting post-mortem degradation. Proteomics 2011; 11:1264-76. [PMID: 21319303 DOI: 10.1002/pmic.201000423] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 10/11/2010] [Accepted: 12/20/2010] [Indexed: 11/07/2022]
Abstract
The hypothalamus is the central regulatory region of the brain that links the nervous system to the endocrine system via the pituitary gland. It synthesizes and secretes neuropeptide hormones, which in turn act to stimulate or inhibit the secretion of pituitary hormones. We have undertaken a detailed MS investigation of the peptides present in the bovine hypothalamus by adapting a novel heat stabilization methodology, which improved peptide discovery to direct our studies into the molecular mechanisms involved in bovine reproduction. The untreated samples contained large numbers of protein degradation products that interfered with the analysis of the neuropeptides. In the thermally stabilized samples, we were able to identify many more neuropeptides that are known to be expressed in the bovine hypothalamus. Furthermore, we have characterized a range of post-translational modifications that indicate the presence of processed intact mature neuropeptides in the stabilized tissue samples, whereas we detected many trimmed or truncated peptides resulting from post-mortem degradation in the untreated tissue samples. Altogether, using an optimized workflow, we were able to identify 140 candidate neuropeptides. We also nominate six new candidate neuropeptides derived from proSAAS, secretogranin-2 and proTRH.
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Gupta N, Bark SJ, Lu WD, Taupenot L, O'Connor DT, Pevzner P, Hook V. Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing. J Proteome Res 2010; 9:5065-75. [PMID: 20704348 DOI: 10.1021/pr100358b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Neuropeptides are required for cell-cell communication in the regulation of physiological and pathological processes. While selected neuropeptides of known biological activities have been studied, global analyses of the endogenous profile of human peptide products derived from prohormones by proteolytic processing in vivo are largely unknown. Therefore, this study utilized the global, unbiased approach of mass spectrometry-based neuropeptidomics to define peptide profiles in secretory vesicles, isolated from human adrenal medullary pheochromocytoma of the sympathetic nervous system. The low molecular weight pool of secretory vesicle peptides was subjected to nano-LC-MS/MS with ion trap and QTOF mass spectrometry analyzed by different database search tools (InsPecT and Spectrum Mill). Peptides were generated by processing of prohormones at dibasic cleavage sites as well as at nonbasic residues. Significantly, peptide profiling provided novel insight into newly identified peptide products derived from proenkephalin, pro-NPY, proSAAS, CgA, CgB, and SCG2 prohormones. Previously unidentified intervening peptide domains of prohormones were observed, thus providing new knowledge of human neuropeptidomes generated from precursors. The global peptidomic approach of this study demonstrates the complexity of diverse neuropeptides present in human secretory vesicles for cell-cell communication.
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Affiliation(s)
- Nitin Gupta
- Bioinformatics Graduate Program, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
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A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome. J Proteome Res 2010; 9:990-6. [PMID: 20000637 DOI: 10.1021/pr900885k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Peptidomics is the identification and study of the in vivo biologically active peptide profile. A combination of high performance liquid chromatography, mass spectrometry, and bioinformatics tools such as database search engines are commonly used to perform the analysis. We report a methodology based on a database system holding the completed translated genome, whereby de novo sequencing and genome-wide database searching are combined. The methodology was applied to the sea urchin neuropeptidome resulting in a 30% increase in identification rate.
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Scholz B, Alm H, Mattsson A, Nilsson A, Kultima K, Savitski MM, Fälth M, Sköld K, Brunström B, Andren PE, Dencker L. Neuropeptidomic analysis of the embryonic Japanese quail diencephalon. BMC DEVELOPMENTAL BIOLOGY 2010; 10:30. [PMID: 20298575 PMCID: PMC2851587 DOI: 10.1186/1471-213x-10-30] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 03/18/2010] [Indexed: 11/10/2022]
Abstract
Background Endogenous peptides such as neuropeptides are involved in numerous biological processes in the fully developed brain but very little is known about their role in brain development. Japanese quail is a commonly used bird model for studying sexual dimorphic brain development, especially adult male copulatory behavior in relation to manipulations of the embryonic endocrine system. This study uses a label-free liquid chromatography mass spectrometry approach to analyze the influence of age (embryonic days 12 vs 17), sex and embryonic day 3 ethinylestradiol exposure on the expression of multiple endogenous peptides in the developing diencephalon. Results We identified a total of 65 peptides whereof 38 were sufficiently present in all groups for statistical analysis. Age was the most defining variable in the data and sex had the least impact. Most identified peptides were more highly expressed in embryonic day 17. The top candidates for EE2 exposure and sex effects were neuropeptide K (downregulated by EE2 in males and females), gastrin-releasing peptide (more highly expressed in control and EE2 exposed males) and gonadotropin-inhibiting hormone related protein 2 (more highly expressed in control males and displaying interaction effects between age and sex). We also report a new potential secretogranin-2 derived neuropeptide and previously unknown phosphorylations in the C-terminal flanking protachykinin 1 neuropeptide. Conclusions This study is the first larger study on endogenous peptides in the developing brain and implies a previously unknown role for a number of neuropeptides in middle to late avian embryogenesis. It demonstrates the power of label-free liquid chromatography mass spectrometry to analyze the expression of multiple endogenous peptides and the potential to detect new putative peptide candidates in a developmental model.
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Affiliation(s)
- Birger Scholz
- Department of Pharmaceutical Biosciences, division of toxicology, Uppsala University, The Biomedical Center, Husargatan 3, Box 594, SE-75124 Uppsala, Sweden.
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Menschaert G, Vandekerckhove TTM, Landuyt B, Hayakawa E, Schoofs L, Luyten W, Van Criekinge W. Spectral clustering in peptidomics studies helps to unravel modification profile of biologically active peptides and enhances peptide identification rate. Proteomics 2009; 9:4381-8. [PMID: 19658089 DOI: 10.1002/pmic.200900248] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
When studying the set of biologically active peptides (the so-called peptidome) of a cell type, organ, or entire organism, the identification of peptides is mostly attempted by MS. However, identification rates are often dismally unsatisfactory. A great deal of failed or missed identifications may be attributable to the wealth of modifications on peptides, some of which may originate from in vivo post-translational processes to activate the molecule, whereas others could be introduced during the tissue preparation procedures. Preliminary knowledge of the modification profile of specific peptidome samples would greatly improve identification rates. To this end we developed an approach that performs clustering of mass spectra in a way that allows us to group spectra having similar peak patterns over significant segments. Comparing members of one spectral group enables us to assess the modifications (expressed as mass shifts in Dalton) present in a peptidome sample. The clustering algorithm in this study is called Bonanza, and it was applied to MALDI-TOF/TOF MS spectra from the mouse. Peptide identification rates went up from 17 to 36% for 278 spectra obtained from the pancreatic islets and from 21 to 43% for 163 pituitary spectra. Spectral clustering with subsequent advanced database search may result in the discovery of new biologically active peptides and modifications thereof, as shown by this report indeed.
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Affiliation(s)
- Gerben Menschaert
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium.
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Wang J, Jiang X, Sturm RM, Li L. Combining tissue extraction and off-line capillary electrophoresis matrix-assisted laser desorption/ionization Fourier transform mass spectrometry for neuropeptide analysis in individual neuronal organs using 2,5-dihydroxybenzoic acid as a multi-functional agent. J Chromatogr A 2009; 1216:8283-8. [PMID: 19473662 PMCID: PMC2783529 DOI: 10.1016/j.chroma.2009.04.085] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Revised: 04/25/2009] [Accepted: 04/28/2009] [Indexed: 01/20/2023]
Abstract
In this study we report an improved protocol that combines simplified sample preparation and micro-scale separation for mass spectrometric analysis of neuropeptides from individual neuroendocrine organs of crab Cancer borealis. A simple, one-step extraction method with commonly used matrix-assisted laser desorption/ionization (MALDI) matrix, 2,5-dihydroxybenzoic acid (DHB), in saturated aqueous solution, is employed for improved extraction of neuropeptides. Furthermore, a novel use of DHB as background electrolyte for capillary electrophoresis (CE) separation in the off-line coupling of CE to MALDI-Fourier transform mass spectrometric (FT-MS) detection is also explored. The new CE electrolyte exhibits full compatibility with MALDI-MS analysis of neuropeptides in that both the peptide extraction process and MALDI detection utilize DHB. In addition, enhanced resolving power and improved sensitivity are also observed for CE-MALDI-MS of peptide mixture analysis. Collectively, the use of DHB has simplified the extraction and reduced the sample loss by elimination of homogenizing, drying, and desalting processes. In the mean time, the concurrent use of DHB as CE separation buffer and subsequent MALDI matrix offers improved spectral quality by eliminating the interferences from typical CE electrolyte in MALDI detection.
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Affiliation(s)
- Junhua Wang
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA
| | - Xiaoyue Jiang
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA
| | - Robert M. Sturm
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA
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Lee JE, Atkins N, Hatcher NG, Zamdborg L, Gillette MU, Sweedler JV, Kelleher NL. Endogenous peptide discovery of the rat circadian clock: a focused study of the suprachiasmatic nucleus by ultrahigh performance tandem mass spectrometry. Mol Cell Proteomics 2009; 9:285-97. [PMID: 19955084 DOI: 10.1074/mcp.m900362-mcp200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Understanding how a small brain region, the suprachiasmatic nucleus (SCN), can synchronize the body's circadian rhythms is an ongoing research area. This important time-keeping system requires a complex suite of peptide hormones and transmitters that remain incompletely characterized. Here, capillary liquid chromatography and FTMS have been coupled with tailored software for the analysis of endogenous peptides present in the SCN of the rat brain. After ex vivo processing of brain slices, peptide extraction, identification, and characterization from tandem FTMS data with <5-ppm mass accuracy produced a hyperconfident list of 102 endogenous peptides, including 33 previously unidentified peptides, and 12 peptides that were post-translationally modified with amidation, phosphorylation, pyroglutamylation, or acetylation. This characterization of endogenous peptides from the SCN will aid in understanding the molecular mechanisms that mediate rhythmic behaviors in mammals.
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Affiliation(s)
- Ji Eun Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Altelaar AFM, Mohammed S, Brans MAD, Adan RAH, Heck AJR. Improved identification of endogenous peptides from murine nervous tissue by multiplexed peptide extraction methods and multiplexed mass spectrometric analysis. J Proteome Res 2009; 8:870-6. [PMID: 19152261 DOI: 10.1021/pr800449n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, mass spectrometry (MS) based techniques have made their entrance in the analysis of endogenous peptides extracted from nervous tissue. In this study, we introduce a novel peptide extraction procedure using 8 M urea, next to the more established extraction method that uses acetic acid. The extracted peptide mixtures are analyzed by both high-resolution nanoLC MS/MS using collision induced dissociation (CID) on an LTQ-Orbitrap and nanoLC electron transfer induced dissociation (ETD) on a linear ion trap. The combined use of the two extraction methods significantly increased the yield of identified endogenous neuropeptides. The multiplexed use of high mass accuracy mass spectrometry and the ETD fragmentation technique further increased the yield and confidence of peptide identifications. Furthermore, reduction of disulfide bridges during sample preparation was essential in the identification of several endogenous peptides containing cysteine disulfide bonds. Through this study, we identified in total 142 peptides in extracts of the mouse pituitary tissue, whereby 43 uniquely in the urea extract and 11 uniquely in the acetic acid extract. A large number of detected endogenous peptides were reported previously, but we confidently identified 22 unreported peptides that possess characteristics of endogenous peptides and are thus interesting targets to be explored further.
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Affiliation(s)
- A F Maarten Altelaar
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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Rossbach U, Nilsson A, Fälth M, Kultima K, Zhou Q, Hallberg M, Gordh T, Andren PE, Nyberg F. A quantitative peptidomic analysis of peptides related to the endogenous opioid and tachykinin systems in nucleus accumbens of rats following naloxone-precipitated morphine withdrawal. J Proteome Res 2009; 8:1091-8. [PMID: 19159213 DOI: 10.1021/pr800669g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have applied a recently developed label-free mass spectrometry based peptidomic approach to identify and quantify a variety of endogenous peptides from rat nucleus accumbens following withdrawal in naloxone-precipitated, morphine-dependent rats of two separate strains. We focused on maturated, partially processed and truncated peptides derived from the peptide precursors proenkephalin, prodynorphin and preprotachykinin. The expression of several identified peptides was dependent on strain and was affected during morphine withdrawal.
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Affiliation(s)
- Uwe Rossbach
- Department of Pharmaceutical Biosciences, Uppsala University, SE-751 24, Uppsala, Sweden
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Svensson M, Borén M, Sköld K, Fälth M, Sjögren B, Andersson M, Svenningsson P, Andrén PE. Heat Stabilization of the Tissue Proteome: A New Technology for Improved Proteomics. J Proteome Res 2009; 8:974-81. [DOI: 10.1021/pr8006446] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Marcus Svensson
- Denator AB, Uppsala Science Park, Dag Hammarskjölds väg 32a, 751 83, Uppsala, Sweden, Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, Box 583, 751 23 Uppsala, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 171 77 Stockholm, Sweden, and Department of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University, Box 594, 751 24 Uppsala, Sweden
| | - Mats Borén
- Denator AB, Uppsala Science Park, Dag Hammarskjölds väg 32a, 751 83, Uppsala, Sweden, Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, Box 583, 751 23 Uppsala, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 171 77 Stockholm, Sweden, and Department of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University, Box 594, 751 24 Uppsala, Sweden
| | - Karl Sköld
- Denator AB, Uppsala Science Park, Dag Hammarskjölds väg 32a, 751 83, Uppsala, Sweden, Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, Box 583, 751 23 Uppsala, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 171 77 Stockholm, Sweden, and Department of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University, Box 594, 751 24 Uppsala, Sweden
| | - Maria Fälth
- Denator AB, Uppsala Science Park, Dag Hammarskjölds väg 32a, 751 83, Uppsala, Sweden, Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, Box 583, 751 23 Uppsala, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 171 77 Stockholm, Sweden, and Department of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University, Box 594, 751 24 Uppsala, Sweden
| | - Benita Sjögren
- Denator AB, Uppsala Science Park, Dag Hammarskjölds väg 32a, 751 83, Uppsala, Sweden, Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, Box 583, 751 23 Uppsala, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 171 77 Stockholm, Sweden, and Department of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University, Box 594, 751 24 Uppsala, Sweden
| | - Malin Andersson
- Denator AB, Uppsala Science Park, Dag Hammarskjölds väg 32a, 751 83, Uppsala, Sweden, Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, Box 583, 751 23 Uppsala, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 171 77 Stockholm, Sweden, and Department of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University, Box 594, 751 24 Uppsala, Sweden
| | - Per Svenningsson
- Denator AB, Uppsala Science Park, Dag Hammarskjölds väg 32a, 751 83, Uppsala, Sweden, Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, Box 583, 751 23 Uppsala, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 171 77 Stockholm, Sweden, and Department of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University, Box 594, 751 24 Uppsala, Sweden
| | - Per E. Andrén
- Denator AB, Uppsala Science Park, Dag Hammarskjölds väg 32a, 751 83, Uppsala, Sweden, Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, Box 583, 751 23 Uppsala, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 171 77 Stockholm, Sweden, and Department of Pharmaceutical Biosciences, Division of Toxicology, Uppsala University, Box 594, 751 24 Uppsala, Sweden
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Nilsson A, Fälth M, Zhang X, Kultima K, Sköld K, Svenningsson P, Andrén PE. Striatal alterations of secretogranin-1, somatostatin, prodynorphin, and cholecystokinin peptides in an experimental mouse model of Parkinson disease. Mol Cell Proteomics 2009; 8:1094-104. [PMID: 19131325 DOI: 10.1074/mcp.m800454-mcp200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The principal causative pathology of Parkinson disease is the progressive degeneration of dopaminergic neurons in the substantia nigra pars compacta projecting to the striatum in the brain. The information regarding the expression of neuropeptides in parkinsonism is very limited. Here we have elucidated striatal neuropeptide mechanisms in experimental parkinsonism using the unilateral 6-hydroxydopamine model to degenerate dopamine neurons. A thoroughly controlled sample preparation technique together with a peptidomics approach and targeted neuropeptide sequence collections enabled sensitive detection, identification, and relative quantitation of a great number of endogenous neuropeptides. Previously not recognized alterations in neuropeptide levels were identified in the unilateral lesioned mice with or without subchronic 3,4-dihydroxy-L-phenylalanine administration, the conventional treatment of Parkinson disease. Several of these peptides originated from the same precursor such as secretogranin-1, somatostatin, prodynorphin, and cholecystokinin. Disease-related biotransformation of precursors into individual peptides was observed in the experimental model of Parkinson disease. Several previously unreported potentially biologically active peptides were also identified from the striatal samples. This study provides further evidence that neuropeptides take part in mediating the central nervous system failure associated with Parkinson disease.
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Affiliation(s)
- Anna Nilsson
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Uppsala University, SE-75123 Uppsala, Sweden
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41
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Zhang X, Che FY, Berezniuk I, Sonmez K, Toll L, Fricker LD. Peptidomics of Cpe(fat/fat) mouse brain regions: implications for neuropeptide processing. J Neurochem 2008; 107:1596-613. [PMID: 19014391 DOI: 10.1111/j.1471-4159.2008.05722.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Quantitative peptidomics was used to compare levels of peptides in wild type (WT) and Cpe(fat/fat) mice, which lack carboxypeptidase E (CPE) activity because of a point mutation. Six different brain regions were analyzed: amygdala, hippocampus, hypothalamus, prefrontal cortex, striatum, and thalamus. Altogether, 111 neuropeptides or other peptides derived from secretory pathway proteins were identified in WT mouse brain extracts by tandem mass spectrometry, and another 47 peptides were tentatively identified based on mass and other criteria. Most secretory pathway peptides were much lower in Cpe(fat/fat) mouse brain, relative to WT mouse brain, indicating that CPE plays a major role in their biosynthesis. Other peptides were only partially reduced in the Cpe(fat/fat) mice, indicating that another enzyme (presumably carboxypeptidase D) contributes to their biosynthesis. Approximately 10% of the secretory pathway peptides were present in the Cpe(fat/fat) mouse brain at levels similar to those in WT mouse brain. Many peptides were greatly elevated in the Cpe(fat/fat) mice; these peptide processing intermediates with C-terminal Lys and/or Arg were generally not detectable in WT mice. Taken together, these results indicate that CPE contributes, either directly or indirectly, to the production of the majority of neuropeptides.
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Affiliation(s)
- Xin Zhang
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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42
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Kochetov AV. Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. Bioessays 2008; 30:683-91. [PMID: 18536038 DOI: 10.1002/bies.20771] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is widely suggested that a eukaryotic mRNA typically contains one translation start site and encodes a single functional protein product. However, according to current points of view on translation initiation mechanisms, eukaryotic ribosomes can recognize several alternative translation start sites and the number of experimentally verified examples of alternative translation is growing rapidly. Also, the frequent occurrence of alternative translation events and their functional significance are supported by the results of computational evaluations. The functional role of alternative translation and its contribution to eukaryotic proteome complexity are discussed.
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Fälth M, Svensson M, Nilsson A, Sköld K, Fenyö D, Andren PE. Validation of Endogenous Peptide Identifications Using a Database of Tandem Mass Spectra. J Proteome Res 2008; 7:3049-53. [DOI: 10.1021/pr800036d] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maria Fälth
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden, and The Rockefeller University, 1230 York Avenue, New York, New York 10065
| | - Marcus Svensson
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden, and The Rockefeller University, 1230 York Avenue, New York, New York 10065
| | - Anna Nilsson
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden, and The Rockefeller University, 1230 York Avenue, New York, New York 10065
| | - Karl Sköld
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden, and The Rockefeller University, 1230 York Avenue, New York, New York 10065
| | - David Fenyö
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden, and The Rockefeller University, 1230 York Avenue, New York, New York 10065
| | - Per E. Andren
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry, Biomedical Centre, Box 583, Uppsala University, SE-75123 Uppsala, Sweden, and The Rockefeller University, 1230 York Avenue, New York, New York 10065
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44
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Clynen E, Baggerman G, Husson SJ, Landuyt B, Schoofs L. Peptidomics in drug research. Expert Opin Drug Discov 2008; 3:425-40. [DOI: 10.1517/17460441.3.4.425] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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