1
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Fricker LD. Neuropeptidomics of Genetically Defined Cell Types in Mouse Brain. Methods Mol Biol 2024; 2758:213-225. [PMID: 38549016 DOI: 10.1007/978-1-0716-3646-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Peptidomic techniques are powerful tools to identify peptides in a biological sample. In the case of brain, which contains a complex mixture of cell types, standard peptidomics procedures reveal the major peptides in a dissected brain region. It is difficult to obtain information on peptides within a specific cell type using standard approaches, unless that cell type can be isolated. This protocol describes a targeted peptidomic approach that uses affinity chromatography to purify peptides that are substrates of carboxypeptidase E (CPE), an enzyme present in the secretory pathway of neuroendocrine cells. Many CPE products function as neuropeptides and/or peptide hormones, and therefore represent an important subset of the peptidome. Because CPE removes C-terminal Lys and Arg residues from peptide processing intermediates, organisms lacking CPE show a large decrease in the levels of the mature forms of most neuropeptides and peptide hormones, and a very large increase in the levels of the processing intermediates that contain C-terminal Lys and/or Arg (i.e., the CPE substrates). These CPE substrates can be purified on an anhydrotrypsin-agarose affinity resin, which specifically binds peptides with C-terminal basic residues. When this method is used with mice lacking CPE activity in genetically defined cell types, it allows the detection of peptides specifically produced in that cell type.
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Affiliation(s)
- Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA.
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2
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Fridjonsdottir E, Nilsson A, Fricker LD, Andrén PE. Two Different Strategies for Stabilization of Brain Tissue and Extraction of Neuropeptides. Methods Mol Biol 2024; 2758:49-60. [PMID: 38549007 DOI: 10.1007/978-1-0716-3646-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neuropeptides are bioactive peptides that are synthesized and secreted by neurons in signaling pathways in the brain. Peptides and proteins are extremely vulnerable to proteolytic cleavage when their biological surrounding changes. This makes neuropeptidomics challenging due to the rapid alterations that occur to the peptidome after harvesting of brain tissue samples. For a successful neuropeptidomic study, the biological tissue sample analyzed should resemble the living state as much as possible. Heat stabilization has been proven to inhibit postmortem degradation by denaturing proteolytic enzymes, hence increasing identification rates of neuropeptides. Here, we describe two different stabilization protocols for rodent brain samples that increase the number of intact mature neuropeptides and minimize interference from degradation products of abundant proteins. Additionally, we present an extraction protocol that aims to extract a wide range of hydrophilic and hydrophobic neuropeptides by sequentially using an aqueous and an organic extraction medium.
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Affiliation(s)
- Elva Fridjonsdottir
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Nilsson
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Per E Andrén
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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3
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Abid MSR, Qiu H, Checco JW. Label-Free Quantitation of Endogenous Peptides. Methods Mol Biol 2024; 2758:125-150. [PMID: 38549012 PMCID: PMC11027169 DOI: 10.1007/978-1-0716-3646-6_7] [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: 04/02/2024]
Abstract
Liquid chromatography-mass spectrometry (LC-MS)-based peptidomics methods allow for the detection and identification of many peptides in a complex biological mixture in an untargeted manner. Quantitative peptidomics approaches allow for comparisons of peptide abundance between different samples, allowing one to draw conclusions about peptide differences as a function of experimental treatment or physiology. While stable isotope labeling is a powerful approach for quantitative proteomics and peptidomics, advances in mass spectrometry instrumentation and analysis tools have allowed label-free methods to gain popularity in recent years. In a general label-free quantitative peptidomics experiment, peak intensity information for each peptide is compared across multiple LC-MS runs. Here, we outline a general approach for label-free quantitative peptidomics experiments, including steps for sample preparation, LC-MS data acquisition, data processing, and statistical analysis. Special attention is paid to address run-to-run variability, which can lead to several major problems in label-free experiments. Overall, our method provides researchers with a framework for the development of their own quantitative peptidomics workflows applicable to quantitation of peptides from a wide variety of different biological sources.
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Affiliation(s)
| | - Haowen Qiu
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA.
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4
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Fan KT, Hsu CW, Chen YR. Mass spectrometry in the discovery of peptides involved in intercellular communication: From targeted to untargeted peptidomics approaches. MASS SPECTROMETRY REVIEWS 2023; 42:2404-2425. [PMID: 35765846 DOI: 10.1002/mas.21789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Endogenous peptide hormones represent an essential class of biomolecules, which regulate cell-cell communications in diverse physiological processes of organisms. Mass spectrometry (MS) has been developed to be a powerful technology for identifying and quantifying peptides in a highly efficient manner. However, it is difficult to directly identify these peptide hormones due to their diverse characteristics, dynamic regulations, low abundance, and existence in a complicated biological matrix. Here, we summarize and discuss the roles of targeted and untargeted MS in discovering peptide hormones using bioassay-guided purification, bioinformatics screening, or the peptidomics-based approach. Although the peptidomics approach is expected to discover novel peptide hormones unbiasedly, only a limited number of successful cases have been reported. The critical challenges and corresponding measures for peptidomics from the steps of sample preparation, peptide extraction, and separation to the MS data acquisition and analysis are also discussed. We also identify emerging technologies and methods that can be integrated into the discovery platform toward the comprehensive study of endogenous peptide hormones.
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Affiliation(s)
- Kai-Ting Fan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Wei Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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5
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Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
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Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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6
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Mousavi S, Qiu H, Heinis FI, Abid MSR, Andrews MT, Checco JW. Short-Term Administration of Common Anesthetics Does Not Dramatically Change the Endogenous Peptide Profile in the Rat Pituitary. ACS Chem Neurosci 2022; 13:2888-2896. [PMID: 36126283 PMCID: PMC9547841 DOI: 10.1021/acschemneuro.2c00359] [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: 01/20/2023] Open
Abstract
Cell-cell signaling peptides (e.g., peptide hormones, neuropeptides) are among the largest class of cellular transmitters and regulate a variety of physiological processes. To identify and quantify the relative abundances of cell-cell signaling peptides in different physiological states, liquid chromatography-mass spectrometry-based peptidomics workflows are commonly utilized on freshly dissected tissues. In such animal experiments, the administration of general anesthetics is an important step for many research projects. However, acute anesthetic administration may rapidly change the measured abundance of transmitter molecules and metabolites, especially in the brain and endocrine system, which would confound experimental results. The aim of this study was to evaluate the effect of short-term (<5 min) anesthetic administration on the measured abundance of cell-cell signaling peptides, as evaluated by a typical peptidomics workflow. To accomplish this goal, we compared endogenous peptide abundances in the rat pituitary following administration of 5% isoflurane, 200 mg/kg sodium pentobarbital, or no anesthetic administration. Label-free peptidomics analysis demonstrated that acute use of isoflurane changed the levels of a small number of peptides, primarily degradation products of the hormone somatotropin, but did not influence the levels of most other peptide hormones. Acute use of sodium pentobarbital had negligible impact on the relative abundance of all measured peptides. Overall, our results suggest that anesthetics used in pituitary peptidomics studies do not dramatically confound observed results.
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Affiliation(s)
- Somayeh Mousavi
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Haowen Qiu
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Frazer I. Heinis
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Md Shadman Ridwan Abid
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Matthew T. Andrews
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - James W. Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE 68588, United States
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7
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Baijnath S, Kaya I, Nilsson A, Shariatgorji R, Andrén PE. Advances in spatial mass spectrometry enable in-depth neuropharmacodynamics. Trends Pharmacol Sci 2022; 43:740-753. [DOI: 10.1016/j.tips.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/06/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022]
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8
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Foreman RE, George AL, Reimann F, Gribble FM, Kay RG. Peptidomics: A Review of Clinical Applications and Methodologies. J Proteome Res 2021; 20:3782-3797. [PMID: 34270237 DOI: 10.1021/acs.jproteome.1c00295] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Improvements in both liquid chromatography (LC) and mass spectrometry (MS) instrumentation have greatly enhanced proteomic and small molecule metabolomic analysis in recent years. Less focus has been on the improved capability to detect and quantify small bioactive peptides, even though the exact sequences of the peptide species produced can have important biological consequences. Endogenous bioactive peptide hormones, for example, are generated by the targeted and regulated cleavage of peptides from their prohormone sequence. This process may include organ specific variants, as proglucagon is converted to glucagon in the pancreas but glucagon-like peptide-1 (GLP-1) in the small intestine, with glucagon raising, whereas GLP-1, as an incretin, lowering blood glucose. Therefore, peptidomics workflows must preserve the structure of the processed peptide products to prevent the misidentification of ambiguous peptide species. The poor in vivo and in vitro stability of peptides in biological matrices is a major factor that needs to be considered when developing methods to study them. The bioinformatic analysis of peptidomics data sets requires the inclusion of specific post-translational modifications, which are critical for the function of many bioactive peptides. This review aims to discuss and contrast the various extraction, analytical, and bioinformatics approaches used for human peptidomics studies in a multitude of matrices.
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Affiliation(s)
- Rachel E Foreman
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Amy L George
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Frank Reimann
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Fiona M Gribble
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
| | - Richard G Kay
- University of Cambridge Metabolic Research Laboratories, Level 4, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge CB2 0QQ, U.K
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9
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Shariatgorji R, Nilsson A, Fridjonsdottir E, Strittmatter N, Dannhorn A, Svenningsson P, Goodwin RJA, Odell LR, Andrén PE. Spatial visualization of comprehensive brain neurotransmitter systems and neuroactive substances by selective in situ chemical derivatization mass spectrometry imaging. Nat Protoc 2021; 16:3298-3321. [PMID: 34075230 DOI: 10.1038/s41596-021-00538-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/05/2021] [Indexed: 02/04/2023]
Abstract
Molecule-specific techniques such as MALDI and desorption electrospray ionization mass spectrometry imaging enable direct and simultaneous mapping of biomolecules in tissue sections in a single experiment. However, neurotransmitter imaging in the complex environment of biological samples remains challenging. Our covalent charge-tagging approach using on-tissue chemical derivatization of primary and secondary amines and phenolic hydroxyls enables comprehensive mapping of neurotransmitter networks. Here, we present robust and easy-to-use chemical derivatization protocols that facilitate quantitative and simultaneous molecular imaging of complete neurotransmitter systems and drugs in diverse biological tissue sections with high lateral resolution. This is currently not possible with any other imaging technique. The protocol, using fluoromethylpyridinium and pyrylium reagents, describes all steps from tissue preparation (~1 h), chemical derivatization (1-2 h), data collection (timing depends on the number of samples and lateral resolution) and data analysis and interpretation. The specificity of the chemical reaction can also help users identify unknown chemical identities. Our protocol can reveal the cellular locations in which signaling molecules act and thus shed light on the complex responses that occur after the administration of drugs or during the course of a disease.
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Affiliation(s)
- Reza Shariatgorji
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry Imaging, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Spatial Mass Spectrometry, Uppsala University, Uppsala, Sweden
| | - Anna Nilsson
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry Imaging, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Spatial Mass Spectrometry, Uppsala University, Uppsala, Sweden
| | - Elva Fridjonsdottir
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry Imaging, Uppsala University, Uppsala, Sweden
| | - Nicole Strittmatter
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Andreas Dannhorn
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Per Svenningsson
- Department of Clinical Neuroscience, Section of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Richard J A Goodwin
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Luke R Odell
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Per E Andrén
- Department of Pharmaceutical Biosciences, Medical Mass Spectrometry Imaging, Uppsala University, Uppsala, Sweden.
- Science for Life Laboratory, Spatial Mass Spectrometry, Uppsala University, Uppsala, Sweden.
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10
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Abstract
Proteasomes are large, multicatalytic protein complexes that cleave cellular proteins into peptides. There are many distinct forms of proteasomes that differ in catalytically active subunits, regulatory subunits, and associated proteins. Proteasome inhibitors are an important class of drugs for the treatment of multiple myeloma and mantle cell lymphoma, and they are being investigated for other diseases. Bortezomib (Velcade) was the first proteasome inhibitor to be approved by the US Food and Drug Administration. Carfilzomib (Kyprolis) and ixazomib (Ninlaro) have recently been approved, and more drugs are in development. While the primary mechanism of action is inhibition of the proteasome, the downstream events that lead to selective cell death are not entirely clear. Proteasome inhibitors have been found to affect protein turnover but at concentrations that are much higher than those achieved clinically, raising the possibility that some of the effects of proteasome inhibitors are mediated by other mechanisms.
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Affiliation(s)
- Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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11
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Affiliation(s)
- Gary B Smejkal
- a Core Services Laboratory , Focus Proteomics , Hudson , NH , USA
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12
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Teixeira CMM, Correa CN, Iwai LK, Ferro ES, Castro LMD. Characterization of Intracellular Peptides from Zebrafish (Danio rerio) Brain. Zebrafish 2019; 16:240-251. [DOI: 10.1089/zeb.2018.1718] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | - Leo Kei Iwai
- Special Laboratory of Applied Toxinology, Center of Toxins, Immune Response and Cell Signaling, Butantan Institute, São Paulo, Brazil
| | - Emer Suavinho Ferro
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo, Brazil
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13
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Brognaro E. Glioblastoma Unique Features Drive the Ways for Innovative Therapies in the Trunk-branch Era. Folia Med (Plovdiv) 2019. [DOI: 10.3897/folmed.61.e34900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Glioblastoma multiforme is a solid tumor with particular aspects due to its organ of origin and its development modalities. The brain is very sensitive to oxygen and glucose deprivation and it is the only organ that cannot be either transplanted or entirely removed. Furthermore, many clues and recent indirect experimental evidence indicate that the micro-infiltration of the whole brain parenchyma occurs in very early stages of tumor bulk growth or likely even before. As a consequence, the primary glioblastoma (IDH-wildtype, WHO 2016) is the only tumor where the malignant (i.e. distantly infiltrating the organ of origin) and deadly (i.e. leading cause to patient’s death) phases coincide and overlap in one single phase of its natural history. To date, the prognosis of optimally treated glioblastoma patients remains dismal despite recent fundamental progress in neurosurgical techniques which are enabling better maximal safe resection and survival outcome. Intratumor variegated heterogeneity of glioblastoma bulk due to trunk-branch evolution and very early micro-infiltration and settlement of neoplastic cells in the entire brain parenchyma are the reasons for resistance to current therapeutic treatments. With the aim of future innovative and effective therapies, this paper deals with the unique glioblastoma features, the appropriate research methods as well as the strategies to follow to overcome current causes of resistance.
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14
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Svirkova A, Turyanskaya A, Perneczky L, Streli C, Marchetti-Deschmann M. Multimodal imaging of undecalcified tissue sections by MALDI MS and μXRF. Analyst 2019; 143:2587-2595. [PMID: 29737333 DOI: 10.1039/c8an00313k] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Matrix-assisted laser desorption/ionisation mass spectrometric imaging (MALDI MSI) is a technique that provides localized information on intact molecules in a sample. Micro X-ray fluorescence (μXRF) imaging allows the examination of the spatial distribution of elements in a sample without any morphological changes. These methods have already been applied separately to different tissues, organs, plants and bacterial films, but, to the best of our knowledge, they have yet to be coupled in a multimodal analysis. In this proof-of-principle study, we established and tested sample preparation strategies, allowing the multimodal analysis of lipids (sphingomyelin and phosphatidylcholines) and elements relevant to bone structures as calcium, phosphorous and sulphur in the very same sample section of a chicken phalanx without tissue decalcification. The results of the investigation of such parameters as adhesive tapes supporting tissue sections, and the sequence of the imaging experiments are presented. We show specific lipid distributions in skin, cartilage, muscle, nail, and the intact morphology of bone by calcium and phosphorus imaging. A combination of molecular and elemental imaging was achieved, thus, providing now for the first time the possibility of gathering MALDI MSI and μXRF information from the very same sample without any washing steps omitting therefore the analytical artifacts that inevitably occur in approaches using consecutive tissue sections. The proposed combination can benefit in research studies regarding bone diseases, osteoporosis, osteoarthritis, cartilage failure, bone/tendon distinguishing, where elemental and lipid interaction play an essential role.
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Affiliation(s)
- Anastasiya Svirkova
- Institute of Chemical Technology and Analytics (CTA), TU Wien, Vienna, Austria.
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15
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Fridjonsdottir E, Nilsson A, Wadensten H, Andrén PE. Brain Tissue Sample Stabilization and Extraction Strategies for Neuropeptidomics. Methods Mol Biol 2019; 1719:41-49. [PMID: 29476502 DOI: 10.1007/978-1-4939-7537-2_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Neuropeptides are bioactive peptides that are synthesized and secreted by neurons in signaling pathways in the brain. Peptides and proteins are extremely vulnerable to proteolytic cleavage when their biological surrounding changes. This makes neuropeptidomics challenging due to the rapid alterations that occur to the peptidome after harvesting of brain tissue samples. For a successful neuropeptidomic study the biological tissue sample analyzed should resemble the premortem state as much as possible. Heat stabilization has been proven to inhibit postmortem degradation by denaturing proteolytic enzymes, hence increasing identification rates of neuropeptides. Here, we describe a stabilization protocol of a frozen tissue specimen that increases the number of intact mature neuropeptides identified and minimizes interference of degradation products from abundant proteins. Additionally, we present an extraction protocol that aims to extract a wide range of hydrophilic and hydrophobic neuropeptides by using both an aqueous and an organic extraction medium.
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Affiliation(s)
- Elva Fridjonsdottir
- Biomolecular Imaging and Proteomics, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Anna Nilsson
- Biomolecular Imaging and Proteomics, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Henrik Wadensten
- Biomolecular Imaging and Proteomics, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Per E Andrén
- Biomolecular Imaging and Proteomics, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden.
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16
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Yang N, Anapindi KDB, Romanova EV, Rubakhin SS, Sweedler JV. Improved identification and quantitation of mature endogenous peptides in the rodent hypothalamus using a rapid conductive sample heating system. Analyst 2018; 142:4476-4485. [PMID: 29098220 DOI: 10.1039/c7an01358b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Measurement, identification, and quantitation of endogenous peptides in tissue samples by mass spectrometry (MS) contribute to our understanding of the complex molecular mechanisms of numerous biological phenomena. For accurate results, it is essential to arrest the postmortem degradation of ubiquitous proteins in samples prior to performing peptidomic measurements. Doing so ensures that the detection of endogenous peptides, typically present at relatively low levels of abundance, is not overwhelmed by protein degradation products. Heat stabilization has been shown to inactivate the enzymes in tissue samples and minimize the presence of protein degradation products in the subsequent peptide extracts. However, the efficacy of different heat treatments to preserve the integrity of full-length endogenous peptides has not been well documented; prior peptidomic studies of heat stabilization methods have not distinguished between the full-length (mature) and numerous truncated (possible artifacts of sampling) forms of endogenous peptides. We show that thermal sample treatment via rapid conductive heat transfer is effective for detection of mature endogenous peptides in fresh and frozen rodent brain tissues. Freshly isolated tissue processing with the commercial Stabilizor T1 heat stabilization system resulted in the confident identification of 65% more full-length mature neuropeptides compared to widely used sample treatment in a hot water bath. This finding was validated by a follow-up quantitative multiple reaction monitoring MS analysis of select neuropeptides. The rapid conductive heating in partial vacuum provided by the Stabilizor T1 effectively reduces protein degradation and decreases the chemical complexity of the sample, as assessed by determining total protein content. This system enabled the detection, identification, and quantitation of neuropeptides related to 22 prohormones expressed in individual rat hypothalami and suprachiasmatic nuclei.
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Affiliation(s)
- Ning Yang
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana 61801, USA.
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17
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Hydrophilic probe in mesoporous pore for selective enrichment of endogenous glycopeptides in biological samples. Anal Chim Acta 2018; 1024:84-92. [DOI: 10.1016/j.aca.2018.04.030] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 12/30/2022]
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18
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Abstract
Imaging provides an insight into biological patho-mechanisms of diseases. However, the link between the imaging phenotype and the underlying molecular processes is often not well understood. Methods such as metabolomics and proteomics reveal detailed information about these processes. Unfortunately, they provide no spatial information and thus cannot be easily correlated with functional imaging. We have developed an image-guided milling machine and unique workflows to precisely isolate tissue samples based on imaging data. The tissue samples remain cooled during the entire procedure, preventing sample degradation. This enables us to correlate, at an unprecedented spatial precision, comprehensive imaging information with metabolomics and proteomics data, leading to a better understanding of diseases. Phenotypic heterogeneity is commonly observed in diseased tissue, specifically in tumors. Multimodal imaging technologies can reveal tissue heterogeneity noninvasively in vivo, enabling imaging-based profiling of receptors, metabolism, morphology, or function on a macroscopic scale. In contrast, in vitro multiomics, immunohistochemistry, or histology techniques accurately characterize these heterogeneities in the cellular and subcellular scales in a more comprehensive but ex vivo manner. The complementary in vivo and ex vivo information would provide an enormous potential to better characterize a disease. However, this requires spatially accurate coregistration of these data by image-driven sampling as well as fast sample-preparation methods. Here, a unique image-guided milling machine and workflow for precise extraction of tissue samples from small laboratory animals or excised organs has been developed and evaluated. The samples can be delineated on tomographic images as volumes of interest and can be extracted with a spatial accuracy better than 0.25 mm. The samples remain cooled throughout the procedure to ensure metabolic stability, a precondition for accurate in vitro analysis.
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Khan AM, Grant AH, Martinez A, Burns GAPC, Thatcher BS, Anekonda VT, Thompson BW, Roberts ZS, Moralejo DH, Blevins JE. Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees. ADVANCES IN NEUROBIOLOGY 2018; 21:101-193. [PMID: 30334222 PMCID: PMC6310046 DOI: 10.1007/978-3-319-94593-4_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This article focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined from brain tissue to the original locations within the brain that they are derived from using digital atlas mapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomic analyses conducted in the mammalian hypothalamus. Following a brief historical overview, we highlight studies that have mined biochemical and molecular information from the hypothalamus and then lay out a strategy for how these data can be linked spatially to the mapped locations in a canonical brain atlas where the data come from, thereby allowing researchers to integrate these data with other datasets across multiple scales. A key methodology that enables atlas-based mapping of extracted datasets-laser-capture microdissection-is discussed in detail, with a view of how this technology is a bridge between systems biology and systems neuroscience.
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Affiliation(s)
- Arshad M Khan
- UTEP Systems Neuroscience Laboratory, University of Texas at El Paso, El Paso, TX, USA.
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA.
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, USA.
| | - Alice H Grant
- UTEP Systems Neuroscience Laboratory, University of Texas at El Paso, El Paso, TX, USA
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
- Graduate Program in Pathobiology, University of Texas at El Paso, El Paso, TX, USA
| | - Anais Martinez
- UTEP Systems Neuroscience Laboratory, University of Texas at El Paso, El Paso, TX, USA
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
- Graduate Program in Pathobiology, University of Texas at El Paso, El Paso, TX, USA
| | - Gully A P C Burns
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA, USA
| | - Brendan S Thatcher
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Vishwanath T Anekonda
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Benjamin W Thompson
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Zachary S Roberts
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Daniel H Moralejo
- Division of Neonatology, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - James E Blevins
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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20
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Fricker L. Affinity Purification of Neuropeptide Precursors from Mice Lacking Carboxypeptidase E Activity. Methods Mol Biol 2018; 1719:199-208. [PMID: 29476513 DOI: 10.1007/978-1-4939-7537-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Peptidomic techniques are powerful tools to identify peptides in a biological sample. This protocol describes a targeted peptidomic approach that uses affinity chromatography to purify peptides that are substrates of carboxypeptidase E (CPE), an enzyme present in the secretory pathway of neuroendocrine cells. Many CPE products function as neuropeptides and/or peptide hormones, and therefore represent an important subset of the peptidome. Because CPE removes C-terminal Lys and Arg residues from peptide-processing intermediates, organisms lacking CPE show a large decrease in the levels of the mature forms of most neuropeptides and peptide hormones, and a very large increase in the levels of the processing intermediates that contain C-terminal Lys and/or Arg (i.e., the CPE substrates). These CPE substrates can be purified on an anhydrotrypsin-agarose affinity resin, which specifically binds peptides with C-terminal basic residues. Not all peptides with basic C-terminal residues within a cell are CPE substrates, and these other peptides will also be purified on the anhydrotrypsin affinity column. However, a comparison of peptides purified from wild-type mice and from mice lacking CPE allows for the rapid identification of CPE substrates based on their large increase in the absence of CPE.
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Affiliation(s)
- Lloyd Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA.
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Abstract
In this final chapter I project my personal perspective on the future of peptidomics. A bird's eye view is shed on the discipline and a bid is made to frame it in the broader arena of the life sciences of tomorrow. Inferring from its present state-of-the-art and from the general direction of some evolutionary trends which are to be discerned, a case is made that peptidomics enjoys full ripeness as a young branch of science today, from which a bright future for the discipline can be predicted.
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Affiliation(s)
- Peter D E M Verhaert
- University of Maastricht Multimodal Molecular Imaging Institute (M4i), Faculty of Health, Medicine & Life Sciences, 50 Universiteitssingel, Maastricht, 6229ER, Netherlands.
- ProteoFormiX, 30 Turnhoutseweg, Beerse, 2340, Belgium.
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22
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Berezniuk I, Rodriguiz RM, Zee ML, Marcus DJ, Pintar J, Morgan DJ, Wetsel WC, Fricker LD. ProSAAS-derived peptides are regulated by cocaine and are required for sensitization to the locomotor effects of cocaine. J Neurochem 2017; 143:268-281. [PMID: 28881029 DOI: 10.1111/jnc.14209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/08/2017] [Accepted: 08/21/2017] [Indexed: 12/11/2022]
Abstract
To identify neuropeptides that are regulated by cocaine, we used a quantitative peptidomic technique to examine the relative levels of neuropeptides in several regions of mouse brain following daily intraperitoneal administration of 10 mg/kg cocaine or saline for 7 days. A total of 102 distinct peptides were identified in one or more of the following brain regions: nucleus accumbens, caudate putamen, frontal cortex, and ventral tegmental area. None of the peptides detected in the caudate putamen or frontal cortex were altered by cocaine administration. Three peptides in the nucleus accumbens and seven peptides in the ventral tegmental area were significantly decreased in cocaine-treated mice. Five of these ten peptides are derived from proSAAS, a secretory pathway protein and neuropeptide precursor. To investigate whether proSAAS peptides contribute to the physiological effects of psychostimulants, we examined acute responses to cocaine and amphetamine in the open field with wild-type (WT) and proSAAS knockout (KO) mice. Locomotion was stimulated more robustly in the WT compared to mutant mice for both psychostimulants. Behavioral sensitization to amphetamine was not maintained in proSAAS KO mice and these mutants failed to sensitize to cocaine. To determine whether the rewarding effects of cocaine were altered, mice were tested in conditioned place preference (CPP). Both WT and proSAAS KO mice showed dose-dependent CPP to cocaine that was not distinguished by genotype. Taken together, these results suggest that proSAAS-derived peptides contribute differentially to the behavioral sensitization to psychostimulants, while the rewarding effects of cocaine appear intact in mice lacking proSAAS.
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Affiliation(s)
- Iryna Berezniuk
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ramona M Rodriguiz
- Department of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, North Carolina, USA
| | - Michael L Zee
- Department of Anesthesiology and Perioperative Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - David J Marcus
- Department of Anesthesiology and Perioperative Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - John Pintar
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Daniel J Morgan
- Department of Anesthesiology and Perioperative Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - William C Wetsel
- Department of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, North Carolina, USA.,Departments of Neurobiology and Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Lloyd D Fricker
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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23
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Lozupone M, Seripa D, Stella E, La Montagna M, Solfrizzi V, Quaranta N, Veneziani F, Cester A, Sardone R, Bonfiglio C, Giannelli G, Bisceglia P, Bringiotti R, Daniele A, Greco A, Bellomo A, Logroscino G, Panza F. Innovative biomarkers in psychiatric disorders: a major clinical challenge in psychiatry. Expert Rev Proteomics 2017; 14:809-824. [DOI: 10.1080/14789450.2017.1375857] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Davide Seripa
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
| | - Eleonora Stella
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Maddalena La Montagna
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Vincenzo Solfrizzi
- Geriatric Medicine-Memory Unit and Rare Disease Centre, University of Bari Aldo Moro, Italy
| | | | - Federica Veneziani
- Psychiatric Unit, Department of Basic Medicine, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Alberto Cester
- Department of Medicine Organization Geriatric Unit, CDCD, Dolo Hospital, Venezia, Italy
| | - Rodolfo Sardone
- Department of Epidemiology and Biostatistics, National Institute of Gastroenterology “Saverio de Bellis”, Research Hospital, Bari, Italy
| | - Caterina Bonfiglio
- Department of Epidemiology and Biostatistics, National Institute of Gastroenterology “Saverio de Bellis”, Research Hospital, Bari, Italy
| | - Gianluigi Giannelli
- Department of Epidemiology and Biostatistics, National Institute of Gastroenterology “Saverio de Bellis”, Research Hospital, Bari, Italy
| | - Paola Bisceglia
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
| | - Roberto Bringiotti
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Daniele
- Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Antonio Greco
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
| | - Antonello Bellomo
- Psychiatric Unit, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Giancarlo Logroscino
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
- Department of Clinical Research in Neurology, University of Bari Aldo Moro, “Pia Fondazione Cardinale G. Panico”, Lecce, Italy
| | - Francesco Panza
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
- Geriatric Unit & Laboratory of Gerontology and Geriatrics, Department of Medical Sciences, IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Foggia, Italy
- Department of Clinical Research in Neurology, University of Bari Aldo Moro, “Pia Fondazione Cardinale G. Panico”, Lecce, Italy
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24
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Scifo E, Calza G, Fuhrmann M, Soliymani R, Baumann M, Lalowski M. Recent advances in applying mass spectrometry and systems biology to determine brain dynamics. Expert Rev Proteomics 2017; 14:545-559. [PMID: 28539064 DOI: 10.1080/14789450.2017.1335200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Neurological disorders encompass various pathologies which disrupt normal brain physiology and function. Poor understanding of their underlying molecular mechanisms and their societal burden argues for the necessity of novel prevention strategies, early diagnostic techniques and alternative treatment options to reduce the scale of their expected increase. Areas covered: This review scrutinizes mass spectrometry based approaches used to investigate brain dynamics in various conditions, including neurodegenerative and neuropsychiatric disorders. Different proteomics workflows for isolation/enrichment of specific cell populations or brain regions, sample processing; mass spectrometry technologies, for differential proteome quantitation, analysis of post-translational modifications and imaging approaches in the brain are critically deliberated. Future directions, including analysis of cellular sub-compartments, targeted MS platforms (selected/parallel reaction monitoring) and use of mass cytometry are also discussed. Expert commentary: Here, we summarize and evaluate current mass spectrometry based approaches for determining brain dynamics in health and diseases states, with a focus on neurological disorders. Furthermore, we provide insight on current trends and new MS technologies with potential to improve this analysis.
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Affiliation(s)
- Enzo Scifo
- a Department of Psychiatry, and of Pharmacology and Toxicology , University of Toronto, Campbell Family Mental Health Research Institute of CAMH , Toronto , Canada
| | - Giulio Calza
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
| | - Martin Fuhrmann
- c Neuroimmunology and Imaging Group , German Center for Neurodegenerative Diseases (DZNE) , Bonn , Germany
| | - Rabah Soliymani
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
| | - Marc Baumann
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
| | - Maciej Lalowski
- b Medicum, Meilahti Clinical Proteomics Core Facility, Biochemistry/Developmental Biology, Faculty of Medicine , FI-00014 University of Helsinki , Helsinki , Finland
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25
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Betsou F, Bulla A, Cho SY, Clements J, Chuaqui R, Coppola D, De Souza Y, De Wilde A, Grizzle W, Guadagni F, Gunter E, Heil S, Hodgkinson V, Kessler J, Kiehntopf M, Kim HS, Koppandi I, Shea K, Singh R, Sobel M, Somiari S, Spyropoulos D, Stone M, Tybring G, Valyi-Nagy K, Van den Eynden G, Wadhwa L. Assays for Qualification and Quality Stratification of Clinical Biospecimens Used in Research: A Technical Report from the ISBER Biospecimen Science Working Group. Biopreserv Biobank 2016; 14:398-409. [PMID: 27046294 PMCID: PMC5896556 DOI: 10.1089/bio.2016.0018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
This technical report presents quality control (QC) assays that can be performed in order to qualify clinical biospecimens that have been biobanked for use in research. Some QC assays are specific to a disease area. Some QC assays are specific to a particular downstream analytical platform. When such a qualification is not possible, QC assays are presented that can be performed to stratify clinical biospecimens according to their biomolecular quality.
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Affiliation(s)
- Fay Betsou
- Integrated BioBank of Luxemburg (IBBL), Luxembourg, Luxembourg
| | - Alexandre Bulla
- Biotheque-SML, Division of Genetics and Laboratory Medicine (DMGL), University Hospital of Geneva, Geneva, Switzerland
| | - Sang Yun Cho
- National Biobank of Korea, Cheongju, South Korea
| | - Judith Clements
- Australian Prostate Cancer Bioresource/Queensland University of Technology, Brisbane, Australia
| | - Rodrigo Chuaqui
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis (DCTD), National Cancer Institute, Rockville, Maryland
| | - Domenico Coppola
- Moffitt Cancer Center, Department of Anatomic Pathology, University of South Florida, Tampa, Florida
| | - Yvonne De Souza
- University of California, San Francisco, AIDS Specimen Bank, San Francisco, California
| | | | | | | | | | - Stacey Heil
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Verity Hodgkinson
- Cancer Research Division, Cancer Council NSW, Woolloomooloo, Australia
| | | | | | - Hee Sung Kim
- Department of Pathology, Chung-Ang University College of Medicine, Dongjak-gu, South Korea
| | | | | | - Rajeev Singh
- Houston Methodist Research Institute, Biorepository, Houston, Texas
| | - Marc Sobel
- American Society for Investigative Pathology, Bethesda, Maryland
| | - Stella Somiari
- Biobank and Biospecimen Science Research, Windber Research Institute, Windber, Pennsylvania
| | - Demetri Spyropoulos
- Department of Pathology and Laboratory Medicine, Children's Research Institute, Medical University of South Carolina, Charleston, South Carolina
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, California
| | | | - Klara Valyi-Nagy
- University of Illinois Biorepository, Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
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26
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Dasgupta S, Yang C, Castro LM, Tashima AK, Ferro ES, Moir RD, Willis IM, Fricker LD. Analysis of the Yeast Peptidome and Comparison with the Human Peptidome. PLoS One 2016; 11:e0163312. [PMID: 27685651 PMCID: PMC5042401 DOI: 10.1371/journal.pone.0163312] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/07/2016] [Indexed: 12/22/2022] Open
Abstract
Peptides function as signaling molecules in species as diverse as humans and yeast. Mass spectrometry-based peptidomics techniques provide a relatively unbiased method to assess the peptidome of biological samples. In the present study, we used a quantitative peptidomic technique to characterize the peptidome of the yeast Saccharomyces cerevisiae and compare it to the peptidomes of mammalian cell lines and tissues. Altogether, 297 yeast peptides derived from 75 proteins were identified. The yeast peptides are similar to those of the human peptidome in average size and amino acid composition. Inhibition of proteasome activity with either bortezomib or epoxomicin led to decreased levels of some yeast peptides, suggesting that these peptides are generated by the proteasome. Approximately 30% of the yeast peptides correspond to the N- or C-terminus of the protein; the human peptidome is also highly represented in N- or C-terminal protein fragments. Most yeast and humans peptides are derived from a subset of abundant proteins, many with functions involving cellular metabolism or protein synthesis and folding. Of the 75 yeast proteins that give rise to peptides, 24 have orthologs that give rise to human and/or mouse peptides and for some, the same region of the proteins are found in the human, mouse, and yeast peptidomes. Taken together, these results support the hypothesis that intracellular peptides may have specific and conserved biological functions.
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Affiliation(s)
- Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, United States of America
| | - Leandro M. Castro
- Biomedical Science Institute, Campus on the São Paulo Coast, São Paulo State University, São Vicente, 11330–900, SP, Brazil
| | - Alexandre K. Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, 04023–901, SP, Brazil
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo, 05508–000, SP, Brazil
| | - Robyn D. Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
| | - Ian M. Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
- * E-mail:
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27
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Canela N, Rodríguez MÁ, Baiges I, Nadal P, Arola L. Foodomics imaging by mass spectrometry and magnetic resonance. Electrophoresis 2016; 37:1748-67. [DOI: 10.1002/elps.201500494] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/22/2015] [Accepted: 01/05/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Núria Canela
- Group of Research on Omic Methodologies (GROM); Universitat Rovira i Virgili; Reus Spain
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
| | - Miguel Ángel Rodríguez
- Group of Research on Omic Methodologies (GROM); Universitat Rovira i Virgili; Reus Spain
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
| | - Isabel Baiges
- Group of Research on Omic Methodologies (GROM); Universitat Rovira i Virgili; Reus Spain
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
| | - Pedro Nadal
- Group of Research on Omic Methodologies (GROM); Universitat Rovira i Virgili; Reus Spain
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
- Centre Tecnològic de Nutriciò i Salut (CTNS); Reus Spain
| | - Lluís Arola
- Centre for Omic Sciences (COS); Universitat Rovira i Virgili; Reus Spain
- Centre Tecnològic de Nutriciò i Salut (CTNS); Reus Spain
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28
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Mulder IA, Esteve C, Wermer MJ, Hoehn M, Tolner EA, van den Maagdenberg AM, McDonnell LA. Funnel-freezing versus heat-stabilization for the visualization of metabolites by mass spectrometry imaging in a mouse stroke model. Proteomics 2016; 16:1652-9. [DOI: 10.1002/pmic.201500402] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/17/2016] [Accepted: 03/03/2016] [Indexed: 01/12/2023]
Affiliation(s)
- Inge A. Mulder
- Department of Neurology; Leiden University Medical Center; Leiden The Netherlands
| | - Clara Esteve
- Center for Proteomics and Metabolomics; Leiden University Medical Center; Leiden The Netherlands
| | - Marieke J.H. Wermer
- Department of Neurology; Leiden University Medical Center; Leiden The Netherlands
| | - Mathias Hoehn
- Department of Radiology; Leiden University Medical Center; Leiden The Netherlands
- Percuros BV; Enschede The Netherlands
- In-vivo-NMR Laboratory; Max Planck Institute for Neurological Research; Cologne Germany
| | - Else A. Tolner
- Department of Neurology; Leiden University Medical Center; Leiden The Netherlands
- Department of Human Genetics; Leiden University Medical Center; Leiden The Netherlands
| | - Arn M.J.M. van den Maagdenberg
- Department of Neurology; Leiden University Medical Center; Leiden The Netherlands
- Department of Human Genetics; Leiden University Medical Center; Leiden The Netherlands
| | - Liam A. McDonnell
- Center for Proteomics and Metabolomics; Leiden University Medical Center; Leiden The Netherlands
- Fondazione Pisana per la Scienza ONLUS; Pisa Italy
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29
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Fricker LD. Limitations of Mass Spectrometry-Based Peptidomic Approaches. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1981-91. [PMID: 26305799 PMCID: PMC6597174 DOI: 10.1007/s13361-015-1231-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/02/2015] [Accepted: 07/03/2015] [Indexed: 05/23/2023]
Abstract
Mass spectrometry-based peptidomic approaches are powerful techniques to detect and identify the peptide content of biological samples. The present study investigated the limitations of peptidomic approaches using trimethylammonium butyrate isotopic tags to quantify relative peptide levels and Mascot searches to identify peptides. Data were combined from previous studies on human cell lines or mouse tissues. The combined databases contain 2155 unique peptides ranging in mass from 444 to 8765 Da, with the vast majority between 1 and 3 kDa. The amino acid composition of the identified peptides generally reflected the frequency in the Eukaryotic proteome with the exception of Cys, which was not present in any of the identified peptides in the free-SH form but was detected at low frequency as a disulfide with Cys residues, a disulfide with glutathione, or as S-cyanocysteine. To test if the low detection rate of peptides smaller than 500 Da, larger than 3 kDa, or containing Cys was a limitation of the peptidomics procedure, tryptic peptides of known proteins were processed for peptidomics using the same approach used for human cell lines and mouse tissues. The identified tryptic peptides ranged from 516 to 2418 Da, whereas the theoretical digest ranged from 217 to 7559 Da. Peptides with Cys were rarely detected and, if present, the Cys was usually modified S-cyanocysteine. Additionally, peptides with mono- and di-iodo Tyr and His were identified. Taken together, there are limitations of peptidomic techniques, and awareness of these limitations is important to properly use and interpret results. Graphical Abstract ᅟ.
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Affiliation(s)
- Lloyd D Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY, 10461, USA.
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30
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Exploring the role of neuropeptide S in the regulation of arousal: a functional anatomical study. Brain Struct Funct 2015; 221:3521-46. [PMID: 26462664 DOI: 10.1007/s00429-015-1117-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/18/2015] [Indexed: 12/13/2022]
Abstract
Neuropeptide S (NPS) is a regulatory peptide expressed by limited number of neurons in the brainstem. The simultaneous anxiolytic and arousal-promoting effect of NPS suggests an involvement in mood control and vigilance, making the NPS-NPS receptor system an interesting potential drug target. Here we examined, in detail, the distribution of NPS-immunoreactive (IR) fiber arborizations in brain regions of rat known to be involved in the regulation of sleep and arousal. Such nerve terminals were frequently apposed to GABAergic/galaninergic neurons in the ventro-lateral preoptic area (VLPO) and to tyrosine hydroxylase-IR neurons in all hypothalamic/thalamic dopamine cell groups. Then we applied the single platform-on-water (mainly REM) sleep deprivation method to study the functional role of NPS in the regulation of arousal. Of the three pontine NPS cell clusters, the NPS transcript levels were increased only in the peri-coerulear group in sleep-deprived animals, but not in stress controls. The density of NPS-IR fibers was significantly decreased in the median preoptic nucleus-VLPO region after the sleep deprivation, while radioimmunoassay and mass spectrometry measurements showed a parallel increase of NPS in the anterior hypothalamus. The expression of the NPS receptor was, however, not altered in the VLPO-region. The present results suggest a selective activation of one of the three NPS-expressing neuron clusters as well as release of NPS in distinct forebrain regions after sleep deprivation. Taken together, our results emphasize a role of the peri-coerulear cluster in the modulation of arousal, and the importance of preoptic area for the action of NPS on arousal and sleep.
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Nilsson A, Goodwin RJA, Shariatgorji M, Vallianatou T, Webborn PJH, Andrén PE. Mass Spectrometry Imaging in Drug Development. Anal Chem 2015; 87:1437-55. [DOI: 10.1021/ac504734s] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Anna Nilsson
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| | - Richard J. A. Goodwin
- Drug Safety & Metabolism, Innovative Medicines, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 OWG, U.K
| | - Mohammadreza Shariatgorji
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| | - Theodosia Vallianatou
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| | - Peter J. H. Webborn
- Drug Safety & Metabolism, Innovative Medicines, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 OWG, U.K
| | - Per E. Andrén
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
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Characterizing the peritumoral brain zone in glioblastoma: a multidisciplinary analysis. J Neurooncol 2015; 122:53-61. [PMID: 25559687 DOI: 10.1007/s11060-014-1695-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/20/2014] [Indexed: 10/24/2022]
Abstract
Glioblastoma (GB) is the most frequent and aggressive type of primary brain tumor. Recurrences are mostly located at the margin of the resection cavity in the peritumoral brain zone (PBZ). Although it is widely believed that infiltrative tumor cells in this zone are responsible for GB recurrence, few studies have examined this zone. In this study, we analyzed PBZ left after surgery with a variety of techniques including radiology, histopathology, flow cytometry, genomic, transcriptomic, proteomic, and primary cell cultures. The resulting PBZ profiles were compared with those of the GB tumor zone and normal brain samples to identify characteristics specific to the PBZ. We found that tumor cell infiltration detected by standard histological analysis was present in almost one third of PBZ taken from an area that was considered normal both on standard MRI and by the neurosurgeon under an operating microscope. The panel of techniques used in this study show that the PBZ, similar to the tumor zone itself, is characterized by substantial inter-patient heterogeneity, which makes it difficult to identify representative markers. Nevertheless, we identified specific alterations in the PBZ such as the presence of selected tumor clones and stromal cells with tumorigenic and angiogenic properties. The study of GB-PBZ is a growing field of interest and this region needs to be characterized further. This will facilitate the development of new, targeted therapies for patients with GB and the development of approaches to refine the per-operative evaluation of the PBZ to optimize the surgical resection of the tumor.
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Mass spectrometric analysis of spatio-temporal dynamics of crustacean neuropeptides. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:798-811. [PMID: 25448012 DOI: 10.1016/j.bbapap.2014.10.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/23/2014] [Accepted: 10/28/2014] [Indexed: 12/13/2022]
Abstract
Neuropeptides represent one of the largest classes of signaling molecules used by nervous systems to regulate a wide range of physiological processes. Over the past several years, mass spectrometry (MS)-based strategies have revolutionized the discovery of neuropeptides in numerous model organisms, especially in decapod crustaceans. Here, we focus our discussion on recent advances in the use of MS-based techniques to map neuropeptides in the spatial domain and monitoring their dynamic changes in the temporal domain. These MS-enabled investigations provide valuable information about the distribution, secretion and potential function of neuropeptides with high molecular specificity and sensitivity. In situ MS imaging and in vivo microdialysis are highlighted as key technologies for probing spatio-temporal dynamics of neuropeptides in the crustacean nervous system. This review summarizes the latest advancement in MS-based methodologies for neuropeptide analysis including typical workflow and sample preparation strategies as well as major neuropeptide families discovered in decapod crustaceans. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Su J, Sandor K, Sköld K, Hökfelt T, Svensson CI, Kultima K. Identification and quantification of neuropeptides in naïve mouse spinal cord using mass spectrometry reveals [des-Ser1]-cerebellin as a novel modulator of nociception. J Neurochem 2014; 130:199-214. [DOI: 10.1111/jnc.12730] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/13/2014] [Accepted: 04/01/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Jie Su
- Department of Physiology and Pharmacology; Karolinska Institutet; Stockholm Sweden
| | - Katalin Sandor
- Department of Physiology and Pharmacology; Karolinska Institutet; Stockholm Sweden
| | - Karl Sköld
- Research and Development; Denator AB; Uppsala Sweden
- Department of Medical Sciences; Cancer Pharmacology and Computational Medicine; Uppsala University; Uppsala Sweden
| | - Tomas Hökfelt
- Department of Neuroscience; Karolinska Institutet; Stockholm Sweden
| | - Camilla I. Svensson
- Department of Physiology and Pharmacology; Karolinska Institutet; Stockholm Sweden
| | - Kim Kultima
- Department of Physiology and Pharmacology; Karolinska Institutet; Stockholm Sweden
- Department of Medical Sciences; Cancer Pharmacology and Computational Medicine; Uppsala University; Uppsala Sweden
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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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Casadonte R, Kriegsmann M, Zweynert F, Friedrich K, Baretton G, Bretton G, Otto M, Deininger SO, Paape R, Belau E, Suckau D, Aust D, Pilarsky C, Kriegsmann J. Imaging mass spectrometry to discriminate breast from pancreatic cancer metastasis in formalin-fixed paraffin-embedded tissues. Proteomics 2014; 14:956-64. [PMID: 24482424 DOI: 10.1002/pmic.201300430] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/17/2013] [Accepted: 12/29/2013] [Indexed: 11/07/2022]
Abstract
Diagnosis of the origin of metastasis is mandatory for adequate therapy. In the past, classification of tumors was based on histology (morphological expression of a complex protein pattern), while supportive immunohistochemical investigation relied only on few "tumor specific" proteins. At present, histopathological diagnosis is based on clinical information, morphology, immunohistochemistry, and may include molecular methods. This process is complex, expensive, requires an experienced pathologist and may be time consuming. Currently, proteomic methods have been introduced in various clinical disciplines. MALDI imaging MS combines detection of numerous proteins with morphological features, and seems to be the ideal tool for objective and fast histopathological tumor classification. To study a special tumor type and to identify predictive patterns that could discriminate metastatic breast from pancreatic carcinoma MALDI imaging MS was applied to multitissue paraffin blocks. A statistical classification model was created using a training set of primary carcinoma biopsies. This model was validated on two testing sets of different breast and pancreatic carcinoma specimens. We could discern breast from pancreatic primary tumors with an overall accuracy of 83.38%, a sensitivity of 85.95% and a specificity of 76.96%. Furthermore, breast and pancreatic liver metastases were tested and classified correctly.
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Fowler CB, O'Leary TJ, Mason JT. Toward improving the proteomic analysis of formalin-fixed, paraffin-embedded tissue. Expert Rev Proteomics 2014; 10:389-400. [PMID: 23992421 DOI: 10.1586/14789450.2013.820531] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Archival formalin-fixed, paraffin-embedded (FFPE) tissue and their associated diagnostic records represent an invaluable source of retrospective proteomic information on diseases for which the clinical outcome and response to treatment are known. However, analysis of archival FFPE tissues by high-throughput proteomic methods has been hindered by the adverse effects of formaldehyde fixation and subsequent tissue histology. This review examines recent methodological advances for extracting proteins from FFPE tissue suitable for proteomic analysis. These methods, based largely upon heat-induced antigen retrieval techniques borrowed from immunohistochemistry, allow at least a qualitative analysis of the proteome of FFPE archival tissues. The authors also discuss recent advances in the proteomic analysis of FFPE tissue; including liquid-chromatography tandem mass spectrometry, reverse phase protein microarrays and imaging mass spectrometry.
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Affiliation(s)
- Carol B Fowler
- Laboratory of Proteomics and Protein Science, Washington DC Veterans Affairs Medical Center, Washington, DC, USA.
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Araújo P, Ferreira MS, de Oliveira DN, Pereira L, Sawaya ACHF, Catharino RR, Mazzafera P. Mass spectrometry imaging: an expeditious and powerful technique for fast in situ lignin assessment in Eucalyptus. Anal Chem 2014; 86:3415-9. [PMID: 24451041 DOI: 10.1021/ac500220r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plant biomass has been suggested as an alternative to produce bioethanol. The recalcitrance of plant biomass to convert cellulose into simpler carbohydrates used in the fermentation process is partially due to lignin, but the standard methods used to analyze lignin composition frequently use toxic solvents and are laborious and time-consuming. MS imaging was used to study lignin in Eucalyptus, since this genus is the main source of cellulose in the world. Hand-cut sections of stems of two Eucalyptus species were covered with silica and directly analyzed by matrix-assisted laser sesorption ionization (MALDI)-imaging mass spectrometry (MS). Information available in the literature about soluble lignin subunits and structures were used to trace their distribution in the sections and using a software image a relative quantification could be made. Matrixes routinely used in MALDI-imaging analysis are not satisfactory to analyze plant material and were efficiently substituted by thin layer chromatography (TLC) grade silica. A total of 22 compounds were detected and relatively quantified. It was also possible to establish a proportion between syringyl and guaiacyl monolignols, characteristic for each species. Because of the simple way that samples are prepared, the MALDI-imaging approach presented here can replace, in routine analysis, complex and laborious MS methods in the study of lignin composition.
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Affiliation(s)
- Pedro Araújo
- Departamento de Biologia Vegetal, Instituto de Biologia, University of Campinas , CP 6109, 13083-970, Campinas, São Paulo, Brazil
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Minerva L, Ceulemans A, Baggerman G, Arckens L. MALDI MS imaging as a tool for biomarker discovery: methodological challenges in a clinical setting. Proteomics Clin Appl 2014; 6:581-95. [PMID: 23090913 DOI: 10.1002/prca.201200033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/12/2022]
Abstract
MALDI MS imaging (MSI) is an analytical tool capable of providing spatial distribution and relative abundance of biomolecules directly in tissue. After 15 years of intense efforts to improve the acquisition and quality of molecular images, MSI has matured into an asset of the proteomic toolbox. The power of MSI lies in the ability to differentiate tissue regions that are not histologically distinct but are characterized by different MS profiles. Recently, MSI has been gaining momentum in biomedical research and has found applications in disease diagnosis and prognosis, biomarker discovery, and drug therapy. Although the technology holds great promise, MSI is still faced with a set of methodological challenges presented by the clinical setting. There is a growing awareness regarding this topic and efforts are being taken to develop clear and practical standards to overcome these challenges. This review presents an overview of MALDI MSI as a biomarker discovery tool and recent methodological progress in the field.
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Affiliation(s)
- Laurens Minerva
- Laboratory of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Leuven, Belgium
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Shariatgorji M, Svenningsson P, Andrén PE. Mass spectrometry imaging, an emerging technology in neuropsychopharmacology. Neuropsychopharmacology 2014; 39:34-49. [PMID: 23966069 PMCID: PMC3857656 DOI: 10.1038/npp.2013.215] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 01/03/2023]
Abstract
Mass spectrometry imaging is a powerful tool for directly determining the distribution of proteins, peptides, lipids, neurotransmitters, metabolites and drugs in neural tissue sections in situ. Molecule-specific imaging can be achieved using various ionization techniques that are suited to different applications but which all yield data with high mass accuracies and spatial resolutions. The ability to simultaneously obtain images showing the distributions of chemical species ranging from metal ions to macromolecules makes it possible to explore the chemical organization of a sample and to correlate the results obtained with specific anatomical features. The imaging of biomolecules has provided new insights into multiple neurological diseases, including Parkinson's and Alzheimer's disease. Mass spectrometry imaging can also be used in conjunction with other imaging techniques in order to identify correlations between changes in the distribution of important chemical species and other changes in the properties of the tissue. Here we review the applications of mass spectrometry imaging in neuroscience research and discuss its potential. The results presented demonstrate that mass spectrometry imaging is a useful experimental method with diverse applications in neuroscience.
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Affiliation(s)
- Mohammadreza Shariatgorji
- Department of Pharmaceutical Biosciences, Biomolecular Imaging and Proteomics, National Laboratory for Mass Spectrometry Imaging, Uppsala University, Uppsala, Sweden
| | - Per Svenningsson
- Department of Neurology and Clinical Neuroscience, Centre for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Per E Andrén
- Department of Pharmaceutical Biosciences, Biomolecular Imaging and Proteomics, National Laboratory for Mass Spectrometry Imaging, Uppsala University, Uppsala, Sweden,Department of Pharmaceutical Biosciences, Biomolecular Imaging and Proteomics, National Laboratory for Mass Spectrometry Imaging, Uppsala University, Box 591, Husargatan 3, Uppsala SE-75124, Sweden, Tel: +46 18 471 7206, Fax: +46 70 167 9334, E-mail:
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Ofer D, Linial M. NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes. ACTA ACUST UNITED AC 2013; 30:931-40. [PMID: 24336809 DOI: 10.1093/bioinformatics/btt725] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
MOTIVATION The evolution of multicellular organisms is associated with increasing variability of molecules governing behavioral and physiological states. This is often achieved by neuropeptides (NPs) that are produced in neurons from a longer protein, named neuropeptide precursor (NPP). The maturation of NPs occurs through a sequence of proteolytic cleavages. The difficulty in identifying NPPs is a consequence of their diversity and the lack of applicable sequence similarity among the short functionally related NPs. RESULTS Herein, we describe Neuropeptide Precursor Identifier (NeuroPID), a machine learning scheme that predicts metazoan NPPs. NeuroPID was trained on hundreds of identified NPPs from the UniProtKB database. Some 600 features were extracted from the primary sequences and processed using support vector machines (SVM) and ensemble decision tree classifiers. These features combined biophysical, chemical and informational-statistical properties of NPs and NPPs. Other features were guided by the defining characteristics of the dibasic cleavage sites motif. NeuroPID reached 89-94% accuracy and 90-93% precision in cross-validation blind tests against known NPPs (with an emphasis on Chordata and Arthropoda). NeuroPID also identified NPP-like proteins from extensively studied model organisms as well as from poorly annotated proteomes. We then focused on the most significant sets of features that contribute to the success of the classifiers. We propose that NPPs are attractive targets for investigating and modulating behavior, metabolism and homeostasis and that a rich repertoire of NPs remains to be identified. AVAILABILITY NeuroPID source code is freely available at http://www.protonet.cs.huji.ac.il/neuropid
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Affiliation(s)
- Dan Ofer
- Department of Biological Chemistry, Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Givat Ram 91904, Israel
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Sköld K, Alm H, Scholz B. The impact of biosampling procedures on molecular data interpretation. Mol Cell Proteomics 2013; 12:1489-501. [PMID: 23382104 PMCID: PMC3675808 DOI: 10.1074/mcp.r112.024869] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 01/17/2013] [Indexed: 01/06/2023] Open
Abstract
The separation between biological and technical variation without extensive use of technical replicates is often challenging, particularly in the context of different forms of protein and peptide modifications. Biosampling procedures in the research laboratory are easier to conduct within a shorter time frame and under controlled conditions as compared with clinical sampling, with the latter often having issues of reproducibility. But is the research laboratory biosampling really less variable? Biosampling introduces within minutes rapid tissue-specific changes in the cellular microenvironment, thus inducing a range of different pathways associated with cell survival. Biosampling involves hypoxia and, depending on the circumstances, hypothermia, circumstances for which there are evolutionarily conserved defense strategies in the range of species and also are relevant for the range of biomedical conditions. It remains unclear to what extent such adaptive processes are reflected in different biosampling procedures or how important they are for the definition of sample quality. Lately, an increasing number of comparative studies on different biosampling approaches, post-mortem effects and pre-sampling biological state, have investigated such immediate early biosampling effects. Commonalities between biosampling effects and a range of ischemia/reperfusion- and hypometabolism/anoxia-associated biological phenomena indicate that even small variations in post-sampling time intervals are likely to introduce a set of nonrandom and tissue-specific effects of experimental importance (both in vivo and in vitro). This review integrates the information provided by these comparative studies and discusses how an adaptive biological perspective in biosampling procedures may be relevant for sample quality issues.
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Affiliation(s)
- Karl Sköld
- From ‡Denator AB, Uppsala Science Park, SE-75183 Uppsala and
| | - Henrik Alm
- the §Department of Pharmaceutical Biosciences, Division of Drug Safety and Toxicology, Uppsala University, SE-75124 Uppsala, Sweden
| | - Birger Scholz
- the §Department of Pharmaceutical Biosciences, Division of Drug Safety and Toxicology, Uppsala University, SE-75124 Uppsala, Sweden
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Kofanova OA, Fack F, Niclou SP, Betsou F. Combined effect of tissue stabilization and protein extraction methods on phosphoprotein analysis. Biopreserv Biobank 2013; 11:161-5. [PMID: 24850093 DOI: 10.1089/bio.2013.0008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Preanalytical conditions applied during sample collection and processing can affect the detection or quantification of unstable phosphoprotein biomarkers. We evaluated the consequences of tissue stabilization and protein extraction methods on phosphoprotein analysis. The effects of stabilization techniques (heat stabilization, snap-freezing) and time on the levels of phosphoproteins, including phospho-Akt, p-ERK 1/2, p-IkBα, p-JNK, and p38 MAPK, were evaluated using a BioPlex phosphoprotein assay. Additionally, two different protein extraction protocols, using different extraction buffers (8 M urea buffer, or Bio-Rad buffer without urea) were tested. For snap-frozen samples, protein extraction yields were comparable with the two buffer systems. For heat-stabilized samples, total protein yields were significantly lower following extraction in non-urea buffer. However, the concentrations of specific phosphoproteins were significantly higher in heat-stabilized samples than in the corresponding snap-frozen samples, indicating that this tissue processing method better preserved phosphoproteins. Significant differences were found between the measured phosphoprotein levels in heat-stabilized and snap-frozen tissue, suggesting that alterations occur very rapidly after tissue excision. Our results suggest that heat stabilization can be used as a tissue processing method for subsequent phosphoprotein analyses, but also suggest that the BioPlex phosphoprotein assay could be used as a possible quality control method to assess tissue sample integrity.
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Proteomic analysis of glioblastomas: what is the best brain control sample? J Proteomics 2013; 85:165-73. [PMID: 23651564 DOI: 10.1016/j.jprot.2013.04.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/01/2013] [Accepted: 04/26/2013] [Indexed: 11/22/2022]
Abstract
UNLABELLED Glioblastoma (GB) is the most frequent and aggressive tumor of the central nervous system. There is currently growing interest in proteomic studies of GB, particularly with the aim of identifying new prognostic or therapeutic response markers. However, comparisons between different proteomic analyses of GB have revealed few common differentiated proteins. The types of control samples used to identify such proteins may in part explain the different results obtained. We therefore tried to determine which control samples would be most suitable for GB proteomic studies. We used an isotope-coded protein labeling (ICPL) method followed by mass spectrometry to reveal and compare the protein patterns of two commonly used types of control sample: GB peritumoral brain zone samples (PBZ) from six patients and epilepsy surgery brain samples (EB) pooled from three patients. The data obtained were processed using AMEN software for network analysis. We identified 197 non-redundant proteins and 35 of them were differentially expressed. Among these 35 differentially expressed proteins, six were over-expressed in PBZ and 29 in EB, showing different proteomic patterns between the two samples. Surprisingly, EB appeared to display a tumoral-like expression pattern in comparison to PBZ. In our opinion, PBZ may be more appropriate control sample for GB proteomic analysis. BIOLOGICAL SIGNIFICANCE This manuscript describes an original study in which we used an isotope-coded protein labeling method followed by mass spectrometry to identify and compare the protein patterns in two types of sample commonly used as control for glioblastoma (GB) proteomic analysis: peritumoral brain zone and brain samples obtained during surgery for epilepsy. The choice of control samples is critical for identifying new prognostic and/or diagnostic markers in GB.
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46
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Frese CK, Boender AJ, Mohammed S, Heck AJR, Adan RAH, Altelaar AFM. Profiling of diet-induced neuropeptide changes in rat brain by quantitative mass spectrometry. Anal Chem 2013; 85:4594-604. [PMID: 23581470 DOI: 10.1021/ac400232y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Neuropeptides are intercellular signal transmitters that play key roles in modulation of many behavioral and physiological processes. Neuropeptide signaling in several nuclei in the hypothalamus contributes to the control of food intake. Additionally, food intake regulation involves neuropeptide signaling in the reward circuitry in the striatum. Here, we analyze neuropeptides extracted from hypothalamus and striatum from rats in four differentially treated dietary groups including a high-fat/high-sucrose diet, mimicking diet-induced obesity. We employ high-resolution tandem mass spectrometry using higher-energy collision dissociation and electron transfer dissociation fragmentation for sensitive identification of more than 1700 unique endogenous peptides, including virtually all key neuropeptides known to be involved in food intake regulation. Label-free quantification of differential neuropeptide expression revealed comparable upregulation of orexigenic and anorexigenic neuropeptides in rats that were fed on a high-fat/high-sucrose diet.
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Affiliation(s)
- Christian K Frese
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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47
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Norris JL, Caprioli RM. Analysis of tissue specimens by matrix-assisted laser desorption/ionization imaging mass spectrometry in biological and clinical research. Chem Rev 2013; 113:2309-42. [PMID: 23394164 PMCID: PMC3624074 DOI: 10.1021/cr3004295] [Citation(s) in RCA: 502] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jeremy L. Norris
- National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, and Department of Biochemistry, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8575
| | - Richard M. Caprioli
- National Research Resource for Imaging Mass Spectrometry, Mass Spectrometry Research Center, and Department of Biochemistry, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232-8575
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48
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Thompson SM, Craven RA, Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue. Proteomics Clin Appl 2013; 7:241-51. [PMID: 23027712 DOI: 10.1002/prca.201200086] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 12/14/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue.
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Affiliation(s)
- Seonaid M Thompson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Molecular Medicine, St. James's University Hospital, United Kingdom
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49
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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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50
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Gelman JS, Dasgupta S, Berezniuk I, Fricker LD. Analysis of peptides secreted from cultured mouse brain tissue. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2408-17. [PMID: 23402728 DOI: 10.1016/j.bbapap.2013.01.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/25/2013] [Accepted: 01/29/2013] [Indexed: 01/02/2023]
Abstract
Peptides represent a major class of cell-cell signaling molecules. Most peptidomic studies have focused on peptides present in brain or other tissues. For a peptide to function in intercellular signaling, it must be secreted. The present study was undertaken to identify the major peptides secreted from mouse brain slices that were cultured in oxygenated buffer for 3-4h. Approximately 75% of the peptides identified in extracts of cultured slices matched the previously reported peptide content of heat-inactivated mouse brain tissue, whereas only 2% matched the peptide content of unheated brain tissue; the latter showed a large number of postmortem changes. As found with extracts of heat-inactivated mouse brain, the extracts of cultured brain slices represented secretory pathway peptides as well as peptides derived from intracellular proteins such as those present in the cytosol and mitochondria. A subset of the peptides detected in the extracts of the cultured slices was detected in the culture media. The vast majority of secreted peptides arose from intracellular proteins and not secretory pathway proteins. The peptide RVD-hemopressin, a CB1 cannabinoid receptor agonist, was detected in culture media, which is consistent with a role for RVD-hemopressin as a non-classical neuropeptide. Taken together with previous studies, the present results show that short-term culture of mouse brain slices is an appropriate system to study peptide secretion, especially the non-conventional pathway(s) by which peptides produced from intracellular proteins are secreted. This article is part of a Special Issue entitled: An Updated Secretome.
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Affiliation(s)
- Julia S Gelman
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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