1
|
McClatchy DB, Powell SB, Yates JR. In vivo mapping of protein-protein interactions of schizophrenia risk factors generates an interconnected disease network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571320. [PMID: 38168169 PMCID: PMC10759996 DOI: 10.1101/2023.12.12.571320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Genetic analyses of Schizophrenia (SCZ) patients have identified thousands of risk factors. In silico protein-protein interaction (PPI) network analysis has provided strong evidence that disrupted PPI networks underlie SCZ pathogenesis. In this study, we performed in vivo PPI analysis of several SCZ risk factors in the rodent brain. Using endogenous antibody immunoprecipitations coupled to mass spectrometry (MS) analysis, we constructed a SCZ network comprising 1612 unique PPI with a 5% FDR. Over 90% of the PPI were novel, reflecting the lack of previous PPI MS studies in brain tissue. Our SCZ PPI network was enriched with known SCZ risk factors, which supports the hypothesis that an accumulation of disturbances in selected PPI networks underlies SCZ. We used Stable Isotope Labeling in Mammals (SILAM) to quantitate phencyclidine (PCP) perturbations in the SCZ network and found that PCP weakened most PPI but also led to some enhanced or new PPI. These findings demonstrate that quantitating PPI in perturbed biological states can reveal alterations to network biology.
Collapse
|
2
|
Puig S, Xue X, Salisbury R, Shelton MA, Kim SM, Hildebrand MA, Glausier JR, Freyberg Z, Tseng GC, Yocum AK, Lewis DA, Seney ML, MacDonald ML, Logan RW. Circadian rhythm disruptions associated with opioid use disorder in synaptic proteomes of human dorsolateral prefrontal cortex and nucleus accumbens. Mol Psychiatry 2023; 28:4777-4792. [PMID: 37674018 PMCID: PMC10914630 DOI: 10.1038/s41380-023-02241-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Opioid craving and relapse vulnerability is associated with severe and persistent sleep and circadian rhythm disruptions. Understanding the neurobiological underpinnings of circadian rhythms and opioid use disorder (OUD) may prove valuable for developing new treatments for opioid addiction. Previous work indicated molecular rhythm disruptions in the human brain associated with OUD, highlighting synaptic alterations in the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc)-key brain regions involved in cognition and reward, and heavily implicated in the pathophysiology of OUD. To provide further insights into the synaptic alterations in OUD, we used mass-spectrometry based proteomics to deeply profile protein expression alterations in bulk tissue and synaptosome preparations from DLPFC and NAc of unaffected and OUD subjects. We identified 55 differentially expressed (DE) proteins in DLPFC homogenates, and 44 DE proteins in NAc homogenates, between unaffected and OUD subjects. In synaptosomes, we identified 161 and 56 DE proteins in DLPFC and NAc, respectively, of OUD subjects. By comparing homogenate and synaptosome protein expression, we identified proteins enriched specifically in synapses that were significantly altered in both DLPFC and NAc of OUD subjects. Across brain regions, synaptic protein alterations in OUD subjects were primarily identified in glutamate, GABA, and circadian rhythm signaling. Using time-of-death (TOD) analyses, where the TOD of each subject is used as a time-point across a 24-h cycle, we were able to map circadian-related changes associated with OUD in synaptic proteomes associated with vesicle-mediated transport and membrane trafficking in the NAc and platelet-derived growth factor receptor beta signaling in DLPFC. Collectively, our findings lend further support for molecular rhythm disruptions in synaptic signaling in the human brain as a key factor in opioid addiction.
Collapse
Affiliation(s)
- Stephanie Puig
- Department of Pharmacology, Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xiangning Xue
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan Salisbury
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Micah A Shelton
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sam-Moon Kim
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mariah A Hildebrand
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jill R Glausier
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - David A Lewis
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marianne L Seney
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew L MacDonald
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Ryan W Logan
- Department of Pharmacology, Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA.
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| |
Collapse
|
3
|
Winnik WM, Padgett W, Pitzer EM, Herr DW. Proteome Profiling of Rat Brain Cortical Changes during Early Postnatal Brain Development. J Proteome Res 2023; 22:2460-2476. [PMID: 37326657 PMCID: PMC10851773 DOI: 10.1021/acs.jproteome.3c00172] [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: 06/17/2023]
Abstract
Label-free quantitation (LFQ) was applied to proteome profiling of rat brain cortical development during the early postnatal period. Male and female rat brain extracts were prepared using a convenient, detergent-free sample preparation technique at postnatal days (PND) 2, 8, 15, and 22. The PND protein ratios were calculated using Proteome Discoverer, and the PND protein change profiles were constructed separately for male and female animals for key presynaptic, postsynaptic, and adhesion brain proteins. The profiles were compared to the analogous profiles assembled from the published mouse and rat cortex proteomic data, including the fractionated-synaptosome data. The PND protein-change trendlines, Pearson correlation coefficient (PCC), and linear regression analysis of the statistically significant PND protein changes were used in the comparative analysis of the datasets. The analysis identified similarities and differences between the datasets. Importantly, there were significant similarities in the comparison of the rat cortex PND (current work) vs mouse (previously published) PND profiles, although in general, a lower abundance of synaptic proteins in mice than in rats was found. The male and female rat cortex PND profiles were expectedly almost identical (98-99% correlation by PCC), which also substantiated this LFQ nanoflow liquid chromatography-high-resolution mass spectrometry approach.
Collapse
Affiliation(s)
- Witold M Winnik
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - William Padgett
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Emily M Pitzer
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - David W Herr
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| |
Collapse
|
4
|
Skinnider MA, Scott NE, Prudova A, Kerr CH, Stoynov N, Stacey RG, Chan QWT, Rattray D, Gsponer J, Foster LJ. An atlas of protein-protein interactions across mouse tissues. Cell 2021; 184:4073-4089.e17. [PMID: 34214469 DOI: 10.1016/j.cell.2021.06.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Cellular processes arise from the dynamic organization of proteins in networks of physical interactions. Mapping the interactome has therefore been a central objective of high-throughput biology. However, the dynamics of protein interactions across physiological contexts remain poorly understood. Here, we develop a quantitative proteomic approach combining protein correlation profiling with stable isotope labeling of mammals (PCP-SILAM) to map the interactomes of seven mouse tissues. The resulting maps provide a proteome-scale survey of interactome rewiring across mammalian tissues, revealing more than 125,000 unique interactions at a quality comparable to the highest-quality human screens. We identify systematic suppression of cross-talk between the evolutionarily ancient housekeeping interactome and younger, tissue-specific modules. Rewired proteins are tightly regulated by multiple cellular mechanisms and are implicated in disease. Our study opens up new avenues to uncover regulatory mechanisms that shape in vivo interactome responses to physiological and pathophysiological stimuli in mammalian systems.
Collapse
Affiliation(s)
- Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nichollas E Scott
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Peter Doherty Institute, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Anna Prudova
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Craig H Kerr
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nikolay Stoynov
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Queenie W T Chan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - David Rattray
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| |
Collapse
|
5
|
Xu Y, Song X, Wang D, Wang Y, Li P, Li J. Proteomic insights into synaptic signaling in the brain: the past, present and future. Mol Brain 2021; 14:37. [PMID: 33596935 PMCID: PMC7888154 DOI: 10.1186/s13041-021-00750-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
Chemical synapses in the brain connect neurons to form neural circuits, providing the structural and functional bases for neural communication. Disrupted synaptic signaling is closely related to a variety of neurological and psychiatric disorders. In the past two decades, proteomics has blossomed as a versatile tool in biological and biomedical research, rendering a wealth of information toward decoding the molecular machinery of life. There is enormous interest in employing proteomic approaches for the study of synapses, and substantial progress has been made. Here, we review the findings of proteomic studies of chemical synapses in the brain, with special attention paid to the key players in synaptic signaling, i.e., the synaptic protein complexes and their post-translational modifications. Looking toward the future, we discuss the technological advances in proteomics such as data-independent acquisition mass spectrometry (DIA-MS), cross-linking in combination with mass spectrometry (CXMS), and proximity proteomics, along with their potential to untangle the mystery of how the brain functions at the molecular level. Last but not least, we introduce the newly developed synaptomic methods. These methods and their successful applications marked the beginnings of the synaptomics era.
Collapse
Affiliation(s)
- Yalan Xu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Xiuyue Song
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Dong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China.
| |
Collapse
|
6
|
Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
Collapse
Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
| |
Collapse
|
7
|
Yates JR. The Journey Is the Reward, a Taoist Proverb: John B. Fenn Award for Distinguished Contribution in Mass Spectrometry Lecture. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1327-1336. [PMID: 32338000 DOI: 10.1021/jasms.0c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This account provided by John Yates describes his incredible path as a scientist, emphasizing key decisions along the way that shaped his career and led to his landmark contributions to the field of mass spectrometry. Although perhaps best known is the development of the SEQUEST algorithm for automated interpretation of tandem mass spectra of peptides, John's achievements have spanned the field of proteomics and had major impact on the ability to address and solve significant biological problems.
Collapse
Affiliation(s)
- John R Yates
- Departments of Molecular Medicine and Neurobiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR302B, LaJolla, California 92037, United States
| |
Collapse
|
8
|
Kim YG, Woo J, Park J, Kim S, Lee YS, Kim Y, Kim SJ. Quantitative Proteomics Reveals Distinct Molecular Signatures of Different Cerebellum-Dependent Learning Paradigms. J Proteome Res 2020; 19:2011-2025. [PMID: 32181667 DOI: 10.1021/acs.jproteome.9b00826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cerebellum improves motor performance by adjusting motor gain appropriately. As de novo protein synthesis is essential for the formation and retention of memories, we hypothesized that motor learning in the opposite direction would induce a distinct pattern of protein expression in the cerebellum. We conducted quantitative proteomic profiling to compare the level of protein expression in the cerebellum at 1 and 24 h after training from mice that underwent different paradigms of cerebellum-dependent oculomotor learning from specific directional changes in motor gain. We quantified a total of 43 proteins that were significantly regulated in each of the three learning paradigms in the cerebellum at 1 and 24 h after learning. In addition, functional enrichment analysis identified protein groups that were differentially enriched or depleted in the cerebellum at 24 h after the three oculomotor learnings, suggesting that distinct biological pathways may be engaged in the formation of three oculomotor memories. Weighted correlation network analysis discovered groups of proteins significantly correlated with oculomotor memory. Finally, four proteins (Snca, Sncb, Cttn, and Stmn1) from the protein group correlated with the learning amount after oculomotor training were validated by Western blot. This study provides a comprehensive and unbiased list of proteins related to three cerebellum-dependent motor learning paradigms, suggesting the distinct nature of protein expression in the cerebellum for each learning paradigm. The proteomics data have been deposited to the ProteomeXchange Consortium with identifiers <PXD008433>.
Collapse
Affiliation(s)
- Yong Gyu Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jongmin Woo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joonho Park
- Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Seoul 151-742, Korea
| | - Sooyong Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yong-Seok Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Interdisciplinary Program in Bioengineering, College of Engineering, Seoul National University, 1 Gwanak-ro, Seoul 151-742, Korea
| | - Sang Jeong Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.,Department of Physiology, Seoul National University College of Medicine, Seoul 03080, Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| |
Collapse
|
9
|
Advances and applications of stable isotope labeling-based methods for proteome relative quantitation. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
10
|
Nam SM, Cho IS, Seo JS, Go TH, Kim JH, Nahm SS, Chang BJ, Lee JH. Ascorbic Acid Attenuates Lead-Induced Alterations in the Synapses in the Developing Rat Cerebellum. Biol Trace Elem Res 2019; 187:142-150. [PMID: 29696534 DOI: 10.1007/s12011-018-1354-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/17/2018] [Indexed: 11/26/2022]
Abstract
We evaluated the effect of lead (Pb) and ascorbic acid treatment of pregnant female rats on cerebellar development in pups. Pb was administered in drinking water (0.2% Pb acetate), and ascorbic acid (100 mg/kg) was administered through oral intubation. Fifteen female rats were randomly classified into control, Pb, and Pb plus ascorbic acid (PA) groups. The treatment of Pb and ascorbic acid treatments were terminated after birth to evaluate the effects on the gestational development of the cerebellum. At postnatal day 21 (PND21), pups were sacrificed, and blood Pb level was analyzed. Blood Pb levels of pups and dams were highest in the Pb group and reduced in the PA group. Immunohistochemistry and immunoblot assays were conducted to study the cerebellar expression levels of synaptic proteins. Along with a significant reduction in Purkinje cells, the reduction in presynaptic (synaptophysin) and postsynaptic (postsynaptic density protein 95, N-methyl-D-aspartate receptor subtype 1) marker proteins was observed in Pb-exposed pups. Ascorbic acid treatment significantly prevented Pb-induced impairment in the cerebellar synaptic proteins. Hypothesizing that brain-derived neurotrophic factor (BDNF) might be affected by Pb exposure given its importance in the regulation of synaptogenesis, we observed a Pb-induced decrease and ascorbic acid-mediated increase of BDNF in the cerebellum. Luxol fast blue staining and myelin basic protein analysis suggest that ascorbic acid treatment ameliorated the Pb exposure-induced reduction in the axonal fibers in the developing cerebellum. Overall, we conclude that ascorbic acid treatment during pregnancy can prevent Pb-induced impairments in the cerebellar development in rats.
Collapse
Affiliation(s)
- Sung Min Nam
- Department of Anatomy, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05030, Republic of Korea
- College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 05030, Republic of Korea
| | - In-Sun Cho
- Department of Anatomy, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05030, Republic of Korea
- Korea Bio-Safety Institute Co. Ltd, Eumseong, Chungbuk, 27600, Republic of Korea
| | - Jin Seok Seo
- Department of Anatomy, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05030, Republic of Korea
| | - Tae-Hun Go
- Department of Anatomy, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05030, Republic of Korea
| | - Ji-Hye Kim
- Department of Rehabilitation Psychology, Seoul Rehabilitation Hospital, Seoul, 03428, Republic of Korea
| | - Sang-Soep Nahm
- Department of Anatomy, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05030, Republic of Korea
- College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 05030, Republic of Korea
| | - Byung-Joon Chang
- Department of Anatomy, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05030, Republic of Korea.
- College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 05030, Republic of Korea.
| | - Jong-Hwan Lee
- Department of Anatomy, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul, 05030, Republic of Korea.
- College of Veterinary Medicine and Veterinary Science Research Institute, Konkuk University, Seoul, 05030, Republic of Korea.
| |
Collapse
|
11
|
McClatchy DB, Yu NK, Martínez-Bartolomé S, Patel R, Pelletier AR, Lavalle-Adam M, Powell SB, Roberto M, Yates JR. Structural Analysis of Hippocampal Kinase Signal Transduction. ACS Chem Neurosci 2018; 9:3072-3085. [PMID: 30053369 DOI: 10.1021/acschemneuro.8b00284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Kinases are a major clinical target for human diseases. Identifying the proteins that interact with kinases in vivo will provide information on unreported substrates and will potentially lead to more specific methods for therapeutic kinase regulation. Here, endogenous immunoprecipitations of evolutionally distinct kinases (i.e., Akt, ERK2, and CAMK2) from rodent hippocampi were analyzed by mass spectrometry to generate three highly confident kinase protein-protein interaction networks. Proteins of similar function were identified in the networks, suggesting a universal model for kinase signaling complexes. Protein interactions were observed between kinases with reported symbiotic relationships. The kinase networks were significantly enriched in genes associated with specific neurodevelopmental disorders providing novel structural connections between these disease-associated genes. To demonstrate a functional relationship between the kinases and the network, pharmacological manipulation of Akt in hippocampal slices was shown to regulate the activity of potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel(HCN1), which was identified in the Akt network. Overall, the kinase protein-protein interaction networks provide molecular insight of the spatial complexity of in vivo kinase signal transduction which is required to achieve the therapeutic potential of kinase manipulation in the brain.
Collapse
Affiliation(s)
- Daniel B. McClatchy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Nam-Kyung Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | | | - Reesha Patel
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Alexander R. Pelletier
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mathieu Lavalle-Adam
- Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Susan B. Powell
- Department of Psychiatry, UCSD, La Jolla, California 92093, United States
| | - Marisa Roberto
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California 92037, United States
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
12
|
Wilson RS, Nairn AC. Cell-Type-Specific Proteomics: A Neuroscience Perspective. Proteomes 2018; 6:51. [PMID: 30544872 PMCID: PMC6313874 DOI: 10.3390/proteomes6040051] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022] Open
Abstract
Cell-type-specific analysis has become a major focus for many investigators in the field of neuroscience, particularly because of the large number of different cell populations found in brain tissue that play roles in a variety of developmental and behavioral disorders. However, isolation of these specific cell types can be challenging due to their nonuniformity and complex projections to different brain regions. Moreover, many analytical techniques used for protein detection and quantitation remain insensitive to the low amounts of protein extracted from specific cell populations. Despite these challenges, methods to improve proteomic yield and increase resolution continue to develop at a rapid rate. In this review, we highlight the importance of cell-type-specific proteomics in neuroscience and the technical difficulties associated. Furthermore, current progress and technological advancements in cell-type-specific proteomics research are discussed with an emphasis in neuroscience.
Collapse
Affiliation(s)
- Rashaun S Wilson
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
| |
Collapse
|
13
|
Reese AT, Pereira FC, Schintlmeister A, Berry D, Wagner M, Hale LP, Wu A, Jiang S, Durand HK, Zhou X, Premont RT, Diehl AM, O'Connell TM, Alberts SC, Kartzinel TR, Pringle RM, Dunn RR, Wright JP, David LA. Microbial nitrogen limitation in the mammalian large intestine. Nat Microbiol 2018; 3:1441-1450. [PMID: 30374168 PMCID: PMC6264799 DOI: 10.1038/s41564-018-0267-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023]
Abstract
Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host-microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.
Collapse
Affiliation(s)
- Aspen T Reese
- Department of Biology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Fátima C Pereira
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - David Berry
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria
| | - Laura P Hale
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Anchi Wu
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Heather K Durand
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Xiyou Zhou
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Richard T Premont
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Anna Mae Diehl
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Thomas M O'Connell
- Department of Otolaryngology - Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Tyler R Kartzinel
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Robert M Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | | | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
| |
Collapse
|
14
|
Gao F, Liu X, Shen Z, Jia X, He H, Gao J, Wu J, Jiang C, Zhou H, Wang Y. Andrographolide Sulfonate Attenuates Acute Lung Injury by Reducing Expression of Myeloperoxidase and Neutrophil-Derived Proteases in Mice. Front Physiol 2018; 9:939. [PMID: 30174607 PMCID: PMC6107831 DOI: 10.3389/fphys.2018.00939] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022] Open
Abstract
Andrographolide sulfonate (Andro-S), a sulfonation derivative of andrographolide, is known to be effective in treating inflammation-related diseases, while the underlying mechanisms and global protein alterations in response to Andro-S remain unknown. This study aimed to investigate the pharmacological effects and potential targets of Andro-S in a murine model of acute lung injury (ALI). ALI was induced by aerosolized lipopolysaccharide (LPS) exposure before treatment with Andro-S. Inflammatory state of each treatment group was determined by histological analysis and quantification of inflammatory markers. Differentially expressed proteins in lung tissues were identified by an iTRAQ-based quantitative proteomic approach and further confirmed by immunohistochemistry analysis. Administration of Andro-S alleviated LPS-induced histological changes in the lung and reduced the expression of inflammatory markers in serum, bronchoalveolar fluid and lung tissues. Proteomic analysis identified 31 differentially expressed proteins from a total of 2,234 quantified proteins in the lung. According to bioinformatics analysis, neutrophil elastase (ELANE), cathepsin G (CTSG) and myeloperoxidase (MPO), three neutrophil-derived proteases related to immune system process and defense responses to fungi were chosen as potential targets of Andro-S. Further immunohistochemistry analysis confirmed the inhibitory effects of Andro-S on LPS-induced ELANE, CTSG and MPO up-regulation. These results indicate that Andro-S suppressed the severity of LPS-induced ALI, possibly by attenuating the expression of and neutrophil-derived proteases.
Collapse
Affiliation(s)
- Fei Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Xing Liu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Ziying Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaohui Jia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Han He
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Jianhong Wu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Chunhong Jiang
- State Key Laboratory of Innovative Natural Medicine and TCM Injections, Ganzhou, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| | - Yiping Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, University of Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
15
|
Quantitative temporal analysis of protein dynamics in cardiac remodeling. J Mol Cell Cardiol 2018; 121:163-172. [PMID: 30009778 DOI: 10.1016/j.yjmcc.2018.07.126] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/20/2018] [Accepted: 07/09/2018] [Indexed: 01/02/2023]
Abstract
Cardiac remodeling (CR) is a complex dynamic process common to many heart diseases. CR is characterized as a temporal progression of global adaptive and maladaptive perturbations. The complex nature of this process clouds a comprehensive understanding of CR, but greater insight into the processes and mechanisms has potential to identify new therapeutic targets. To provide a deeper understanding of this important cardiac process, we applied a new proteomic technique, PALM (Pulse Azidohomoalanine in Mammals), to quantitate the newly-synthesized protein (NSP) changes during the progression of isoproterenol (ISO)-induced CR in the mouse left ventricle. This analysis revealed a complex combination of adaptive and maladaptive alterations at acute and prolonged time points including the identification of proteins not previously associated with CR. We also combined the PALM dataset with our published protein turnover rate dataset to identify putative biochemical mechanisms underlying CR. The novel integration of analyzing NSPs together with their protein turnover rates demonstrated that alterations in specific biological pathways (e.g., inflammation and oxidative stress) are produced by differential regulation of protein synthesis and degradation.
Collapse
|
16
|
Abstract
Koppel & Fainzilber review translatomics and proteomics methods for studying protein synthesis at subcellular resolution.
Collapse
Affiliation(s)
- Indrek Koppel
- Department of Biomolecular Sciences
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
| | - Mike Fainzilber
- Department of Biomolecular Sciences
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
| |
Collapse
|
17
|
Glykys J, Dzhala V, Egawa K, Kahle KT, Delpire E, Staley K. Chloride Dysregulation, Seizures, and Cerebral Edema: A Relationship with Therapeutic Potential. Trends Neurosci 2017; 40:276-294. [PMID: 28431741 DOI: 10.1016/j.tins.2017.03.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 11/18/2022]
Abstract
Pharmacoresistant seizures and cytotoxic cerebral edema are serious complications of ischemic and traumatic brain injury. Intraneuronal Cl- concentration ([Cl-]i) regulation impacts on both cell volume homeostasis and Cl--permeable GABAA receptor-dependent membrane excitability. Understanding the pleiotropic molecular determinants of neuronal [Cl-]i - cytoplasmic impermeant anions, polyanionic extracellular matrix (ECM) glycoproteins, and plasmalemmal Cl- transporters - could help the identification of novel anticonvulsive and neuroprotective targets. The cation/Cl- cotransporters and ECM metalloproteinases may be particularly druggable targets for intervention. We establish here a paradigm that accounts for recent data regarding the complex regulatory mechanisms of neuronal [Cl-]i and how these mechanisms impact on neuronal volume and excitability. We propose approaches to modulate [Cl-]i that are relevant for two common clinical sequela of brain injury: edema and seizures.
Collapse
Affiliation(s)
- Joseph Glykys
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Volodymyr Dzhala
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kiyoshi Egawa
- Department of Pediatrics, Hokkaido University Hospital, Sapporo 0010019, Japan
| | - Kristopher T Kahle
- Departments of Neurosurgery, Pediatrics, and Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Eric Delpire
- Department of Anesthesiology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kevin Staley
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
18
|
Sethi S, Chourasia D, Parhar IS. Approaches for targeted proteomics and its potential applications in neuroscience. J Biosci 2016; 40:607-27. [PMID: 26333406 DOI: 10.1007/s12038-015-9537-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
An extensive guide on practicable and significant quantitative proteomic approaches in neuroscience research is important not only because of the existing overwhelming limitations but also for gaining valuable understanding into brain function and deciphering proteomics from the workbench to the bedside. Early methodologies to understand the functioning of biological systems are now improving with high-throughput technologies, which allow analysis of various samples concurrently, or of thousand of analytes in a particular sample. Quantitative proteomic approaches include both gel-based and non-gel-based methods that can be further divided into different labelling approaches. This review will emphasize the role of existing technologies, their advantages and disadvantages, as well as their applications in neuroscience. This review will also discuss advanced approaches for targeted proteomics using isotope-coded affinity tag (ICAT) coupled with laser capture microdissection (LCM) followed by liquid chromatography tandem mass spectrometric (LC-MS/MS) analysis. This technology can further be extended to single cell proteomics in other areas of biological sciences and can be combined with other 'omics' approaches to reveal the mechanism of a cellular alterations. This approach may lead to further investigation in basic biology, disease analysis and surveillance, as well as drug discovery. Although numerous challenges still exist, we are confident that this approach will increase the understanding of pathological mechanisms involved in neuroendocrinology, neuropsychiatric and neurodegenerative disorders by delivering protein biomarker signatures for brain dysfunction.
Collapse
Affiliation(s)
- Sumit Sethi
- Brain Research Institute, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Selangor Darul Ehsan, Malaysia,
| | | | | |
Collapse
|
19
|
McClatchy DB, Savas JN, Martínez-Bartolomé S, Park SK, Maher P, Powell SB, Yates JR. Global quantitative analysis of phosphorylation underlying phencyclidine signaling and sensorimotor gating in the prefrontal cortex. Mol Psychiatry 2016; 21:205-15. [PMID: 25869802 PMCID: PMC4605830 DOI: 10.1038/mp.2015.41] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 03/02/2015] [Indexed: 01/09/2023]
Abstract
Prepulse inhibition (PPI) is an example of sensorimotor gating and deficits in PPI have been demonstrated in schizophrenia patients. Phencyclidine (PCP) suppression of PPI in animals has been studied to elucidate the pathological elements of schizophrenia. However, the molecular mechanisms underlying PCP treatment or PPI in the brain are still poorly understood. In this study, quantitative phosphoproteomic analysis was performed on the prefrontal cortex from rats that were subjected to PPI after being systemically injected with PCP or saline. PCP downregulated phosphorylation events were significantly enriched in proteins associated with long-term potentiation (LTP). Importantly, this data set identifies functionally novel phosphorylation sites on known LTP-associated signaling molecules. In addition, mutagenesis of a significantly altered phosphorylation site on xCT (SLC7A11), the light chain of system xc-, the cystine/glutamate antiporter, suggests that PCP also regulates the activity of this protein. Finally, new insights were also derived on PPI signaling independent of PCP treatment. This is the first quantitative phosphorylation proteomic analysis providing new molecular insights into sensorimotor gating.
Collapse
Affiliation(s)
| | - Jeffrey N. Savas
- Department of Chemical Physiology, The Scripps Research Institute
| | | | - Sung Kyu Park
- Department of Chemical Physiology, The Scripps Research Institute
| | - Pamela Maher
- Cellular Neurobiology Laboratory, Salk Institute
| | | | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute
- Corresponding Author:
| |
Collapse
|
20
|
Distribution of N-Acetylgalactosamine-Positive Perineuronal Nets in the Macaque Brain: Anatomy and Implications. Neural Plast 2016; 2016:6021428. [PMID: 26881119 PMCID: PMC4735937 DOI: 10.1155/2016/6021428] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/17/2015] [Accepted: 08/26/2015] [Indexed: 11/17/2022] Open
Abstract
Perineuronal nets (PNNs) are extracellular molecules that form around neurons near the end of critical periods during development. They surround neuronal cell bodies and proximal dendrites. PNNs inhibit the formation of new connections and may concentrate around rapidly firing inhibitory interneurons. Previous work characterized the important role of perineuronal nets in plasticity in the visual system, amygdala, and spinal cord of rats. In this study, we use immunohistochemistry to survey the distribution of perineuronal nets in representative areas of the primate brain. We also document changes in PNN prevalence in these areas in animals of different ages. We found that PNNs are most prevalent in the cerebellar nuclei, surrounding >90% of the neurons there. They are much less prevalent in cerebral cortex, surrounding less than 10% of neurons in every area that we examined. The incidence of perineuronal nets around parvalbumin-positive neurons (putative fast-spiking interneurons) varies considerably between different areas in the brain. Our survey indicates that the presence of PNNs may not have a simple relationship with neural plasticity and may serve multiple functions in the central nervous system.
Collapse
|
21
|
Proteomic Analysis of Protein Turnover by Metabolic Whole Rodent Pulse-Chase Isotopic Labeling and Shotgun Mass Spectrometry Analysis. Methods Mol Biol 2016; 1410:293-304. [PMID: 26867752 DOI: 10.1007/978-1-4939-3524-6_18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The analysis of protein half-life and degradation dynamics has proven critically important to our understanding of a broad and diverse set of biological conditions ranging from cancer to neurodegeneration. Historically these protein turnover measures have been performed in cells by monitoring protein levels after "pulse" labeling of newly synthesized proteins and subsequent chase periods. Comparing the level of labeled protein remaining as a function of time to the initial level reveals the protein's half-life. In this method we provide a detailed description of the workflow required for the determination of protein turnover rates on a whole proteome scale in vivo. Our approach starts with the metabolic labeling of whole rodents by restricting all the nitrogen in their diet to exclusively nitrogen-15 in the form of spirulina algae. After near complete organismal labeling with nitrogen-15, the rodents are then switched to a normal nitrogen-14 rich diet for time periods of days to years. Tissues are harvested, the extracts are fractionated, and the proteins are digested to peptides. Peptides are separated by multidimensional liquid chromatography and analyzed by high resolution orbitrap mass spectrometry (MS). The nitrogen-15 containing proteins are then identified and measured by the bioinformatic proteome analysis tools Sequest, DTASelect2, and Census. In this way, our metabolic pulse-chase approach reveals in vivo protein decay rates proteome-wide.
Collapse
|
22
|
McClatchy DB, Ma Y, Liu C, Stein BD, Martínez-Bartolomé S, Vasquez D, Hellberg K, Shaw RJ, Yates JR. Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver-Specific LKB1 Knockout Mice. J Proteome Res 2015; 14:4815-22. [PMID: 26445171 PMCID: PMC4642245 DOI: 10.1021/acs.jproteome.5b00653] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Quantification
of proteomes by mass spectrometry has proven to
be useful to study human pathology recapitulated in cellular or animal
models of disease. Enriching and quantifying newly synthesized proteins
(NSPs) at set time points by mass spectrometry has the potential to
identify important early regulatory or expression changes associated
with disease states or perturbations. NSP can be enriched from proteomes
by employing pulsed introduction of the noncanonical amino acid, azidohomoalanine
(AHA). We demonstrate that pulsed introduction of AHA in the feed
of mice can label and identify NSP from multiple tissues. Furthermore,
we quantitate differences in new protein expression resulting from
CRE-LOX initiated knockout of LKB1 in mouse livers. Overall, the PALM
strategy allows for the first time in vivo labeling of mouse tissues
to differentiate protein synthesis rates at discrete time points.
Collapse
Affiliation(s)
- Daniel B McClatchy
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yuanhui Ma
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chao Liu
- Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences , No. 6 Kexueyuan South Road, Beijing 100190, China
| | - Benjamin D Stein
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Salvador Martínez-Bartolomé
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | | | | | | | - John R Yates
- Department of Chemical Physiology and Molecular and Cellular Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
23
|
Wong VWC, Reid DG, Chow WY, Rajan R, Green M, Brooks RA, Duer MJ. Preparation of highly and generally enriched mammalian tissues for solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 63:119-123. [PMID: 26407607 DOI: 10.1007/s10858-015-9977-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/08/2015] [Indexed: 06/05/2023]
Abstract
An appreciable level of isotope labelling is essential for future NMR structure elucidation of mammalian biomaterials, which are either poorly expressed, or unexpressable, using micro-organisms. We present a detailed protocol for high level (13)C enrichment even in slow turnover murine biomaterials (fur keratin), using a customized diet supplemented with commercial labelled algal hydrolysate and formulated as a gel to minimize wastage, which female mice consumed during pregnancy and lactation. This procedure produced approximately eightfold higher fur keratin labelling in pups, exposed in utero and throughout life to label, than in adults exposed for the same period, showing both the effectiveness, and necessity, of this approach.
Collapse
Affiliation(s)
| | - David G Reid
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Wing Ying Chow
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Rakesh Rajan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Maggie Green
- Central Biomedical Resources, School of Clinical Medicine, University of Cambridge, West Forvie Building, Forvie Site, Robinson Way, Cambridge, CB2 0SZ, UK
| | - Roger A Brooks
- Department of Trauma and Orthopaedic Surgery, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Melinda J Duer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| |
Collapse
|
24
|
Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome. Proc Natl Acad Sci U S A 2015; 112:E4697-706. [PMID: 26307763 DOI: 10.1073/pnas.1502258112] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fragile X syndrome (FXS) is an X-linked neurodevelopmental disorder characterized by severe intellectual disability and other symptoms including autism. Although caused by the silencing of a single gene, Fmr1 (fragile X mental retardation 1), the complexity of FXS pathogenesis is amplified because the encoded protein, FMRP, regulates the activity-dependent translation of numerous mRNAs. Although the mRNAs that associate with FMRP have been extensively studied, little is known regarding the proteins whose expression levels are altered, directly or indirectly, by loss of FMRP during brain development. Here we systematically measured protein expression in neocortical synaptic fractions from Fmr1 knockout (KO) and wild-type (WT) mice at both adolescent and adult stages. Although hundreds of proteins are up-regulated in the absence of FMRP in young mice, this up-regulation is largely diminished in adulthood. Up-regulated proteins included previously unidentified as well as known targets involved in synapse formation and function and brain development and others linked to intellectual disability and autism. Comparison with putative FMRP target mRNAs and autism susceptibility genes revealed substantial overlap, consistent with the idea that the autism endophenotype of FXS is due to a "multiple hit" effect of FMRP loss, particularly within the PSD95 interactome. Through studies of de novo protein synthesis in primary cortical neurons from KO and WT mice, we found that neurons lacking FMRP produce nascent proteins at higher rates, many of which are synaptic proteins and encoded by FMRP target mRNAs. Our results provide a greatly expanded view of protein changes in FXS and identify age-dependent effects of FMRP in shaping the neuronal proteome.
Collapse
|
25
|
Dzhala V, Staley KJ. Acute and chronic efficacy of bumetanide in an in vitro model of posttraumatic epileptogenesis. CNS Neurosci Ther 2014; 21:173-80. [PMID: 25495911 DOI: 10.1111/cns.12369] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Seizures triggered by acute injuries to the developing brain respond poorly to first-line medications that target the inhibitory chloride-permeable GABAA receptor. Neuronal injury is associated with profound increases in cytoplasmic chloride ([Cl(-)]i) resulting in depolarizing GABA signaling, higher seizure propensity and limited efficacy of GABAergic anticonvulsants. The Na(+)-K(+)-2Cl(-) (NKCC1) cotransporter blocker bumetanide reduces [Cl(-)]i and causes more negative GABA equilibrium potential in injured neurons. We therefore tested both the acute and chronic efficacy of bumetanide on early posttraumatic ictal-like epileptiform discharges and epileptogenesis. METHODS Acute hippocampal slices were used as a model of severe traumatic brain injury and posttraumatic epileptogenesis. Hippocampal slices were then incubated for 3 weeks. After a 1-week latent period, slice cultures developed chronic spontaneous ictal-like discharges. The anticonvulsant and anti-epileptogenic efficacy of bumetanide, phenobarbital, and the combination of these drugs was studied. RESULTS Bumetanide reduced the frequency and power of early posttraumatic ictal-like discharges in vitro and enhanced the anticonvulsant efficacy of phenobarbital. Continuous 2-3 weeks administration of bumetanide as well as phenobarbital in combination with bumetanide failed to prevent posttraumatic ictal-like discharges and epileptogenesis. CONCLUSIONS Our data demonstrate a persistent contribution of NKCC1 cotransport in posttraumatic ictal-like activity, presumably as a consequence of chronic alterations in neuronal chloride homeostasis and GABA-mediated inhibition. New strategies for more effective reduction in posttraumatic and seizure-induced [Cl(-)]i accumulation could provide the basis for effective treatments for posttraumatic epileptogenesis and the resultant seizures.
Collapse
Affiliation(s)
- Volodymyr Dzhala
- Neurology Department, Massachusetts General Hospital, Boston, MA, USA
| | | |
Collapse
|
26
|
Khazipov R, Valeeva G, Khalilov I. Depolarizing GABA and developmental epilepsies. CNS Neurosci Ther 2014; 21:83-91. [PMID: 25438879 DOI: 10.1111/cns.12353] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 10/14/2014] [Accepted: 10/20/2014] [Indexed: 12/22/2022] Open
Abstract
Early in development, GABA, which is the main inhibitory neurotransmitter in adult brain, depolarizes immature neurons and exerts dual--excitatory and shunting/inhibitory--effects in the developing neuronal networks. The present review discusses some general questions, including the properties of excitation at depolarizing GABAergic synapse and shunting inhibition by depolarizing GABA; technical issues in exploration of depolarizing GABA using various techniques and preparations, including the developmental aspects of traumatic injury and what is known (or rather unknown) on the actions of GABA in vivo; complex roles of depolarizing GABA in developmental epilepsies, including a contribution of depolarizing GABA to enhanced excitability in the immature networks, caused by repetitive seizures accumulation of intracellular chloride concentration that increases excitatory GABA power and its synchronizing proconvulsive effects, and correction of chloride homeostasis as a potential strategy to treat neonatal seizures.
Collapse
Affiliation(s)
- Roustem Khazipov
- INMED-INSERM U901, Marseille, France; Aix-Marseille University, Marseille, France; Laboratory of Neurobiology, Kazan Federal University, Kazan, Russia
| | | | | |
Collapse
|
27
|
Zhang G, Annan RS, Carr SA, Neubert TA. Overview of peptide and protein analysis by mass spectrometry. ACTA ACUST UNITED AC 2014; 108:10.21.1-10.21.30. [PMID: 25271712 DOI: 10.1002/0471142727.mb1021s108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post-translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide.
Collapse
Affiliation(s)
- Guoan Zhang
- Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York
| | | | | | | |
Collapse
|
28
|
Henrich M, Huber K, Rydzewski L, Kirsten S, Spengler B, Römpp A, Reinacher M. Identification of T cell receptor signaling pathway proteins in a feline large granular lymphoma cell line by liquid chromatography tandem mass spectrometry. Vet Immunol Immunopathol 2014; 161:116-21. [DOI: 10.1016/j.vetimm.2014.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/11/2014] [Accepted: 06/19/2014] [Indexed: 11/25/2022]
|
29
|
Chaube R. Absolute quantitation of post-translational modifications. Front Chem 2014; 2:58. [PMID: 25140300 PMCID: PMC4122087 DOI: 10.3389/fchem.2014.00058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 07/14/2014] [Indexed: 01/22/2023] Open
Affiliation(s)
- Ruchi Chaube
- Department of Medicine and Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland, OH, USA
| |
Collapse
|
30
|
Ficarro SB, Biagi JM, Wang J, Scotcher J, Koleva RI, Card JD, Adelmant G, He H, Askenazi M, Marshall AG, Young NL, Gray NS, Marto JA. Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:636-650. [PMID: 24496597 PMCID: PMC3971929 DOI: 10.1007/s13361-013-0811-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 12/09/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
We assemble a versatile molecular scaffold from simple building blocks to create binary and multiplexed stable isotope reagents for quantitative mass spectrometry. Termed Protected Amine Labels (PAL), these reagents offer multiple analytical figures of merit including, (1) robust targeting of peptide N-termini and lysyl side chains, (2) optimal mass spectrometry ionization efficiency through regeneration of primary amines on labeled peptides, (3) an amino acid-based mass tag that incorporates heavy isotopes of carbon, nitrogen, and oxygen to ensure matched physicochemical and MS/MS fragmentation behavior among labeled peptides, and (4) a molecularly efficient architecture, in which the majority of hetero-atom centers can be used to synthesize a variety of nominal mass and sub-Da isotopologue stable isotope reagents. We demonstrate the performance of these reagents in well-established strategies whereby up to four channels of peptide isotopomers, each separated by 4 Da, are quantified in MS-level scans with accuracies comparable to current commercial reagents. In addition, we utilize the PAL scaffold to create isotopologue reagents in which labeled peptide analogs differ in mass based on the binding energy in carbon and nitrogen nuclei, thereby allowing quantification based on MS or MS/MS spectra. We demonstrate accurate quantification for reagents that support 6-plex labeling and propose extension of this scheme to 9-channels based on a similar PAL scaffold. Finally, we provide exemplar data that extend the application of isotopologe-based quantification reagents to medium resolution, quadrupole time-of-flight mass spectrometers.
Collapse
Affiliation(s)
- Scott B. Ficarro
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Jessica M. Biagi
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Jinhua Wang
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Jenna Scotcher
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL
| | - Rositsa I. Koleva
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Joseph D. Card
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Guillaume Adelmant
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Huan He
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL
| | - Manor Askenazi
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Israel
| | - Alan G. Marshall
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL
| | - Nicolas L. Young
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL
| | - Nathanael S. Gray
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Jarrod A. Marto
- Department of Cancer Biology, Harvard Medical School, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| |
Collapse
|
31
|
Quantitative proteomics of Xenopus laevis embryos: expression kinetics of nearly 4000 proteins during early development. Sci Rep 2014; 4:4365. [PMID: 24626130 PMCID: PMC3953746 DOI: 10.1038/srep04365] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 02/17/2014] [Indexed: 02/07/2023] Open
Abstract
While there is a rich literature on transcription dynamics during the development of many organisms, protein data is limited. We used iTRAQ isotopic labeling and mass spectrometry to generate the largest developmental proteomic dataset for any animal. Expression dynamics of nearly 4,000 proteins of Xenopuslaevis was generated from fertilized egg to neurula embryo. Expression clusters into groups. The cluster profiles accurately reflect the major events that mark changes in gene expression patterns during early Xenopus development. We observed decline in the expression of ten DNA replication factors after the midblastula transition (MBT), including a marked decline of the licensing factor XCdc6. Ectopic expression of XCdc6 leads to apoptosis; temporal changes in this protein are critical for proper development. Measurement of expression in single embryos provided no evidence for significant protein heterogeneity between embryos at the same stage of development.
Collapse
|
32
|
Miller RA, Winrow CJ, Spellman DS, Song Q, Reiss DR, Conway JP, Taylor RR, Coleman PJ, Hendrickson RC, Renger JJ. Quantitative proteomics in laser capture microdissected sleep nuclei from rat brain. J Neurogenet 2014; 28:136-45. [PMID: 24579665 PMCID: PMC4075250 DOI: 10.3109/01677063.2014.883389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The combination of stable isotope labeling of amino acids in mammals (SILAM) and laser capture microdissection (LCM) for selective proteomic analysis of the targeted tissues holds tremendous potential for refined characterization of proteome changes within complex tissues such as the brain. The authors have applied this approach to measure changes in relative protein abundance in ventral tegmental area (VTA) of the rat brain that correlate to pharmacological perturbations. Enriched 13C615N2-lysine was introduced in vivo via diet. These animals were sacrificed during the middle of the 12-hour light period to extract isotopically “heavy” proteins, which were then used as a reference for extracts from dosed, unlabeled rats. Animals were administered an orexin peptide (Ox-B), an orexin receptor antagonist (ORA), or a mixture of both (Ox-B + ORA). All samples were obtained at same phase of the sleep cycle. Labeled-pair identification and differential quantitation provided protein identification and expression ratio data. Five proteins were found to exhibit decreased relative abundance after administration of an ORA, including α-synuclein and rat myelin basic protein. Conversely, six proteins showed increased relative abundance upon antagonist treatment, including 2’,3’-cyclic nucleotide 3’-phosphodiesterase.
Collapse
Affiliation(s)
- Ronald A Miller
- Department of Proteomics, Molecular Profiling and Research Informatics, Merck Research Laboratories , West Point, Pennsylvania , USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Glykys J, Dzhala V, Egawa K, Balena T, Saponjian Y, Kuchibhotla KV, Bacskai BJ, Kahle KT, Zeuthen T, Staley KJ. Local impermeant anions establish the neuronal chloride concentration. Science 2014; 343:670-5. [PMID: 24503855 DOI: 10.1126/science.1245423] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Neuronal intracellular chloride concentration [Cl(-)](i) is an important determinant of γ-aminobutyric acid type A (GABA(A)) receptor (GABA(A)R)-mediated inhibition and cytoplasmic volume regulation. Equilibrative cation-chloride cotransporters (CCCs) move Cl(-) across the membrane, but accumulating evidence suggests factors other than the bulk concentrations of transported ions determine [Cl(-)](i). Measurement of [Cl(-)](i) in murine brain slice preparations expressing the transgenic fluorophore Clomeleon demonstrated that cytoplasmic impermeant anions ([A](i)) and polyanionic extracellular matrix glycoproteins ([A](o)) constrain the local [Cl(-)]. CCC inhibition had modest effects on [Cl(-)](i) and neuronal volume, but substantial changes were produced by alterations of the balance between [A](i) and [A](o). Therefore, CCCs are important elements of Cl(-) homeostasis, but local impermeant anions determine the homeostatic set point for [Cl(-)], and hence, neuronal volume and the polarity of local GABA(A)R signaling.
Collapse
Affiliation(s)
- J Glykys
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
Proteins provide the verbs to biology, and proteomics provides the nouns for their analytical and discovery-driven studies. The term proteomics was coined in the 1990s and deals with the protein complement of the genome-the proteome. Following the classical proteomics era, the development of new mass spectrometric methods for peptide analysis permitted the identification of proteins in peptide mixtures obtained by proteolytic digestion of complex samples, e.g., shotgun proteomics. Since its introduction, shotgun proteomics became the standard technique for the analysis of protein hydrolyzates in a high-throughput way. In this chapter, we provide a survey in shotgun proteomics highlighting instruments and techniques used in modern second and third proteomics generation.
Collapse
Affiliation(s)
- Fabio Cesar Sousa Nogueira
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Av Athos da Silveira Ramos, 149 Bloco A - sala 542 Cidade Universitária, 21941-909, Rio de Janeiro, RJ, Brazil
| | | |
Collapse
|
35
|
Xiong L, Wen Y, Miao X, Yang Z. NT5E and FcGBP as key regulators of TGF-1-induced epithelial-mesenchymal transition (EMT) are associated with tumor progression and survival of patients with gallbladder cancer. Cell Tissue Res 2013; 355:365-74. [PMID: 24310606 PMCID: PMC3921456 DOI: 10.1007/s00441-013-1752-1] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 10/31/2013] [Indexed: 11/28/2022]
Abstract
Epithelial–mesenchymal transitions (EMTs) are essential manifestations of epithelial cell plasticity during tumor progression. Transforming growth factor-β(TGF-β) modulates epithelial plasticity in tumor physiological contexts by inducing EMT, which is associated with the altered expression of genes. In the present study, we used DNA micro-array analysis to search for differentially expressed genes in the TGF-β1 induced gallbladder carcinoma cell line (GBC-SD cells), as compared with normal GBC-SD cells. We identified 225 differentially expressed genes, including 144 that were over-expressed and 81 that were under-expressed in the TGF-β1 induced GBC-SD cells. NT5E (CD73) is the most increased gene, while the Fc fragment of the IgG binding protein (FcGBP) is the most decreased gene. The expression patterns of these two genes in gallbladder adenocarcinoma and chronic cholecystitis tissue were consistent with the micro-array data. Immunochemistry and clinicopathological results showed that the expression of NT5E and FcGBP in gallbladder adenocarcinoma is an independent marker for evaluation of the disease progression, clinical biological behaviors and prognosis. The data from the current study indicate that differential NT5E and FcGBP expressions could be further evaluated as biomarkers for predicting survival of patients with gallbladder cancer and that NT5E and FcGBP could be promising targets in the control of gallbladder cancer progression.
Collapse
Affiliation(s)
- Li Xiong
- Research Laboratory of Hepatobiliary Diseases, Second Xiangya Hospital, Central South University, 139# Middle Renmin road, Changsha, Hunan, 410011, China
| | | | | | | |
Collapse
|
36
|
A perspective on proteomics in cell biology. Trends Cell Biol 2013; 24:257-64. [PMID: 24284280 PMCID: PMC3989996 DOI: 10.1016/j.tcb.2013.10.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 10/14/2013] [Accepted: 10/30/2013] [Indexed: 12/21/2022]
Abstract
Proteomic strategies facilitate system-wide analyses of protein complexes. Isotope labelling allows quantitative measurement of protein properties, not only their identification. There is a major need to organise effective community sharing of the proteomic data mountain. The integration of proteomic data with other online data repositories must be improved.
During the past 15 years mass spectrometry (MS)-based analyses have become established as the method of choice for direct protein identification and measurement. Owing to the remarkable improvements in the sensitivity and resolution of MS instruments, this technology has revolutionised the opportunities available for the system-wide characterisation of proteins, with wide applications across virtually the whole of cell biology. In this article we provide a perspective on the current state of the art and discuss how the future of cell biology research may benefit from further developments and applications in the field of MS and proteomics, highlighting the major challenges ahead for the community in organising the effective sharing and integration of the resulting data mountain.
Collapse
|
37
|
Wan J, Savas JN, Roth AF, Sanders SS, Singaraja RR, Hayden MR, Yates JR, Davis NG. Tracking brain palmitoylation change: predominance of glial change in a mouse model of Huntington's disease. CHEMISTRY & BIOLOGY 2013; 20:1421-34. [PMID: 24211138 PMCID: PMC3880188 DOI: 10.1016/j.chembiol.2013.09.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 08/28/2013] [Accepted: 09/08/2013] [Indexed: 11/25/2022]
Abstract
Protein palmitoylation, a reversible lipid modification of proteins, is widely used in the nervous system, with dysregulated palmitoylation being implicated in a variety of neurological disorders. Described below is ABE/SILAM, a proteomic strategy that couples acyl-biotinyl exchange (ABE) purification of palmitoyl-proteins to whole animal stable isotope labeling (SILAM) to provide an accurate tracking of palmitoylation change within rodent disease models. As a first application, we have used ABE/SILAM to look at Huntington's disease (HD), profiling palmitoylation change in two HD-relevant mouse mutants: the transgenic HD model mouse YAC128 and the hypomorphic Hip14-gt mouse, which has sharply reduced expression for HIP14 (Zdhhc17), a palmitoyl-transferase implicated in the HD disease process. Rather than mapping to the degenerating neurons themselves, the biggest disease changes instead map to astrocytes and oligodendrocytes (i.e., the supporting glial cells).
Collapse
Affiliation(s)
- Junmei Wan
- Department of Pharmacology, Wayne State University, Detroit, MI 48201, USA
| | - Jeffrey N. Savas
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amy F. Roth
- Department of Pharmacology, Wayne State University, Detroit, MI 48201, USA
| | - Shaun S. Sanders
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4 Canada
| | - Roshni R. Singaraja
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4 Canada
| | - Michael R. Hayden
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4 Canada
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas G. Davis
- Department of Pharmacology, Wayne State University, Detroit, MI 48201, USA
| |
Collapse
|
38
|
SILAC Proteomics of Planarians Identifies Ncoa5 as a Conserved Component of Pluripotent Stem Cells. Cell Rep 2013; 5:1142-55. [DOI: 10.1016/j.celrep.2013.10.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/09/2013] [Accepted: 10/21/2013] [Indexed: 12/19/2022] Open
|
39
|
Weng RR, Chu LJ, Shu HW, Wu TH, Chen MC, Chang Y, Tsai YS, Wilson MC, Tsay YG, Goodlett DR, Ng WV. Large precursor tolerance database search - a simple approach for estimation of the amount of spectra with precursor mass shifts in proteomic data. J Proteomics 2013; 91:375-84. [PMID: 23933159 DOI: 10.1016/j.jprot.2013.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 07/08/2013] [Accepted: 07/27/2013] [Indexed: 11/30/2022]
Abstract
UNLABELLED Mass measurement and precursor mass assignment are independent processes in proteomic data acquisition. Due to misassignments to C-13 peak, or for other reasons, extensive precursor mass shifts (i.e., deviations of the measured from calculated precursor neutral masses) in LC-MS/MS data obtained with the high-accuracy LTQ-Orbitrap mass spectrometers have been reported in previous studies. Although computational methods for post-acquisition reassignment to monoisotopic mass have been developed to curate the MS/MS spectra prior to database search, a simpler method for estimating the fraction of spectra with precursor mass shift so as to determine whether the data require curation remains desirable. Here, we provide the evidence that an easy approach, which applies a large precursor tolerance (2.1Da or higher) in SEQUEST search against a forward and decoy protein sequence database and then filters the data with PeptideProphet peptide identification probability (p≥0.9), could detect most of the MS/MS spectra containing inaccurate precursor masses. Furthermore, through the implementation of artificial mass shifts on 4000 randomly selected MS/MS spectra, which originally had accurate precursor mass assigned by the mass spectrometers, we demonstrated that the accuracy of the precursor mass has almost negligible influence on the efficacy and fidelity of peptide identification. BIOLOGICAL SIGNIFICANCE Integral precursor mass shift is a known problem and thus proteomic data should be handled and analyzed properly to avoid losing important protein identification and/or quantification information. A quick and easy approach for estimating the number of MS/MS spectra with inaccurate precursor mass assignments would be helpful for evaluating the performance of the instrument, determining whether the data requires curation prior to database search or should be searched with specific search parameter(s). Here we demonstrated most of the MS/MS spectra with inaccurate mass assignments (integral or non-integral changes) that could be easily identified by database search with large precursor tolerance windows.
Collapse
Affiliation(s)
- Rueyhung Roc Weng
- Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, ROC
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Craft GE, Chen A, Nairn AC. Recent advances in quantitative neuroproteomics. Methods 2013; 61:186-218. [PMID: 23623823 PMCID: PMC3891841 DOI: 10.1016/j.ymeth.2013.04.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 03/29/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023] Open
Abstract
The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.
Collapse
Affiliation(s)
- George E Craft
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Anshu Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Angus C Nairn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
- Yale/NIDA Neuroproteomics Center, Yale University School of Medicine, New Haven, CT, 06508
| |
Collapse
|
41
|
Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 957] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
42
|
Rauniyar N, McClatchy DB, Yates JR. Stable isotope labeling of mammals (SILAM) for in vivo quantitative proteomic analysis. Methods 2013; 61:260-8. [PMID: 23523555 DOI: 10.1016/j.ymeth.2013.03.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 02/20/2013] [Accepted: 03/07/2013] [Indexed: 11/30/2022] Open
Abstract
Metabolic labeling of rodent proteins with ¹⁵N, a heavy stable isotope of nitrogen, provides an efficient way for relative quantitation of differentially expressed proteins. Here we describe a protocol for metabolic labeling of rats with an ¹⁵N-enriched spirulina diet. As a case study, we also demonstrate the application of ¹⁵N-enriched tissue as a common internal standard in quantitative analysis of differentially expressed proteins in neurodevelopment in rats at two different time points, postnatal day 1 and 45. We briefly discuss the bioinformatics tools, ProLucid and Census, which can easily be used in a sequential manner to identify and quantitate relative protein levels on a proteomic scale.
Collapse
Affiliation(s)
- Navin Rauniyar
- Department of Chemical Physiology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | | | | |
Collapse
|
43
|
Yates JR. The revolution and evolution of shotgun proteomics for large-scale proteome analysis. J Am Chem Soc 2013; 135:1629-40. [PMID: 23294060 PMCID: PMC3751590 DOI: 10.1021/ja3094313] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mass spectrometry has evolved at an exponential rate over the last 100 years. Innovations in the development of mass spectrometers have created powerful instruments capable of analyzing a wide range of targets, from rare atoms and molecules to very large molecules, such as a proteins, protein complexes, and DNA. These performance gains have been driven by sustaining innovations, punctuated by the occasional disruptive innovation. The use of mass spectrometry for proteome analysis was driven by disruptive innovations that created a capability for large-scale analysis of proteins and modifications.
Collapse
Affiliation(s)
- John R. Yates
- 10550 North Torrey Pines, SR11, Department of Chemical Physiology, The Scripps Research Institute, LaJolla, CA 92037, TEL: (858) 784-8862
| |
Collapse
|
44
|
In vivo quantitative proteomics of somatosensory cortical synapses shows which protein levels are modulated by sensory deprivation. Proc Natl Acad Sci U S A 2013; 110:E726-35. [PMID: 23382246 DOI: 10.1073/pnas.1300424110] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Postnatal bilateral whisker trimming was used as a model system to test how synaptic proteomes are altered in barrel cortex by sensory deprivation during synaptogenesis. Using quantitative mass spectrometry, we quantified more than 7,000 synaptic proteins and identified 89 significantly reduced and 161 significantly elevated proteins in sensory-deprived synapses, 22 of which were validated by immunoblotting. More than 95% of quantified proteins, including abundant synaptic proteins such as PSD-95 and gephyrin, exhibited no significant difference under high- and low-activity rearing conditions, suggesting no tissue-wide changes in excitatory or inhibitory synaptic density. In contrast, several proteins that promote mature spine morphology and synaptic strength, such as excitatory glutamate receptors and known accessory factors, were reduced significantly in deprived synapses. Immunohistochemistry revealed that the reduction in SynGAP1, a postsynaptic scaffolding protein, was restricted largely to layer I of barrel cortex in sensory-deprived rats. In addition, protein-degradation machinery such as proteasome subunits, E2 ligases, and E3 ligases, accumulated significantly in deprived synapses, suggesting targeted synaptic protein degradation under sensory deprivation. Importantly, this screen identified synaptic proteins whose levels were affected by sensory deprivation but whose synaptic roles have not yet been characterized in mammalian neurons. These data demonstrate the feasibility of defining synaptic proteomes under different sensory rearing conditions and could be applied to elucidate further molecular mechanisms of sensory development.
Collapse
|
45
|
Vogt A, Fuerholzner B, Kinkl N, Boldt K, Ueffing M. Isotope coded protein labeling coupled immunoprecipitation (ICPL-IP): a novel approach for quantitative protein complex analysis from native tissue. Mol Cell Proteomics 2012; 12:1395-406. [PMID: 23268931 DOI: 10.1074/mcp.o112.023648] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
High confidence definition of protein interactions is an important objective toward the understanding of biological systems. Isotope labeling in combination with affinity-based isolation of protein complexes has increased in accuracy and reproducibility, yet, larger organisms--including humans--are hardly accessible to metabolic labeling and thus, a major limitation has been its restriction to small animals, cell lines, and yeast. As composition as well as the stoichiometry of protein complexes can significantly differ in primary tissues, there is a great demand for methods capable to combine the selectivity of affinity-based isolation as well as the accuracy and reproducibility of isotope-based labeling with its application toward analysis of protein interactions from intact tissue. Toward this goal, we combined isotope coded protein labeling (ICPL)(1) with immunoprecipitation (IP) and quantitative mass spectrometry (MS). ICPL-IP allows sensitive and accurate analysis of protein interactions from primary tissue. We applied ICPL-IP to immuno-isolate protein complexes from bovine retinal tissue. Protein complexes of immunoprecipitated β-tubulin, a highly abundant protein with known interactors as well as the lowly expressed small GTPase RhoA were analyzed. The results of both analyses demonstrate sensitive and selective identification of known as well as new protein interactions by our method.
Collapse
Affiliation(s)
- Andreas Vogt
- Institute for Ophthalmic Research, Division of Experimental Ophthalmology and Medical Proteome Center, University of Tuebingen, D-72076 Tuebingen, Germany
| | | | | | | | | |
Collapse
|
46
|
Rauniyar N, Gao B, McClatchy DB, Yates JR. Comparison of protein expression ratios observed by sixplex and duplex TMT labeling method. J Proteome Res 2012; 12:1031-9. [PMID: 23214967 DOI: 10.1021/pr3008896] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Stable isotope labeling via isobaric derivatization of peptides is a universally applicable approach that enables concurrent identification and quantification of proteins in different samples using tandem mass spectrometry. In this study, we evaluated the performance of amine-reactive isobaric tandem mass tag (TMT), available as duplex and sixplex sets, with regard to their ability to elucidate protein expression changes. Using rat brain tissue from two different developmental time points, postnatal day 1 (p1) and 45 (p45), as a model system, we compared the protein expression ratios (p45/p1) observed using duplex TMT tags in triplicate measurements versus sixplex tag in a single LC-MS/MS analysis. A correlation of 0.79 in relative protein abundance was observed in the proteins quantified by these two sets of reagents. However, more proteins passed the criteria for significant fold change (-1.0 ≤ log(2) ratio (p45/p1) ≥ +1.0 and p < 0.05) in the sixplex analysis. Nevertheless, in both methods most proteins showing significant fold change were identified by multiple spectra, increasing their quantification precision. Additionally, the fold change in p45 rats against p1, observed in TMT experiments, was corroborated by a metabolic labeling strategy where relative quantification of differentially expressed proteins was obtained using (15)N-labeled p45 rats as an internal standard.
Collapse
Affiliation(s)
- Navin Rauniyar
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | | | |
Collapse
|
47
|
|
48
|
Filiou MD, Varadarajulu J, Teplytska L, Reckow S, Maccarrone G, Turck CW. The 15N isotope effect in Escherichia coli: a neutron can make the difference. Proteomics 2012; 12:3121-8. [PMID: 22887715 DOI: 10.1002/pmic.201200209] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 06/25/2012] [Accepted: 08/04/2012] [Indexed: 12/22/2022]
Abstract
Several techniques based on stable isotope labeling are used for quantitative MS. These include stable isotope metabolic labeling methods for cells in culture as well as live organisms with the assumption that the stable isotope has no effect on the proteome. Here, we investigate the (15) N isotope effect on Escherichia coli cultures that were grown in either unlabeled ((14) N) or (15) N-labeled media by LC-ESI-MS/MS-based relative protein quantification. Consistent protein expression level differences and altered growth rates were observed between (14) N and (15) N-labeled cultures. Furthermore, targeted metabolite analyses revealed altered metabolite levels between (14) N and (15) N-labeled bacteria. Our data demonstrate for the first time that the introduction of the (15) N isotope affects protein and metabolite levels in E. coli and underline the importance of implementing controls for unbiased protein quantification using stable isotope labeling techniques.
Collapse
Affiliation(s)
- Michaela D Filiou
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Munich, Germany
| | | | | | | | | | | |
Collapse
|
49
|
Brunner AM, Tweedie-Cullen RY, Mansuy IM. Epigenetic modifications of the neuroproteome. Proteomics 2012; 12:2404-20. [PMID: 22696459 DOI: 10.1002/pmic.201100672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 03/12/2012] [Accepted: 04/12/2012] [Indexed: 01/17/2023]
Abstract
In the central nervous system, epigenetic processes are involved in a multitude of brain functions ranging from the development and differentiation of the nervous system through to higher-order cognitive processes such as learning and memory. This review summarises the current state of the art for the proteomic analysis of the epigenetic regulation of gene expression, in particular the PTM of histones, in the brain and cellular model systems. It describes the MS technologies that have helped the identification and analysis of histones, histone variants and PTMs in the brain. Strategies for the isolation of histones that allow the qualitative analysis of PTMs and their combinatorial patterns are introduced, methods for the relative and absolute quantification of histone PTMs are described, and future challenges are discussed.
Collapse
Affiliation(s)
- Andrea M Brunner
- Brain Research Institute, University of Zürich and Department of Biology, ETH Zürich, Zürich, Switzerland
| | | | | |
Collapse
|
50
|
Culver BP, Savas JN, Park SK, Choi JH, Zheng S, Zeitlin SO, Yates JR, Tanese N. Proteomic analysis of wild-type and mutant huntingtin-associated proteins in mouse brains identifies unique interactions and involvement in protein synthesis. J Biol Chem 2012; 287:21599-614. [PMID: 22556411 DOI: 10.1074/jbc.m112.359307] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Huntington disease is a neurodegenerative disorder caused by a CAG repeat amplification in the gene huntingtin (HTT) that is reflected by a polyglutamine expansion in the Htt protein. Nearly 20 years of research have uncovered roles for Htt in a wide range of cellular processes, and many of these discoveries stemmed from the identification of Htt-interacting proteins. However, no study has employed an impartial and comprehensive strategy to identify proteins that differentially associate with full-length wild-type and mutant Htt in brain tissue, the most relevant sample source to the disease condition. We analyzed Htt affinity-purified complexes from wild-type and HTT mutant juvenile mouse brain from two different biochemical fractions by tandem mass spectrometry. We compared variations in protein spectral counts relative to Htt to identify those proteins that are the most significantly contrasted between wild-type and mutant Htt purifications. Previously unreported Htt interactions with Myo5a, Prkra (PACT), Gnb2l1 (RACK1), Rps6, and Syt2 were confirmed by Western blot analysis. Gene Ontology analysis of these and other Htt-associated proteins revealed a statistically significant enrichment for proteins involved in translation among other categories. Furthermore, Htt co-sedimentation with polysomes in cytoplasmic mouse brain extracts is dependent upon the presence of intact ribosomes. Finally, wild-type or mutant Htt overexpression inhibits cap-dependent translation of a reporter mRNA in an in vitro system. Cumulatively, these data support a new role for Htt in translation and provide impetus for further study into the link between protein synthesis and Huntington disease pathogenesis.
Collapse
Affiliation(s)
- Brady P Culver
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | | | | | | | | | | | | | | |
Collapse
|