1
|
Wang Z, Liu PK, Li L. A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics. ACS MEASUREMENT SCIENCE AU 2024; 4:315-337. [PMID: 39184361 PMCID: PMC11342459 DOI: 10.1021/acsmeasuresciau.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 08/27/2024]
Abstract
Recent advancements in mass spectrometry (MS) have revolutionized quantitative proteomics, with multiplex isotope labeling emerging as a key strategy for enhancing accuracy, precision, and throughput. This tutorial review offers a comprehensive overview of multiplex isotope labeling techniques, including precursor-based, mass defect-based, reporter ion-based, and hybrid labeling methods. It details their fundamental principles, advantages, and inherent limitations along with strategies to mitigate the limitation of ratio-distortion. This review will also cover the applications and latest progress in these labeling techniques across various domains, including cancer biomarker discovery, neuroproteomics, post-translational modification analysis, cross-linking MS, and single-cell proteomics. This Review aims to provide guidance for researchers on selecting appropriate methods for their specific goals while also highlighting the potential future directions in this rapidly evolving field.
Collapse
Affiliation(s)
- Zicong Wang
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Peng-Kai Liu
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Lachman
Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Wisconsin
Center for NanoBioSystems, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| |
Collapse
|
2
|
Kater MSJ, Baumgart KF, Badia-Soteras A, Heistek TS, Carney KE, Timmerman AJ, van Weering JRT, Smit AB, van der Knaap MS, Mansvelder HD, Verheijen MHG, Min R. A novel role for MLC1 in regulating astrocyte-synapse interactions. Glia 2023; 71:1770-1785. [PMID: 37002718 DOI: 10.1002/glia.24368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023]
Abstract
Loss of function of the astrocyte membrane protein MLC1 is the primary genetic cause of the rare white matter disease Megalencephalic Leukoencephalopathy with subcortical Cysts (MLC), which is characterized by disrupted brain ion and water homeostasis. MLC1 is prominently present around fluid barriers in the brain, such as in astrocyte endfeet contacting blood vessels and in processes contacting the meninges. Whether the protein plays a role in other astrocyte domains is unknown. Here, we show that MLC1 is present in distal astrocyte processes, also known as perisynaptic astrocyte processes (PAPs) or astrocyte leaflets, which closely interact with excitatory synapses in the CA1 region of the hippocampus. We find that the PAP tip extending toward excitatory synapses is shortened in Mlc1-null mice. This affects glutamatergic synaptic transmission, resulting in a reduced rate of spontaneous release events and slower glutamate re-uptake under challenging conditions. Moreover, while PAPs in wildtype mice retract from the synapse upon fear conditioning, we reveal that this structural plasticity is disturbed in Mlc1-null mice, where PAPs are already shorter. Finally, Mlc1-null mice show reduced contextual fear memory. In conclusion, our study uncovers an unexpected role for the astrocyte protein MLC1 in regulating the structure of PAPs. Loss of MLC1 alters excitatory synaptic transmission, prevents normal PAP remodeling induced by fear conditioning and disrupts contextual fear memory expression. Thus, MLC1 is a new player in the regulation of astrocyte-synapse interactions.
Collapse
Affiliation(s)
- Mandy S J Kater
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, The Netherlands
| | - Katharina F Baumgart
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Aina Badia-Soteras
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, The Netherlands
| | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Karen E Carney
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, The Netherlands
| | - A Jacob Timmerman
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jan R T van Weering
- Department of Human Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam University Medical Centers, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, The Netherlands
| | - Marjo S van der Knaap
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mark H G Verheijen
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, The Netherlands
| | - Rogier Min
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
3
|
Kater MSJ, Badia-Soteras A, van Weering JRT, Smit AB, Verheijen MHG. Electron microscopy analysis of astrocyte-synapse interactions shows altered dynamics in an Alzheimer's disease mouse model. Front Cell Neurosci 2023; 17:1085690. [PMID: 36779013 PMCID: PMC9908992 DOI: 10.3389/fncel.2023.1085690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction Astrocyte-synapse bi-directional communication is required for neuronal development and synaptic plasticity. Astrocytes structurally interact with synapses using their distal processes also known as leaflets or perisynaptic astrocytic processes (PAPs). We recently showed that these PAPs are retracted from hippocampal synapses, and involved in the consolidation of fear memory. However, whether astrocytic synaptic coverage is affected when memory is impaired is unknown. Methods Here, we describe in detail an electron microscopy method that makes use of a large number of 2D images to investigate structural astrocyte-synapse interaction in paraformaldehyde fixed brain tissue of mice. Results and discussion We show that fear memory-induced synaptic activation reduces the interaction between the PAPs and the presynapse, but not the postsynapse, accompanied by retraction of the PAP tip from the synaptic cleft. Interestingly, this retraction is absent in the APP/PS1 mouse model of Alzheimer's disease, supporting the concept that alterations in astrocyte-synapse coverage contribute to memory processing.
Collapse
Affiliation(s)
- Mandy S. J. Kater
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Aina Badia-Soteras
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Jan R. T. van Weering
- Department of Human Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Amsterdam University Medical Center, Vrije Universiteit Medical Center, Amsterdam, Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Mark H. G. Verheijen
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands,*Correspondence: Mark H. G. Verheijen,
| |
Collapse
|
4
|
Nasseri GG, Matin N, Wild AR, Tosefsky K, Flibotte S, Stacey RG, Hollman RB, Foster LJ, Bamji SX. Synaptic activity-dependent changes in the hippocampal palmitoylome. Sci Signal 2022; 15:eadd2519. [PMID: 36473050 DOI: 10.1126/scisignal.add2519] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dynamic protein S-palmitoylation is critical for neuronal function, development, and synaptic plasticity. Synaptic activity-dependent changes in palmitoylation have been reported for a small number of proteins. Here, we characterized the palmitoylome in the hippocampi of male mice before and after context-dependent fear conditioning. Of the 121 differentially palmitoylated proteins identified, just over half were synaptic proteins, whereas others were associated with metabolic functions, cytoskeletal organization, and signal transduction. The synapse-associated proteins generally exhibited increased palmitoylation after fear conditioning. In contrast, most of the proteins that exhibited decreased palmitoylation were associated with metabolic processes. Similar results were seen in cultured rat hippocampal neurons in response to chemically induced long-term potentiation. Furthermore, we found that the palmitoylation of one of the synaptic proteins, plasticity-related gene-1 (PRG-1), also known as lipid phosphate phosphatase-related protein type 4 (LPPR4), was important for synaptic activity-induced insertion of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) into the postsynaptic membrane. The findings identify proteins whose dynamic palmitoylation may regulate their role in synaptic plasticity, learning, and memory.
Collapse
Affiliation(s)
- Glory G Nasseri
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nusrat Matin
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Angela R Wild
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Kira Tosefsky
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Stephane Flibotte
- Life Sciences Institute Bioinformatics Facility, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - R Greg Stacey
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rocio B Hollman
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Shernaz X Bamji
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| |
Collapse
|
5
|
Activity-dependent translation dynamically alters the proteome of the perisynaptic astrocyte process. Cell Rep 2022; 41:111474. [PMID: 36261025 PMCID: PMC9624251 DOI: 10.1016/j.celrep.2022.111474] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 06/16/2022] [Accepted: 09/19/2022] [Indexed: 01/07/2023] Open
Abstract
Within eukaryotic cells, translation is regulated independent of transcription, enabling nuanced, localized, and rapid responses to stimuli. Neurons respond transcriptionally and translationally to synaptic activity. Although transcriptional responses are documented in astrocytes, here we test whether astrocytes have programmed translational responses. We show that seizure activity rapidly changes the transcripts on astrocyte ribosomes, some predicted to be downstream of BDNF signaling. In acute slices, we quantify the extent to which cues of neuronal activity activate translation in astrocytes and show that this translational response requires the presence of neurons, indicating that the response is non-cell autonomous. We also show that this induction of new translation extends into the periphery of astrocytes. Finally, synaptic proteomics show that new translation is required for changes that occur in perisynaptic astrocyte protein composition after fear conditioning. Regulation of translation in astrocytes by neuronal activity suggests an additional mechanism by which astrocytes may dynamically modulate nervous system functioning.
Collapse
|
6
|
León A, Aparicio GI, Scorticati C. Neuronal Glycoprotein M6a: An Emerging Molecule in Chemical Synapse Formation and Dysfunction. Front Synaptic Neurosci 2021; 13:661681. [PMID: 34017241 PMCID: PMC8129562 DOI: 10.3389/fnsyn.2021.661681] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/07/2021] [Indexed: 12/27/2022] Open
Abstract
The cellular and molecular mechanisms underlying neuropsychiatric and neurodevelopmental disorders show that most of them can be categorized as synaptopathies-or damage of synaptic function and plasticity. Synaptic formation and maintenance are orchestrated by protein complexes that are in turn regulated in space and time during neuronal development allowing synaptic plasticity. However, the exact mechanisms by which these processes are managed remain unknown. Large-scale genomic and proteomic projects led to the discovery of new molecules and their associated variants as disease risk factors. Neuronal glycoprotein M6a, encoded by the GPM6A gene is emerging as one of these molecules. M6a has been involved in neuron development and synapse formation and plasticity, and was also recently proposed as a gene-target in various neuropsychiatric disorders where it could also be used as a biomarker. In this review, we provide an overview of the structure and molecular mechanisms by which glycoprotein M6a participates in synapse formation and maintenance. We also review evidence collected from patients carrying mutations in the GPM6A gene; animal models, and in vitro studies that together emphasize the relevance of M6a, particularly in synapses and in neurological conditions.
Collapse
Affiliation(s)
| | | | - Camila Scorticati
- Instituto de Investigaciones Biotecnológicas “Rodolfo A. Ugalde”, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (IIBio-UNSAM-CONICET), Buenos Aires, Argentina
| |
Collapse
|
7
|
Kim CH, Kim S, Kim SH, Roh J, Jin H, Song B. Role of densin-180 in mouse ventral hippocampal neurons in 24-hr retention of contextual fear conditioning. Brain Behav 2020; 10:e01891. [PMID: 33064361 PMCID: PMC7749528 DOI: 10.1002/brb3.1891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/01/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Densin-180 interacts with postsynaptic molecules including calcium/calmodulin-dependent protein kinase IIα (CaMKIIα) but its function in learning and memory process has been unclear. METHODS To investigate a role of hippocampal densin-180 in contextual fear conditioning (CFC) learning and memory processes, knockdown (KD) of densin-180 in hippocampal subareas was applied. RESULTS First, ventral hippocampal (vHC) densin-180 KD impaired single-trial CFC (stCFC) memory one day later. stCFC caused freezing behaviors to reach the peak about one hour later in both control and KD mice, but then freezing was disappeared at 2 hr postshock in KD mice. Second, stCFC caused an immediate and transient reduction of vHC densin-180 in control mice, which was not observed in KD mice. Third, stCFC caused phosphorylated-T286 (p-T286) CaMKIIα to change similarly to densin-180, but p-T305 CaMKIIα was increased 1 hr later in control mice. In KD mice, these effects were gone. Moreover, both basal levels of p-T286 and p-T305 CaMKIIα were reduced without change in total CaMKIIα in KD mice. Fourth, we found double-trial CFC (dtCFC) memory acquisition and retrieval kinetics were different from those of stCFC in vHC KD mice. In addition, densin-180 in dorsal hippocampal area appeared to play its unique role during the very early retrieval period of both CFC memories. CONCLUSION This study shows that vHC densin-180 is necessary for stCFC memory formation and retrieval and suggests that both densin-180 and p-T305 CaMKIIα at 1 ~ 2 hr postshock are important for stCFC memory formation. We conclude that roles of hippocampal neuronal densin-180 in CFC are temporally dynamic and differential depending on the pattern of conditioning stimuli and its location along the dorsoventral axis of hippocampal formation.
Collapse
Affiliation(s)
- Chong-Hyun Kim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, Korea.,Neuroscience Program, Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Korea
| | - Seoyul Kim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, Korea.,Neuroscience Program, Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Korea
| | - Su-Hyun Kim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, Korea.,Neuroscience Program, Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Korea
| | - Jongtae Roh
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, Korea.,Neuroscience Program, Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Korea
| | - Harin Jin
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, Korea.,Neuroscience Program, Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Korea
| | - Bokyung Song
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, Korea.,Neuroscience Program, Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, Korea
| |
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
|
Pandya NJ, Seeger C, Babai N, Gonzalez-Lozano MA, Mack V, Lodder JC, Gouwenberg Y, Mansvelder HD, Danielson UH, Li KW, Heine M, Spijker S, Frischknecht R, Smit AB. Noelin1 Affects Lateral Mobility of Synaptic AMPA Receptors. Cell Rep 2019; 24:1218-1230. [PMID: 30067977 PMCID: PMC6088136 DOI: 10.1016/j.celrep.2018.06.102] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/26/2018] [Accepted: 06/26/2018] [Indexed: 11/24/2022] Open
Abstract
Lateral diffusion on the neuronal plasma membrane of the AMPA-type glutamate receptor (AMPAR) serves an important role in synaptic plasticity. We investigated the role of the secreted glycoprotein Noelin1 (Olfactomedin-1 or Pancortin) in AMPAR lateral mobility and its dependence on the extracellular matrix (ECM). We found that Noelin1 interacts with the AMPAR with high affinity, however, without affecting rise- and decay time and desensitization properties. Noelin1 co-localizes with synaptic and extra-synaptic AMPARs and is expressed at synapses in an activity-dependent manner. Single-particle tracking shows that Noelin1 reduces lateral mobility of both synaptic and extra-synaptic GluA1-containing receptors and affects short-term plasticity. While the ECM does not constrain the synaptic pool of AMPARs and acts only extrasynaptically, Noelin1 contributes to synaptic potentiation by limiting AMPAR mobility at synaptic sites. This is the first evidence for the role of a secreted AMPAR-interacting protein on mobility of GluA1-containing receptors and synaptic plasticity. Noelin1 interacts with high affinity to AMPA receptors (AMPARs) Noelin1 is secreted upon cellular stimulation (Extra)synaptic AMPAR mobility, but not channel properties, are affected by Noelin1 Reducing synaptic AMPAR lateral mobility by Noelin1 limits synaptic plasticity
Collapse
Affiliation(s)
- Nikhil J Pandya
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Christian Seeger
- Beactica AB, Virdings allé 2, 754 50 Uppsala, Sweden; Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Norbert Babai
- Department of Biology, Animal Physiology, Friedrich Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Miguel A Gonzalez-Lozano
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Volker Mack
- Department of CNS Diseases Research, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach (an der Riss), Germany
| | - Johannes C Lodder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Yvonne Gouwenberg
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - U Helena Danielson
- Beactica AB, Virdings allé 2, 754 50 Uppsala, Sweden; Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands
| | - Martin Heine
- Research Group Molecular Physiology, Leibniz Institute for Neurobiology, Brenneckestrasse 6, 39118 Magdeburg, Germany
| | - Sabine Spijker
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands.
| | - Renato Frischknecht
- Department of Biology, Animal Physiology, Friedrich Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany; Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Brenneckestrasse 6, 39118 Magdeburg, Germany
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands.
| |
Collapse
|
10
|
Çetereisi D, Kramvis I, Gebuis T, van der Loo RJ, Gouwenberg Y, Mansvelder HD, Li KW, Smit AB, Spijker S. Gpr158 Deficiency Impacts Hippocampal CA1 Neuronal Excitability, Dendritic Architecture, and Affects Spatial Learning. Front Cell Neurosci 2019; 13:465. [PMID: 31749686 PMCID: PMC6843000 DOI: 10.3389/fncel.2019.00465] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/30/2019] [Indexed: 11/30/2022] Open
Abstract
G-protein-coupled receptor 158 (Gpr158) is highly expressed in striatum, hippocampus and prefrontal cortex. It gained attention as it was implicated in physiological responses to stress and depression. Recently, Gpr158 has been shown to act as a pathway-specific synaptic organizer in the hippocampus, required for proper mossy fiber-CA3 neurocircuitry establishment, structure, and function. Although rodent Gpr158 expression is highest in CA3, considerable expression occurs in CA1 especially after the first postnatal month. Here, we combined hippocampal-dependent behavioral paradigms with subsequent electrophysiological and morphological analyses from the same group of mice to assess the effects of Gpr158 deficiency on CA1 physiology and function. We demonstrate deficits in spatial memory acquisition and retrieval in the Morris water maze paradigm, along with deficits in the acquisition of extinction memory in the passive avoidance test in Gpr158 KO mice. Electrophysiological recordings from CA1 pyramidal neurons revealed normal basal excitatory and inhibitory synaptic transmission, however, Schaffer collateral stimulation yielded dramatically reduced post-synaptic currents. Interestingly, intrinsic excitability of CA1 pyramidals was found increased, potentially acting as a compensatory mechanism to the reductions in Schaffer collateral-mediated drive. Both ex vivo and in vitro, neurons deficient for or with lowered levels of Gpr158 exhibited robust reductions in dendritic architecture and complexity, i.e., reduced length, surface, bifurcations, and branching. This effect was localized in the apical but not basal dendrites of adult CA1 pyramidals, indicative of compartment-specific alterations. A significant positive correlation between spatial memory acquisition and extent of complexity of CA1 pyramidals was found. Taken together, we provide first evidence of significant disruptions in hippocampal CA1 neuronal dendritic architecture and physiology, driven by Gpr158 deficiency. Importantly, the hippocampal neuronal morphology deficits appear to support the impairments in spatial memory acquisition observed in Gpr158 KO mice.
Collapse
Affiliation(s)
- Demirhan Çetereisi
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Ioannis Kramvis
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Titia Gebuis
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Rolinka J. van der Loo
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Yvonne Gouwenberg
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Huibert D. Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Sabine Spijker
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| |
Collapse
|
11
|
Koopmans F, Pandya NJ, Franke SK, Phillippens IHCMH, Paliukhovich I, Li KW, Smit AB. Comparative Hippocampal Synaptic Proteomes of Rodents and Primates: Differences in Neuroplasticity-Related Proteins. Front Mol Neurosci 2018; 11:364. [PMID: 30333727 PMCID: PMC6176546 DOI: 10.3389/fnmol.2018.00364] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/13/2018] [Indexed: 01/20/2023] Open
Abstract
Key to the human brain’s unique capacities are a myriad of neural cell types, specialized molecular expression signatures, and complex patterns of neuronal connectivity. Neurons in the human brain communicate via well over a quadrillion synapses. Their specific contribution might be key to the dynamic activity patterns that underlie primate-specific cognitive function. Recently, functional differences were described in transmission capabilities of human and rat synapses. To test whether unique expression signatures of synaptic proteins are at the basis of this, we performed a quantitative analysis of the hippocampal synaptic proteome of four mammalian species, two primates, human and marmoset, and two rodents, rat and mouse. Abundance differences down to 1.15-fold at an FDR-corrected p-value of 0.005 were reliably detected using SWATH mass spectrometry. The high measurement accuracy of SWATH allowed the detection of a large group of differentially expressed proteins between individual species and rodent vs. primate. Differentially expressed proteins between rodent and primate were found highly enriched for plasticity-related proteins.
Collapse
Affiliation(s)
- Frank Koopmans
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Nikhil J Pandya
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Sigrid K Franke
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Biomedical Primate Research Centre, Rijswijk, Netherlands
| | | | - Iryna Paliukhovich
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
12
|
von Ziegler LM, Selevsek N, Tweedie-Cullen RY, Kremer E, Mansuy IM. Subregion-Specific Proteomic Signature in the Hippocampus for Recognition Processes in Adult Mice. Cell Rep 2018; 22:3362-3374. [DOI: 10.1016/j.celrep.2018.02.079] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 01/05/2018] [Accepted: 02/21/2018] [Indexed: 12/15/2022] Open
|
13
|
Houyoux N, Wattiez R, Ris L. A proteomic analysis of contextual fear conditioned rats reveals dynamic modifications in neuron and oligodendrocyte protein expression in the dentate gyrus. Eur J Neurosci 2017; 46:2177-2189. [PMID: 28833751 DOI: 10.1111/ejn.13664] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 11/30/2022]
Abstract
Contextual memory is an intricate process involving synaptic plasticity and network rearrangement. Both are governed by many molecular processes including phosphorylation and modulation of protein expression. However, little is known about the molecules involved in it. Here, we exploited the advantages of a quantitative proteomic approach to identify a great number of molecules in the rat dentate gyrus after a contextual fear conditioning session. Our results allowed us to highlight protein expression patterns, not only related to neuroplasticity, but also to myelin structure, such as myelin basic protein and myelin proteolipid protein showing a decrease in expression. Validation of the modification in protein expression reveals a dynamic profile during the 48 h following the fear conditioning session. The expression of proteins involved in neurite outgrowth, such as BASP-1 and calcineurin B1, and in synaptic structure and function, VAMP2 and RAB3C, was increased in the dentate gyrus of rats submitted to fear conditioning compared to controls. We showed that the increase in BASP-1 protein was specific to fear conditioning learning as it was not present in immediate-shock rats, neither in rats exposed to a novel environment without being shocked. As myelin is known to stabilise synaptic network, the decrease in myelin proteins suggests a neuroglia interactive process taking place in the dentate gyrus in the 24 h following contextual fear learning, which has never been demonstrated before. These results therefore open the way to the study of new plasticity mechanisms underlying learning and memory.
Collapse
Affiliation(s)
- Nicolas Houyoux
- Proteomics and Microbiology Department, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Laurence Ris
- Department of Neuroscience, Research Institute for Biosciences, University of Mons, 20 Place du Parc, 7000, Mons, Belgium
| |
Collapse
|
14
|
Liu X, Guo Z, Liu W, Sun W, Ma C. Differential proteome analysis of hippocampus and temporal cortex using label-free based 2D-LC-MS/MS. J Proteomics 2017. [PMID: 28627465 DOI: 10.1016/j.jprot.2017.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hippocampus and temporal cortex are important brain regions, which play distinct, but complimentary roles in mediating learning and memory. Herein, we utilized label-free differential proteome strategy to explore function of normal human hippocampus and temporal cortex in learning and memory. As a result, a total of 5529 and 5702 proteins were identified in hippocampus and temporal cortex, respectively, 516 of which were significantly differential expressed, with abundance span 5 orders of magnitudes. Pathways analysis showed that temporal cortex was involved in growth of axons growth and synapse density regulation, through which could regulate long-term potentiation and long-term retention of trace memory. Hippocampus was involved in regulation of cell survival and cell viability, and regulates neurons proliferation by actin dynamics changes, through which involved in both short-term memory and long-term memory. Four selected differential proteins were further validated by Western blot and immunohistochemistry. For the first time, we identified proteins and associated pathways of hippocampus and temporal cortex in human cognition process using proteomic strategy, which would provide references for generating corresponding insights in hippocampus and temporal cortex-related cognitive function. The original data files can be downloaded at http://211.102.209.254/page/PSV023.html;?url=1489542083729AFHp (password: kYxh). SIGNIFICANCE This study explored the potential molecular mechanism of hippocampus and temporal cortex in human cognition function using proteomics strategy, which will offer a baseline reference for further cognitive disorders study and reveal insights into physiology of temporal cortex and hippocampus.
Collapse
Affiliation(s)
- Xiaoyan Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Zhengguang Guo
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
| |
Collapse
|
15
|
Pontes AH, de Sousa MV. Mass Spectrometry-Based Approaches to Understand the Molecular Basis of Memory. Front Chem 2016; 4:40. [PMID: 27790611 PMCID: PMC5064248 DOI: 10.3389/fchem.2016.00040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/27/2016] [Indexed: 01/15/2023] Open
Abstract
The central nervous system is responsible for an array of cognitive functions such as memory, learning, language, and attention. These processes tend to take place in distinct brain regions; yet, they need to be integrated to give rise to adaptive or meaningful behavior. Since cognitive processes result from underlying cellular and molecular changes, genomics and transcriptomics assays have been applied to human and animal models to understand such events. Nevertheless, genes and RNAs are not the end products of most biological functions. In order to gain further insights toward the understanding of brain processes, the field of proteomics has been of increasing importance in the past years. Advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS) have enabled the identification and quantification of thousands of proteins with high accuracy and sensitivity, fostering a revolution in the neurosciences. Herein, we review the molecular bases of explicit memory in the hippocampus. We outline the principles of mass spectrometry (MS)-based proteomics, highlighting the use of this analytical tool to study memory formation. In addition, we discuss MS-based targeted approaches as the future of protein analysis.
Collapse
Affiliation(s)
- Arthur H Pontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia Brasilia, Brazil
| | - Marcelo V de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia Brasilia, Brazil
| |
Collapse
|
16
|
Michopoulos V, Vester A, Neigh G. Posttraumatic stress disorder: A metabolic disorder in disguise? Exp Neurol 2016; 284:220-229. [PMID: 27246996 PMCID: PMC5056806 DOI: 10.1016/j.expneurol.2016.05.038] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 05/24/2016] [Accepted: 05/26/2016] [Indexed: 12/30/2022]
Abstract
Posttraumatic stress disorder (PTSD) is a heterogeneous psychiatric disorder that affects individuals exposed to trauma and is highly co-morbid with other adverse health outcomes, including cardiovascular disease and obesity. The unique pathophysiological feature of PTSD is the inability to inhibit fear responses, such that individuals suffering from PTSD re-experience traumatic memories and are unable to control psychophysiological responses to trauma-associated stimuli. However, underlying alterations in sympathetic nervous system activity, neuroendocrine systems, and metabolism associated with PTSD are similar to those present in traditional metabolic disorders, such as obesity and diabetes. The current review highlights existing clinical, translational, and preclinical data that support the notion that underneath the primary indication of impaired fear inhibition, PTSD is itself also a metabolic disorder and proposes altered function of inflammatory responses as a common underlying mechanism. The therapeutic implications of treating PTSD as a whole-body condition are significant, as targeting any underlying biological system whose activity is altered in both PTSD and metabolic disorders, (i.e. HPA axis, sympathetic nervous systems, inflammation) may elicit symptomatic relief in individuals suffering from these whole-body adverse outcomes.
Collapse
Affiliation(s)
- Vasiliki Michopoulos
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States; Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Aimee Vester
- Department of Environmental Health Sciences, Rollins School of Public Health, Atlanta, GA, United States
| | - Gretchen Neigh
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, United States; Yerkes National Primate Research Center, Atlanta, GA, United States; Department of Physiology, Emory University School of Medicine, Atlanta, GA, United States.
| |
Collapse
|
17
|
Kähne T, Richter S, Kolodziej A, Smalla KH, Pielot R, Engler A, Ohl FW, Dieterich DC, Seidenbecher C, Tischmeyer W, Naumann M, Gundelfinger ED. Proteome rearrangements after auditory learning: high-resolution profiling of synapse-enriched protein fractions from mouse brain. J Neurochem 2016; 138:124-38. [PMID: 27062398 PMCID: PMC5089584 DOI: 10.1111/jnc.13636] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 03/23/2016] [Accepted: 04/01/2016] [Indexed: 01/09/2023]
Abstract
Learning and memory processes are accompanied by rearrangements of synaptic protein networks. While various studies have demonstrated the regulation of individual synaptic proteins during these processes, much less is known about the complex regulation of synaptic proteomes. Recently, we reported that auditory discrimination learning in mice is associated with a relative down-regulation of proteins involved in the structural organization of synapses in various brain regions. Aiming at the identification of biological processes and signaling pathways involved in auditory memory formation, here, a label-free quantification approach was utilized to identify regulated synaptic junctional proteins and phosphoproteins in the auditory cortex, frontal cortex, hippocampus, and striatum of mice 24 h after the learning experiment. Twenty proteins, including postsynaptic scaffolds, actin-remodeling proteins, and RNA-binding proteins, were regulated in at least three brain regions pointing to common, cross-regional mechanisms. Most of the detected synaptic proteome changes were, however, restricted to individual brain regions. For example, several members of the Septin family of cytoskeletal proteins were up-regulated only in the hippocampus, while Septin-9 was down-regulated in the hippocampus, the frontal cortex, and the striatum. Meta analyses utilizing several databases were employed to identify underlying cellular functions and biological pathways. Data are available via ProteomeExchange with identifier PXD003089. How does the protein composition of synapses change in different brain areas upon auditory learning? We unravel discrete proteome changes in mouse auditory cortex, frontal cortex, hippocampus, and striatum functionally implicated in the learning process. We identify not only common but also area-specific biological pathways and cellular processes modulated 24 h after training, indicating individual contributions of the regions to memory processing.
Collapse
Affiliation(s)
- Thilo Kähne
- Institute of Experimental Internal Medicine, Medical School, Otto von Guericke University, Magdeburg, Germany
| | - Sandra Richter
- Institute of Experimental Internal Medicine, Medical School, Otto von Guericke University, Magdeburg, Germany
| | - Angela Kolodziej
- Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany.,Institute of Biology, Otto von Guericke University, Magdeburg, Germany
| | - Karl-Heinz Smalla
- Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Rainer Pielot
- Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany
| | | | - Frank W Ohl
- Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany.,Institute of Biology, Otto von Guericke University, Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Daniela C Dieterich
- Center for Behavioral Brain Sciences, Magdeburg, Germany.,Institute of Pharmacology and Toxicology, Medical School, Otto von Guericke University, Magdeburg, Germany
| | - Constanze Seidenbecher
- Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Wolfgang Tischmeyer
- Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical School, Otto von Guericke University, Magdeburg, Germany
| | - Eckart D Gundelfinger
- Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany.,Molecular Neuroscience, Medical School, Otto von Guericke University, Magdeburg, Germany.,German Center for Neurodegenerative Diseases, Magdeburg, Germany
| |
Collapse
|
18
|
Quantitative proteomics reveals protein kinases and phosphatases in the individual phases of contextual fear conditioning in the C57BL/6J mouse. Behav Brain Res 2016; 303:208-17. [DOI: 10.1016/j.bbr.2015.12.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/14/2015] [Accepted: 12/18/2015] [Indexed: 12/20/2022]
|
19
|
Dieterich DC, Kreutz MR. Proteomics of the Synapse--A Quantitative Approach to Neuronal Plasticity. Mol Cell Proteomics 2016; 15:368-81. [PMID: 26307175 PMCID: PMC4739661 DOI: 10.1074/mcp.r115.051482] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/29/2015] [Indexed: 11/06/2022] Open
Abstract
The advances in mass spectrometry based proteomics in the past 15 years have contributed to a deeper appreciation of protein networks and the composition of functional synaptic protein complexes. However, research on protein dynamics underlying core mechanisms of synaptic plasticity in brain lag far behind. In this review, we provide a synopsis on proteomic research addressing various aspects of synaptic function. We discuss the major topics in the study of protein dynamics of the chemical synapse and the limitations of current methodology. We highlight recent developments and the future importance of multidimensional proteomics and metabolic labeling. Finally, emphasis is given on the conceptual framework of modern proteomics and its current shortcomings in the quest to gain a deeper understanding of synaptic plasticity.
Collapse
Affiliation(s)
- Daniela C Dieterich
- From the ‡Institute for Pharmacology and Toxicology, Otto-von-Guericke University Magdeburg, Germany; Research Group Neuralomics, Leibniz Institute for Neurobiology Magdeburg, Germany; ¶Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.
| | - Michael R Kreutz
- §RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany; ¶Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.
| |
Collapse
|
20
|
Lenselink AM, Rotaru DC, Li KW, van Nierop P, Rao-Ruiz P, Loos M, van der Schors R, Gouwenberg Y, Wortel J, Mansvelder HD, Smit AB, Spijker S. Strain Differences in Presynaptic Function: PROTEOMICS, ULTRASTRUCTURE, AND PHYSIOLOGY OF HIPPOCAMPAL SYNAPSES IN DBA/2J AND C57Bl/6J MICE. J Biol Chem 2015; 290:15635-15645. [PMID: 25911096 DOI: 10.1074/jbc.m114.628776] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 12/25/2022] Open
Abstract
The inbred strains C57BL/6J and DBA/2J (DBA) display striking differences in a number of behavioral tasks depending on hippocampal function, such as contextual memory. Historically, this has been explained through differences in postsynaptic protein expression underlying synaptic transmission and plasticity. We measured the synaptic hippocampal protein content (iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) and mass spectrometry), CA1 synapse ultrastructural morphology, and synaptic functioning in adult C57BL/6J and DBA mice. DBA mice showed a prominent decrease in the Ras-GAP calcium-sensing protein RASAL1. Furthermore, expression of several presynaptic markers involved in exocytosis, such as syntaxin (Stx1b), Ras-related proteins (Rab3a/c), and rabphilin (Rph3a), was reduced. Ultrastructural analysis of CA1 hippocampal synapses showed a significantly lower number of synaptic vesicles and presynaptic cluster size in DBA mice, without changes in postsynaptic density or active zone. In line with this compromised presynaptic morphological and molecular phenotype in DBA mice, we found significantly lower paired-pulse facilitation and enhanced short term depression of glutamatergic synapses, indicating a difference in transmitter release and/or refilling mechanisms. Taken together, our data suggest that in addition to strain-specific postsynaptic differences, the change in dynamic properties of presynaptic transmitter release may underlie compromised synaptic processing related to cognitive functioning in DBA mice.
Collapse
Affiliation(s)
- A Mariette Lenselink
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Diana C Rotaru
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands; Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Ka Wan Li
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Pim van Nierop
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Priyanka Rao-Ruiz
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Maarten Loos
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Roel van der Schors
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Yvonne Gouwenberg
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Joke Wortel
- Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - August B Smit
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands
| | - Sabine Spijker
- Departments of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam, The Netherlands.
| |
Collapse
|