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Mousavi S, Qiu H, Heinis FI, Bredahl EC, Ridwan Abid MS, Clifton AD, Andrews MT, Checco JW. Effects of Anesthetic Administration on Rat Hypothalamus and Cerebral Cortex Peptidome. ACS Chem Neurosci 2023; 14:3986-3992. [PMID: 37879091 PMCID: PMC10872895 DOI: 10.1021/acschemneuro.3c00499] [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: 10/27/2023] Open
Abstract
Prohormone-derived neuropeptides act as cell-cell signaling molecules to mediate a wide variety of biological processes in the animal brain. Mass spectrometry-based peptidomic experiments are valuable approaches to gain insight into the dynamics of individual peptides under different physiological conditions or experimental treatments. However, the use of anesthetics during animal procedures may confound experimental peptide measurements, especially in the brain, where anesthetics act. Here, we investigated the effects of the commonly used anesthetics isoflurane and sodium pentobarbital on the peptide profile in the rodent hypothalamus and cerebral cortex, as assessed by label-free quantitative peptidomics. Our results showed that neither anesthetic dramatically alters peptide levels, although extended isoflurane exposure did cause changes in a small number of prohormone-derived peptides in the cerebral cortex. Overall, our results demonstrate that acute anesthetic administration can be utilized in peptidomic experiments of the hypothalamus and cerebral cortex without greatly affecting the measured peptide profiles.
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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
| | - Eric C. Bredahl
- Department of Exercise Science and Pre-Health Professions, Creighton University, Omaha, NE 68178, United States
| | - Md Shadman Ridwan Abid
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Ashley D. Clifton
- 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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Qiu TA, Lee CJ, Huang C, Lee DK, Rubakhin SS, Romanova EV, Sweedler JV. Biodistribution and racemization of gut-absorbed L/D-alanine in germ-free mice. Commun Biol 2023; 6:851. [PMID: 37587187 PMCID: PMC10432453 DOI: 10.1038/s42003-023-05209-y] [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] [Received: 01/02/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Microbiome-derived metabolites are important for the microbiome-gut-brain axis and the discovery of new disease treatments. D-Alanine (D-Ala) is found in many animals as a potential co-agonist of the N-methyl-D-aspartate receptors (NMDAR), receptors widely used in the nervous and endocrine systems. The gut microbiome, diet and putative endogenous synthesis are the potential sources of D-Ala in animals, although there is no direct evidence to show the distribution and racemization of gut-absorbed L-/D-Ala with regards to host-microbe interactions in mammals. In this work, we utilized germ-free mice to control the interference from microbiota and isotopically labeled L-/D-Ala to track their biodistribution and racemization in vivo. Results showed time-dependent biodistribution of gut-absorbed D-Ala, particularly accumulation of gut-absorbed D-Ala in pancreatic tissues, brain, and pituitary. No endogenous synthesis of D-Ala via racemization was observed in germ-free mice. The sources of D-Ala in mice were revealed as microbiota and diet, but not endogenous racemization. This work indicates the importance of further investigating the in vivo biological functions of gut-microbiome derived D-Ala, particularly on NMDAR-related activities, for D-Ala as a potential signaling molecules in the microbiome-gut-brain axis.
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Affiliation(s)
- Tian Autumn Qiu
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Cindy J Lee
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Chen Huang
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Dong-Kyu Lee
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Stanislav S Rubakhin
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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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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4
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Tillmaand EG, Anapindi KDB, De La Toba EA, Guo CJ, Krebs J, Lenhart AE, Liu Q, Sweedler JV. Quantitative Characterization of the Neuropeptide Level Changes in Dorsal Horn and Dorsal Root Ganglia Regions of the Murine Itch Models. J Proteome Res 2020; 19:1248-1257. [PMID: 31957451 PMCID: PMC7060821 DOI: 10.1021/acs.jproteome.9b00758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chronic itch can be extremely devastating and, in many cases, difficult to treat. One challenge in treating itch disorders is the limited understanding of the multitude of chemical players involved in the communication of itch sensation from the peripheral to the central nervous system. Neuropeptides are intercellular signaling molecules that are known to be involved in the transmission of itch signals from primary afferent neurons, which detect itch in the skin, to higher-order circuits in the spinal cord and brain. To investigate the role of neuropeptides in transmitting itch signals, we generated two mouse models of chronic itch-Acetone-Ether-Water (AEW, dry skin) and calcipotriol (MC903, atopic dermatitis). For peptide identification and quantitation, we analyzed the peptide content of dorsal root ganglia (DRG) and dorsal horn (DH) tissues from chronically itchy mice using liquid chromatography coupled to tandem mass spectrometry. De novo-assisted database searching facilitated the identification and quantitation of 335 peptides for DH MC903, 318 for DH AEW, 266 for DRG MC903, and 271 for DRG AEW. Of these quantifiable peptides, we detected 30 that were differentially regulated in the tested models, after accounting for multiple testing correction (q ≤ 0.1). These include several peptide candidates derived from neuropeptide precursors, such as proSAAS, protachykinin-1, proenkephalin, and calcitonin gene-related peptide, some of them previously linked to itch. The peptides identified in this study may help elucidate our understanding about these debilitating disorders. Data are available via ProteomeXchange with identifier PXD015949.
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Affiliation(s)
- Emily G. Tillmaand
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Krishna D. B. Anapindi
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Eduardo A. De La Toba
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Changxiong J. Guo
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Jessica Krebs
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Ashley E. Lenhart
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Qin Liu
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Jonathan V. Sweedler
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
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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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6
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Park HM, Satta R, Davis RG, Goo YA, LeDuc RD, Fellers RT, Greer JB, Romanova EV, Rubakhin SS, Tai R, Thomas PM, Sweedler JV, Kelleher NL, Patrie SM, Lasek AW. Multidimensional Top-Down Proteomics of Brain-Region-Specific Mouse Brain Proteoforms Responsive to Cocaine and Estradiol. J Proteome Res 2019; 18:3999-4012. [PMID: 31550894 DOI: 10.1021/acs.jproteome.9b00481] [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: 11/29/2022]
Abstract
Cocaine addiction afflicts nearly 1 million adults in the United States, and to date, there are no known treatments approved for this psychiatric condition. Women are particularly vulnerable to developing a cocaine use disorder and suffer from more serious cardiac consequences than men when using cocaine. Estrogen is one biological factor contributing to the increased risk for females to develop problematic cocaine use. Animal studies have demonstrated that estrogen (17β-estradiol or E2) enhances the rewarding properties of cocaine. Although E2 affects the dopamine system, the molecular and cellular mechanisms of E2-enhanced cocaine reward have not been characterized. In this study, quantitative top-down proteomics was used to measure intact proteins in specific regions of the female mouse brain after mice were trained for cocaine-conditioned place preference, a behavioral test of cocaine reward. Several proteoform changes occurred in the ventral tegmental area after combined cocaine and E2 treatments, with the most numerous proteoform alterations on myelin basic protein, indicating possible changes in white matter structure. There were also changes in histone H4, protein phosphatase inhibitors, cholecystokinin, and calmodulin proteoforms. These observations provide insight into estrogen signaling in the brain and may guide new approaches to treating women with cocaine use disorder.
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Affiliation(s)
- Hae-Min Park
- Departments of Chemistry, Molecular Biosciences, and The Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Rosalba Satta
- Department of Psychiatry , University of Illinois at Chicago , 1601 West Taylor Street , Chicago , Illinois 60612 , United States
| | - Roderick G Davis
- Departments of Chemistry, Molecular Biosciences, and The Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Young Ah Goo
- Departments of Chemistry, Molecular Biosciences, and The Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Richard D LeDuc
- Departments of Chemistry, Molecular Biosciences, and The Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Ryan T Fellers
- Departments of Chemistry, Molecular Biosciences, and The Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Joseph B Greer
- Departments of Chemistry, Molecular Biosciences, and The Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Elena V Romanova
- Department of Chemistry , University of Illinois , Urbana-Champaign, 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Stanislav S Rubakhin
- Department of Chemistry , University of Illinois , Urbana-Champaign, 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Rex Tai
- Department of Psychiatry , University of Illinois at Chicago , 1601 West Taylor Street , Chicago , Illinois 60612 , United States
| | - Paul M Thomas
- Departments of Chemistry, Molecular Biosciences, and The Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Jonathan V Sweedler
- Department of Chemistry , University of Illinois , Urbana-Champaign, 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences, and The Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Steven M Patrie
- Departments of Chemistry, Molecular Biosciences, and The Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Amy W Lasek
- Department of Psychiatry , University of Illinois at Chicago , 1601 West Taylor Street , Chicago , Illinois 60612 , United States
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7
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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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8
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Segura-Uribe JJ, Farfán-García ED, Guerra-Araiza C, Ciprés-Flores FJ, García-dela Torre P, Soriano-Ursúa MA. Differences in brain regions of three mice strains identified by label-free micro-Raman. SPECTROSCOPY LETTERS 2018. [DOI: 10.1080/00387010.2018.1473883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Julia Jeanett Segura-Uribe
- Departamento de Fisiología, Departamento de Bioquímica y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
- Unidad de Investigación Médica en Enfermedades Neurológicas, Hospital de Especialidades. Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Eunice Dalet Farfán-García
- Departamento de Fisiología, Departamento de Bioquímica y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Christian Guerra-Araiza
- Unidad de Investigación Médica en Farmacología, Hospital de Especialidades. Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Fabiola Jimena Ciprés-Flores
- Departamento de Fisiología, Departamento de Bioquímica y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Paola García-dela Torre
- Unidad de Investigación Médica en Enfermedades Neurológicas, Hospital de Especialidades. Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Marvin Antonio Soriano-Ursúa
- Departamento de Fisiología, Departamento de Bioquímica y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
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9
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Zhou Y, Kreek MJ. Involvement of Activated Brain Stress Responsive Systems in Excessive and "Relapse" Alcohol Drinking in Rodent Models: Implications for Therapeutics. J Pharmacol Exp Ther 2018; 366:9-20. [PMID: 29669731 PMCID: PMC5988024 DOI: 10.1124/jpet.117.245621] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/16/2018] [Indexed: 02/06/2023] Open
Abstract
Addictive diseases, including addiction to alcohol, pose massive public health costs. Addiction is a chronic relapsing disease caused by both the direct effects induced by drugs and persistent neuroadaptations at the molecular, cellular, and behavioral levels. These drug-type specific neuroadaptations are brought on largely by the reinforcing effects of drugs on the central nervous system and environmental stressors. Results from animal experiments have demonstrated important interactions between alcohol and stress-responsive systems. Addiction to specific drugs such as alcohol, psychostimulants, and opioids shares some common direct or downstream effects on the brain's stress-responsive systems, including arginine vasopressin and its V1b receptors, dynorphin and the κ-opioid receptors, pro-opiomelanocortin/β-endorphin and the μ-opioid receptors, and the endocannabinoids. Further study of these systems through laboratory-based and translational research could lead to the discovery of novel treatment targets and the early optimization of interventions (for example, combination) for the pharmacologic therapy of alcoholism.
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Affiliation(s)
- Yan Zhou
- Laboratory of Biology of Addictive Diseases, Rockefeller University, New York, New York
| | - Mary Jeanne Kreek
- Laboratory of Biology of Addictive Diseases, Rockefeller University, New York, New York
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10
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Monroe EB, Annangudi SP, Wadhams AA, Richmond TA, Yang N, Southey BR, Romanova EV, Schoofs L, Baggerman G, Sweedler JV. Exploring the Sea Urchin Neuropeptide Landscape by Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:923-934. [PMID: 29667164 PMCID: PMC5943159 DOI: 10.1007/s13361-018-1898-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/04/2017] [Accepted: 12/16/2017] [Indexed: 05/08/2023]
Abstract
Neuropeptides are essential cell-to-cell signaling messengers and serve important regulatory roles in animals. Although remarkable progress has been made in peptide identification across the Metazoa, for some phyla such as Echinodermata, limited neuropeptides are known and even fewer have been verified on the protein level. We employed peptidomic approaches using bioinformatics and mass spectrometry (MS) to experimentally confirm 23 prohormones and to characterize a new prohormone in nervous system tissue from Strongylocentrotus purpuratus, the purple sea urchin. Ninety-three distinct peptides from known and novel prohormones were detected with MS from extracts of the radial nerves, many of which are reported or experimentally confirmed here for the first time, representing a large-scale study of neuropeptides from the phylum Echinodermata. Many of the identified peptides and their precursor proteins have low homology to known prohormones from other species/phyla and are unique to the sea urchin. By pairing bioinformatics with MS, the capacity to characterize novel peptides and annotate prohormone genes is enhanced. Graphical Abstract.
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Affiliation(s)
- Eric B Monroe
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Suresh P Annangudi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andinet A Wadhams
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Timothy A Richmond
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ning Yang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Liliane Schoofs
- Functional Genomics and Proteomics Unit, KU Leuven, 3000, Leuven, Belgium
| | - Geert Baggerman
- ProMeta Interfacultary Center for Proteomics and Metabolomics, KU Leuven, 3000, Leuven, Belgium
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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11
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Davis RG, Park HM, Kim K, Greer JB, Fellers RT, LeDuc RD, Romanova EV, Rubakhin SS, Zombeck JA, Wu C, Yau PM, Gao P, van Nispen AJ, Patrie SM, Thomas PM, Sweedler JV, Rhodes JS, Kelleher NL. Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains. Anal Chem 2018; 90:3802-3810. [PMID: 29481055 DOI: 10.1021/acs.analchem.7b04108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Over the past decade, advances in mass spectrometry-based proteomics have accelerated brain proteome research aimed at studying the expression, dynamic modification, interaction and function of proteins in the nervous system that are associated with physiological and behavioral processes. With the latest hardware and software improvements in top-down mass spectrometry, the technology has expanded from mere protein profiling to high-throughput identification and quantification of intact proteoforms. Murine systems are broadly used as models to study human diseases. Neuroscientists specifically study the mouse brain from inbred strains to help understand how strain-specific genotype and phenotype affect development, functioning, and disease progression. This work describes the first application of label-free quantitative top-down proteomics to the analysis of the mouse brain proteome. Operating in discovery mode, we determined physiochemical differences in brain tissue from four healthy inbred strains, C57BL/6J, DBA/2J, FVB/NJ, and BALB/cByJ, after probing their intact proteome in the 3.5-30 kDa mass range. We also disseminate these findings using a new tool for top-down proteomics, TDViewer and cataloged them in a newly established Mouse Brain Proteoform Atlas. The analysis of brain tissues from the four strains identified 131 gene products leading to the full characterization of 343 of the 593 proteoforms identified. Within the results, singly and doubly phosphorylated ARPP-21 proteoforms, known to inhibit calmodulin, were differentially expressed across the four strains. Gene ontology (GO) analysis for detected differentially expressed proteoforms also helps to illuminate the similarities and dissimilarities in phenotypes among these inbred strains.
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Affiliation(s)
- Roderick G Davis
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Hae-Min Park
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Kyunggon Kim
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Joseph B Greer
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Ryan T Fellers
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Richard D LeDuc
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Elena V Romanova
- Department of Chemistry , University of Illinois, Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Stanislav S Rubakhin
- Department of Chemistry , University of Illinois, Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Jonathan A Zombeck
- Department of Psychology , University of Illinois, Urbana-Champaign , 405 North Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Cong Wu
- Department of Chemistry , University of Illinois, Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Peter M Yau
- Roy J. Carver Biotechnology Center, Protein Sciences Facility , University of Illinois, Urbana-Champaign , 505 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Peng Gao
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Alexandra J van Nispen
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Steven M Patrie
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Paul M Thomas
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Jonathan V Sweedler
- Department of Chemistry , University of Illinois, Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Justin S Rhodes
- Department of Psychology , University of Illinois, Urbana-Champaign , 405 North Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
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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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13
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Hu CK, Southey BR, Romanova EV, Maruska KP, Sweedler JV, Fernald RD. Identification of prohormones and pituitary neuropeptides in the African cichlid, Astatotilapia burtoni. BMC Genomics 2016; 17:660. [PMID: 27543050 PMCID: PMC4992253 DOI: 10.1186/s12864-016-2914-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 07/06/2016] [Indexed: 12/14/2022] Open
Abstract
Background Cichlid fishes have evolved remarkably diverse reproductive, social, and feeding behaviors. Cell-to-cell signaling molecules, notably neuropeptides and peptide hormones, are known to regulate these behaviors across vertebrates. This class of signaling molecules derives from prohormone genes that have undergone multiple duplications and losses in fishes. Whether and how subfunctionalization, neofunctionalization, or losses of neuropeptides and peptide hormones have contributed to fish behavioral diversity is largely unknown. Information on fish prohormones has been limited and is complicated by the whole genome duplication of the teleost ancestor. We combined bioinformatics, mass spectrometry-enabled peptidomics, and molecular techniques to identify the suite of neuropeptide prohormones and pituitary peptide products in Astatotilapia burtoni, a well-studied member of the diverse African cichlid clade. Results Utilizing the A. burtoni genome, we identified 148 prohormone genes, with 21 identified as a single copy and 39 with at least 2 duplicated copies. Retention of prohormone duplicates was therefore 41 %, which is markedly above previous reports for the genome-wide average in teleosts. Beyond the expected whole genome duplication, differences between cichlids and mammals can be attributed to gene loss in tetrapods and additional duplication after divergence. Mass spectrometric analysis of the pituitary identified 620 unique peptide sequences that were matched to 120 unique proteins. Finally, we used in situ hybridization to localize the expression of galanin, a prohormone with exceptional sequence divergence in cichlids, as well as the expression of a proopiomelanocortin, prohormone that has undergone an additional duplication in some bony fish lineages. Conclusion We characterized the A. burtoni prohormone complement. Two thirds of prohormone families contain duplications either from the teleost whole genome duplication or a more recent duplication. Our bioinformatic and mass spectrometric findings provide information on a major vertebrate clade that will further our understanding of the functional ramifications of these prohormone losses, duplications, and sequence changes across vertebrate evolution. In the context of the cichlid radiation, these findings will also facilitate the exploration of neuropeptide and peptide hormone function in behavioral diversity both within A. burtoni and across cichlid and other fish species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2914-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caroline K Hu
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.,Present address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Elena V Romanova
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Karen P Maruska
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Russell D Fernald
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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14
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Ong TH, Romanova EV, Roberts-Galbraith RH, Yang N, Zimmerman TA, Collins JJ, Lee JE, Kelleher NL, Newmark PA, Sweedler JV. Mass Spectrometry Imaging and Identification of Peptides Associated with Cephalic Ganglia Regeneration in Schmidtea mediterranea. J Biol Chem 2016; 291:8109-20. [PMID: 26884331 PMCID: PMC4825013 DOI: 10.1074/jbc.m115.709196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Indexed: 12/21/2022] Open
Abstract
Tissue regeneration is a complex process that involves a mosaic of molecules that vary spatially and temporally. Insights into the chemical signaling underlying this process can be achieved with a multiplex and untargeted chemical imaging method such as mass spectrometry imaging (MSI), which can enablede novostudies of nervous system regeneration. A combination of MSI and multivariate statistics was used to differentiate peptide dynamics in the freshwater planarian flatwormSchmidtea mediterraneaat different time points during cephalic ganglia regeneration. A protocol was developed to makeS. mediterraneatissues amenable for MSI. MS ion images of planarian tissue sections allow changes in peptides and unknown compounds to be followed as a function of cephalic ganglia regeneration. In conjunction with fluorescence imaging, our results suggest that even though the cephalic ganglia structure is visible after 6 days of regeneration, the original chemical composition of these regenerated structures is regained only after 12 days. Differences were observed in many peptides, such as those derived from secreted peptide 4 and EYE53-1. Peptidomic analysis further identified multiple peptides from various known prohormones, histone proteins, and DNA- and RNA-binding proteins as being associated with the regeneration process. Mass spectrometry data also facilitated the identification of a new prohormone, which we have named secreted peptide prohormone 20 (SPP-20), and is up-regulated during regeneration in planarians.
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Affiliation(s)
- Ta-Hsuan Ong
- From the Department of Chemistry, and the Beckman Institute
| | | | - Rachel H Roberts-Galbraith
- the Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
| | - Ning Yang
- From the Department of Chemistry, and the Beckman Institute
| | | | - James J Collins
- the Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
| | - Ji Eun Lee
- From the Department of Chemistry, and the Beckman Institute
| | - Neil L Kelleher
- the Departments of Chemistry and Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60611
| | - Phillip A Newmark
- the Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, and
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