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Schwab K, Lauer D, Magbagbeolu M, Theuring F, Gasiorowska A, Zadrozny M, Harrington CR, Wischik CM, Niewiadomska G, Riedel G. Hydromethylthionine rescues synaptic SNARE proteins in a mouse model of tauopathies: Interference by cholinesterase inhibitors. Brain Res Bull 2024; 212:110955. [PMID: 38677558 DOI: 10.1016/j.brainresbull.2024.110955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/14/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
In clinical trials for Alzheimer's disease (AD), hydromethylthionine mesylate (HMTM) showed reduced efficacy when administered as an add-on to symptomatic treatments, while it produced a significant improvement of cognitive function when taken as monotherapy. Interference of cholinesterase inhibition with HMTM was observed also in a tau transgenic mouse model, where rivastigmine reduced the pharmacological activity of HMTM at multiple brain levels including hippocampal acetylcholine release, synaptosomal glutamate release and mitochondrial activity. Here, we examined the effect of HMTM, given alone or in combination with the acetylcholinesterase inhibitor, rivastigmine, at the level of expression of selected pre-synaptic proteins (syntaxin-1; SNAP-25, VAMP-2, synaptophysin-1, synapsin-1, α-synuclein) in brain tissue harvested from tau-transgenic Line 1 (L1) and wild-type mice using immunohistochemistry. L1 mice overexpress the tau-core unit that induces tau aggregation and results in an AD-like phenotype. Synaptic proteins were lower in hippocampus and cortex but greater in basal forebrain regions in L1 compared to wild-type mice. HMTM partially normalised the expression pattern of several of these proteins in basal forebrain. This effect was diminished when HMTM was administered in combination with rivastigmine, where mean protein expression seemed supressed. This was further confirmed by group-based correlation network analyses where important levels of co-expression correlations in basal forebrain regions were lost in L1 mice and partially re-established when HMTM was given alone but not in combination with rivastigmine. These data indicate a reduction in pharmacological activity of HMTM when given as an add-on therapy, a result that is consistent with the responses observed in the clinic. Attenuation of the therapeutic effects of HMTM by cholinergic treatments may have important implications for other potential AD therapies.
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Affiliation(s)
- Karima Schwab
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; Institute of Pharmacology, Charité - Universitätsmedizin Berlin, Hessische Str. 3-4, Berlin 10115, Germany
| | - Dilyara Lauer
- Institute of Pharmacology, Charité - Universitätsmedizin Berlin, Hessische Str. 3-4, Berlin 10115, Germany
| | - Mandy Magbagbeolu
- Institute of Pharmacology, Charité - Universitätsmedizin Berlin, Hessische Str. 3-4, Berlin 10115, Germany
| | - Franz Theuring
- Institute of Pharmacology, Charité - Universitätsmedizin Berlin, Hessische Str. 3-4, Berlin 10115, Germany
| | - Anna Gasiorowska
- Clinical and Research Department of Applied Physiology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Maciej Zadrozny
- Clinical and Research Department of Applied Physiology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Charles R Harrington
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; TauRx Therapeutics Ltd., 395 King Street, Aberdeen AB24 5RP, UK
| | - Claude M Wischik
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK; TauRx Therapeutics Ltd., 395 King Street, Aberdeen AB24 5RP, UK
| | - Grażyna Niewiadomska
- Clinical and Research Department of Applied Physiology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Gernot Riedel
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
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2
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Kaizuka T, Suzuki T, Kishi N, Tamada K, Kilimann MW, Ueyama T, Watanabe M, Shimogori T, Okano H, Dohmae N, Takumi T. Remodeling of the postsynaptic proteome in male mice and marmosets during synapse development. Nat Commun 2024; 15:2496. [PMID: 38548776 PMCID: PMC10979008 DOI: 10.1038/s41467-024-46529-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
Postsynaptic proteins play crucial roles in synaptic function and plasticity. During brain development, alterations in synaptic number, shape, and stability occur, known as synapse maturation. However, the postsynaptic protein composition changes during development are not fully understood. Here, we show the trajectory of the postsynaptic proteome in developing male mice and common marmosets. Proteomic analysis of mice at 2, 3, 6, and 12 weeks of age shows that proteins involved in synaptogenesis are differentially expressed during this period. Analysis of published transcriptome datasets shows that the changes in postsynaptic protein composition in the mouse brain after 2 weeks of age correlate with gene expression changes. Proteomic analysis of marmosets at 0, 2, 3, 6, and 24 months of age show that the changes in the marmoset brain can be categorized into two parts: the first 2 months and after that. The changes observed in the first 2 months are similar to those in the mouse brain between 2 and 12 weeks of age. The changes observed in marmoset after 2 months old include differential expression of synaptogenesis-related molecules, which hardly overlap with that in mice. Our results provide a comprehensive proteomic resource that underlies developmental synapse maturation in rodents and primates.
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Affiliation(s)
- Takeshi Kaizuka
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Noriyuki Kishi
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
| | - Kota Tamada
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan
| | - Manfred W Kilimann
- Max Planck Institute for Experimental Medicine, Göttingen, 37075, Germany
| | - Takehiko Ueyama
- Laboratory of Molecular Pharmacology, Biosignal Research Center, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Kita, Sapporo, 060-8638, Japan
| | | | - Hideyuki Okano
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, 160-8585, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan.
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan.
- RIKEN Center for Biosystems Dynamics Research, Chuo, Kobe, 650-0047, Japan.
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3
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Kaizuka T, Hirouchi T, Saneyoshi T, Shirafuji T, Collins MO, Grant SGN, Hayashi Y, Takumi T. FAM81A is a postsynaptic protein that regulates the condensation of postsynaptic proteins via liquid-liquid phase separation. PLoS Biol 2024; 22:e3002006. [PMID: 38452102 PMCID: PMC10919877 DOI: 10.1371/journal.pbio.3002006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/17/2024] [Indexed: 03/09/2024] Open
Abstract
Proteome analyses of the postsynaptic density (PSD), a proteinaceous specialization beneath the postsynaptic membrane of excitatory synapses, have identified several thousands of proteins. While proteins with predictable functions have been well studied, functionally uncharacterized proteins are mostly overlooked. In this study, we conducted a comprehensive meta-analysis of 35 PSD proteome datasets, encompassing a total of 5,869 proteins. Employing a ranking methodology, we identified 97 proteins that remain inadequately characterized. From this selection, we focused our detailed analysis on the highest-ranked protein, FAM81A. FAM81A interacts with PSD proteins, including PSD-95, SynGAP, and NMDA receptors, and promotes liquid-liquid phase separation of those proteins in cultured cells or in vitro. Down-regulation of FAM81A in cultured neurons causes a decrease in the size of PSD-95 puncta and the frequency of neuronal firing. Our findings suggest that FAM81A plays a crucial role in facilitating the interaction and assembly of proteins within the PSD, and its presence is important for maintaining normal synaptic function. Additionally, our methodology underscores the necessity for further characterization of numerous synaptic proteins that still lack comprehensive understanding.
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Affiliation(s)
- Takeshi Kaizuka
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
- Centre for Clinical Brain Sciences, Chancellor’s Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
| | - Taisei Hirouchi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeo Saneyoshi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toshihiko Shirafuji
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
| | - Mark O. Collins
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- biOMICS Facility, Mass Spectrometry Centre, University of Sheffield, Sheffield, United Kingdom
| | - Seth G. N. Grant
- Centre for Clinical Brain Sciences, Chancellor’s Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
- RIKEN Center for Biosystems Dynamics Research, Chuo, Kobe, Japan
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4
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ARRAY TOMOGRAPHY: 15 YEARS OF SYNAPTIC ANALYSIS. Neuronal Signal 2022; 6:NS20220013. [PMID: 36187224 PMCID: PMC9512143 DOI: 10.1042/ns20220013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
Synapses are minuscule, intricate structures crucial for the correct communication between neurons. In the 125 years since the term synapse was first coined, we have advanced a long way when it comes to our understanding of how they work and what they do. Most of the fundamental discoveries have been invariably linked to advances in technology. However, due to their size, delicate structural integrity and their sheer number, our knowledge of synaptic biology has remained somewhat elusive and their role in neurodegenerative diseases still remains largely unknown. Here, we briefly discuss some of the imaging technologies used to study synapses and focus on the utility of the high-resolution imaging technique array tomography (AT). We introduce the AT technique and highlight some of the ways it is utilised with a particular focus on its power for analysing synaptic composition and pathology in human post-mortem tissue. We also discuss some of the benefits and drawbacks of techniques for imaging synapses and highlight some recent advances in the study of form and function by combining physiology and high-resolution synaptic imaging.
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5
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Coupling of GABA Metabolism to Mitochondrial Glucose Phosphorylation. Neurochem Res 2021; 47:470-480. [PMID: 34623563 DOI: 10.1007/s11064-021-03463-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 09/15/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
Glucose and oxygen (O2) are vital to the brain. Glucose metabolism and mitochondria play a pivotal role in this process, culminating in the increase of reactive O2 species. Hexokinase (HK) is a key enzyme on glucose metabolism and is coupled to the brain mitochondrial redox modulation by recycling ADP for oxidative phosphorylation (OXPHOS). GABA shunt is an alternative pathway to GABA metabolism that increases succinate levels, a Krebs cycle intermediate. Although glucose and GABA metabolisms are intrinsically connected, their interplay coordinating mitochondrial function is poorly understood. Here, we hypothesize that the HK and the GABA shunt interact to control mitochondrial metabolism differently in the cortex and the hypothalamus. The GABA shunt stimulated mitochondrial O2 consumption and H2O2 production higher in hypothalamic synaptosomes (HSy) than cortical synaptosomes (CSy). The GABA shunt increased the HK coupled to OXPHOS activity in both population of synaptosomes, but the rate of activation was higher in HSy than CSy. Significantly, malonate and vigabatrin blocked the effects of the GABA shunt in the HK activity coupled to OXPHOS. It indicates that the glucose phosphorylation is linked to GABA and Krebs cycle reactions. Together, these data shed light on the HK and SDH role on the metabolism of each region fed by GABA turnover, which depends on the neurons' metabolic route.
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6
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Qian C, Wu Z, Sun R, Yu H, Zeng J, Rao Y, Li Y. Localization, proteomics, and metabolite profiling reveal a putative vesicular transporter for UDP-glucose. eLife 2021; 10:65417. [PMID: 34269178 PMCID: PMC8373376 DOI: 10.7554/elife.65417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/15/2021] [Indexed: 11/27/2022] Open
Abstract
Vesicular neurotransmitter transporters (VNTs) mediate the selective uptake and enrichment of small-molecule neurotransmitters into synaptic vesicles (SVs) and are therefore a major determinant of the synaptic output of specific neurons. To identify novel VNTs expressed on SVs (thus identifying new neurotransmitters and/or neuromodulators), we conducted localization profiling of 361 solute carrier (SLC) transporters tagging with a fluorescent protein in neurons, which revealed 40 possible candidates through comparison with a known SV marker. We parallelly performed proteomics analysis of immunoisolated SVs and identified seven transporters in overlap. Ultrastructural analysis further supported that one of the transporters, SLC35D3, localized to SVs. Finally, by combining metabolite profiling with a radiolabeled substrate transport assay, we identified UDP-glucose as the principal substrate for SLC35D3. These results provide new insights into the functional role of SLC transporters in neurotransmission and improve our understanding of the molecular diversity of chemical transmitters.
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Affiliation(s)
- Cheng Qian
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhaofa Wu
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.,PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Rongbo Sun
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.,PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Huasheng Yu
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.,PKU-IDG/McGovern Institute for Brain Research, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Jianzhi Zeng
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.,PKU-IDG/McGovern Institute for Brain Research, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Yi Rao
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.,PKU-IDG/McGovern Institute for Brain Research, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China.,Chinese Institute for Brain Research, Beijing, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.,PKU-IDG/McGovern Institute for Brain Research, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China.,Chinese Institute for Brain Research, Beijing, China
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7
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Di Paolo A, Garat J, Eastman G, Farias J, Dajas-Bailador F, Smircich P, Sotelo-Silveira JR. Functional Genomics of Axons and Synapses to Understand Neurodegenerative Diseases. Front Cell Neurosci 2021; 15:686722. [PMID: 34248504 PMCID: PMC8267896 DOI: 10.3389/fncel.2021.686722] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 01/02/2023] Open
Abstract
Functional genomics studies through transcriptomics, translatomics and proteomics have become increasingly important tools to understand the molecular basis of biological systems in the last decade. In most cases, when these approaches are applied to the nervous system, they are centered in cell bodies or somatodendritic compartments, as these are easier to isolate and, at least in vitro, contain most of the mRNA and proteins present in all neuronal compartments. However, key functional processes and many neuronal disorders are initiated by changes occurring far away from cell bodies, particularly in axons (axopathologies) and synapses (synaptopathies). Both neuronal compartments contain specific RNAs and proteins, which are known to vary depending on their anatomical distribution, developmental stage and function, and thus form the complex network of molecular pathways required for neuron connectivity. Modifications in these components due to metabolic, environmental, and/or genetic issues could trigger or exacerbate a neuronal disease. For this reason, detailed profiling and functional understanding of the precise changes in these compartments may thus yield new insights into the still intractable molecular basis of most neuronal disorders. In the case of synaptic dysfunctions or synaptopathies, they contribute to dozens of diseases in the human brain including neurodevelopmental (i.e., autism, Down syndrome, and epilepsy) as well as neurodegenerative disorders (i.e., Alzheimer's and Parkinson's diseases). Histological, biochemical, cellular, and general molecular biology techniques have been key in understanding these pathologies. Now, the growing number of omics approaches can add significant extra information at a high and wide resolution level and, used effectively, can lead to novel and insightful interpretations of the biological processes at play. This review describes current approaches that use transcriptomics, translatomics and proteomic related methods to analyze the axon and presynaptic elements, focusing on the relationship that axon and synapses have with neurodegenerative diseases.
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Affiliation(s)
- Andres Di Paolo
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Proteínas y Ácidos Nucleicos, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquin Garat
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Guillermo Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Polo de Desarrollo Universitario “Espacio de Biología Vegetal del Noreste”, Centro Universitario Regional Noreste, Universidad de la República (UdelaR), Tacuarembó, Uruguay
| | - Federico Dajas-Bailador
- School of Life Sciences, Medical School Building, University of Nottingham, Nottingham, United Kingdom
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - José Roberto Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
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8
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Aiken J, Holzbaur ELF. Cytoskeletal regulation guides neuronal trafficking to effectively supply the synapse. Curr Biol 2021; 31:R633-R650. [PMID: 34033795 DOI: 10.1016/j.cub.2021.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The development and proper function of the brain requires the formation of highly complex neuronal circuitry. These circuits are shaped from synaptic connections between neurons and must be maintained over a lifetime. The formation and continued maintenance of synapses requires accurate trafficking of presynaptic and postsynaptic components along the axon and dendrite, respectively, necessitating deliberate and specialized delivery strategies to replenish essential synaptic components. Maintenance of synaptic transmission also requires readily accessible energy stores, produced in part by localized mitochondria, that are tightly regulated with activity level. In this review, we focus on recent developments in our understanding of the cytoskeletal environment of axons and dendrites, examining how local regulation of cytoskeletal dynamics and organelle trafficking promotes synapse-specific delivery and plasticity. These new insights shed light on the complex and coordinated role that cytoskeletal elements play in establishing and maintaining neuronal circuitry.
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Affiliation(s)
- Jayne Aiken
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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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.
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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.
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10
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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.
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Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
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11
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Pazos Obregón F, Palazzo M, Soto P, Guerberoff G, Yankilevich P, Cantera R. An improved catalogue of putative synaptic genes defined exclusively by temporal transcription profiles through an ensemble machine learning approach. BMC Genomics 2019; 20:1011. [PMID: 31870293 PMCID: PMC6929295 DOI: 10.1186/s12864-019-6380-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/09/2019] [Indexed: 11/25/2022] Open
Abstract
Background Assembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Previously, we had trained an ensemble machine learning model to assign a probability of having synaptic function to every protein-coding gene in Drosophila melanogaster. This approach resulted in the publication of a catalogue of 893 genes which we postulated to be very enriched in genes with a still undocumented synaptic function. Since then, the scientific community has experimentally identified 79 new synaptic genes. Here we use these new empirical data to evaluate our original prediction. We also implement a series of changes to the training scheme of our model and using the new data we demonstrate that this improves its predictive power. Finally, we added the new synaptic genes to the training set and trained a new model, obtaining a new, enhanced catalogue of putative synaptic genes. Results The retrospective analysis demonstrate that our original catalogue was significantly enriched in new synaptic genes. When the changes to the training scheme were implemented using the original training set we obtained even higher enrichment. Finally, applying the new training scheme with a training set including the 79 new synaptic genes, resulted in an enhanced catalogue of putative synaptic genes. Here we present this new catalogue and announce that a regularly updated version will be available online at: http://synapticgenes.bnd.edu.uy Conclusions We show that training an ensemble of machine learning classifiers solely with the whole-body temporal transcription profiles of known synaptic genes resulted in a catalogue with a significant enrichment in undiscovered synaptic genes. Using new empirical data provided by the scientific community, we validated our original approach, improved our model an obtained an arguably more precise prediction. This approach reduces the number of genes to be tested through hypothesis-driven experimentation and will facilitate our understanding of neuronal function. Availability http://synapticgenes.bnd.edu.uy
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Affiliation(s)
- Flavio Pazos Obregón
- Neurodevelopmental Biology Department, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
| | - Martín Palazzo
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Pablo Soto
- Neurodevelopmental Biology Department, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Gustavo Guerberoff
- Instituto de Matemática y Estadística "Prof. Ing. Rafael Laguardia", Facultad de Ingeniería, UDELAR, Montevideo, Uruguay
| | - Patricio Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Rafael Cantera
- Neurodevelopmental Biology Department, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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12
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Ramos-Miguel A, Barakauskas V, Alamri J, Miyauchi M, Barr AM, Beasley CL, Rosoklija G, Mann JJ, Dwork AJ, Moradian A, Morin GB, Honer WG. The SNAP25 Interactome in Ventromedial Caudate in Schizophrenia Includes the Mitochondrial Protein ARF1. Neuroscience 2019; 420:97-111. [PMID: 30610939 DOI: 10.1016/j.neuroscience.2018.12.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 12/11/2022]
Abstract
Abnormalities of SNAP25 (synaptosome-associated protein 25) amount and protein-protein interactions occur in schizophrenia, and may contribute to abnormalities of neurotransmitter release in patients. However, presynaptic terminal function depends on multiple subcellular mechanisms, including energy provided by mitochondria. To explore the SNAP25 interactome in schizophrenia, we immunoprecipitated SNAP25 along with interacting proteins from the ventromedial caudate of 15 cases of schizophrenia and 13 controls. Proteins were identified with mass spectrometry-based proteomics. As well as 15 SNARE- (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) associated proteins, we identified 17 mitochondria-associated and four other proteins. The mitochondrial small GTPase ARF1 (ADP-ribosylation factor 1) was identified in eight schizophrenia SNAP25 immunoprecipitates and none from controls (P = 0.004). Although the ARF1-SNAP25 interaction may be increased, immunoblotting demonstrated 21% lower ARF1-21 (21 kiloDaltons) in schizophrenia samples (P = 0.04). In contrast, the mitochondrial protein UQCRC1 (ubiquinol-cytochrome c reductase core protein 1) did not differ. Lower ARF1-21 levels were associated with the previously reported increased SNAP25-syntaxin interaction in schizophrenia (r = -0.39, P = 0.04). Additional immunoprecipitation studies confirmed the ARF1-21-SNAP25 interaction, independent of UQCRC1. Both ARF1 and SNAP25 were localized to synaptosomes. Confocal microscopy demonstrated co-localization of ARF1 and SNAP25, and further suggested fivefold enrichment of ARF1 in synaptosomes containing an excitatory marker (vesicular glutamate transporter) compared with synaptosomes containing an inhibitory marker (vesicular GABA transporter). The present findings suggest an association between abnormalities of SNARE proteins involved with vesicular neurotransmission and the mitochondrial protein ARF1 that may contribute to the pathophysiology of schizophrenia.
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Affiliation(s)
- Alfredo Ramos-Miguel
- BC Mental Health and Addictions Research Institute, 938 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC V6T 2A1, Canada; Department of Pharmacology, University of the Basque Country, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Barrio Sarriena, s/n, 48940 Leioa, Biscay, Spain
| | - Vilte Barakauskas
- BC Mental Health and Addictions Research Institute, 938 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, 2J9-4500 Oak St., Vancouver, BC V6H 3B1, Canada
| | - Jehan Alamri
- BC Mental Health and Addictions Research Institute, 938 West 28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Masatoshi Miyauchi
- BC Mental Health and Addictions Research Institute, 938 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC V6T 2A1, Canada
| | - Alasdair M Barr
- BC Mental Health and Addictions Research Institute, 938 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Anesthesiology, Pharmacology, & Therapeutics, University of British Columbia, 2176 Health Sciences Mall Vancouver, BC V6T 1Z3, Canada
| | - Clare L Beasley
- BC Mental Health and Addictions Research Institute, 938 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC V6T 2A1, Canada
| | - Gorazd Rosoklija
- Department of Psychiatry, Columbia University, 1051 Riverside Drive, New York, NY 10032, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, 1051 Riverside Drive, New York, NY 10032, USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, 1051 Riverside Drive, New York, NY 10032, USA
| | - Annie Moradian
- Department of Medical Genetics, University of British Columbia, C234-4500 Oak St., Vancouver, BC V6H 3B1, Canada
| | - Gregg B Morin
- Department of Medical Genetics, University of British Columbia, C234-4500 Oak St., Vancouver, BC V6H 3B1, Canada
| | - William G Honer
- BC Mental Health and Addictions Research Institute, 938 West 28th Ave, Vancouver, BC V5Z 4H4, Canada; Department of Psychiatry, University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC V6T 2A1, Canada.
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13
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Maeder CI, Kim JI, Liang X, Kaganovsky K, Shen A, Li Q, Li Z, Wang S, Xu XZS, Li JB, Xiang YK, Ding JB, Shen K. The THO Complex Coordinates Transcripts for Synapse Development and Dopamine Neuron Survival. Cell 2018; 174:1436-1449.e20. [PMID: 30146163 DOI: 10.1016/j.cell.2018.07.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 05/11/2018] [Accepted: 07/26/2018] [Indexed: 01/07/2023]
Abstract
Synaptic vesicle and active zone proteins are required for synaptogenesis. The molecular mechanisms for coordinated synthesis of these proteins are not understood. Using forward genetic screens, we identified the conserved THO nuclear export complex (THOC) as an important regulator of presynapse development in C. elegans dopaminergic neurons. In THOC mutants, synaptic messenger RNAs are retained in the nucleus, resulting in dramatic decrease of synaptic protein expression, near complete loss of synapses, and compromised dopamine function. CRE binding protein (CREB) interacts with THOC to mark synaptic transcripts for efficient nuclear export. Deletion of Thoc5, a THOC subunit, in mouse dopaminergic neurons causes severe defects in synapse maintenance and subsequent neuronal death in the substantia nigra compacta. These cellular defects lead to abrogated dopamine release, ataxia, and animal death. Together, our results argue that nuclear export mechanisms can select specific mRNAs and be a rate-limiting step for neuronal differentiation and survival.
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Affiliation(s)
- Celine I Maeder
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Jae-Ick Kim
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xing Liang
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Konstantin Kaganovsky
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ao Shen
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Zhaoyu Li
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sui Wang
- Department of Opthalmology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - X Z Shawn Xu
- Life Sciences Institute and Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yang Kevin Xiang
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Jun B Ding
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Kang Shen
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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14
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Benito I, Casañas JJ, Montesinos ML. Proteomic Analysis of Synaptoneurosomes Highlights the Relevant Role of Local Translation in the Hippocampus. Proteomics 2018; 18:e1800005. [PMID: 29923338 DOI: 10.1002/pmic.201800005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/19/2018] [Indexed: 11/12/2022]
Abstract
Several proteomic analyses have been performed on synaptic fractions isolated from cortex or even total brain, resulting in preparations with a high synaptic heterogeneity and complexity. Synaptoneurosomes (SNs) are subcellular membranous elements that contain sealed pre- and post-synaptic components. They are obtained by subcellular fractionation of brain homogenates and serve as a suitable model to study many aspects of the synapse physiology. Here the proteomic content of SNs isolated from hippocampus of adult mice, a brain region involved in memory that presents lower synaptic heterogeneity than cortex, is reported. Interestingly, in addition to pre- and post-synaptic proteins, proteins involved in RNA binding and translation are overrepresented in this preparation. These results validate the protocol previously reported for SNs isolation, and, as reported by other authors, highlight the relevance of local synaptic translation for hippocampal physiology.
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Affiliation(s)
- Itziar Benito
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, Sevilla, E-41009, Spain.,Instituto de Biomedicina de Sevilla, IBIS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla,, Sevilla, E-41013, Spain.,Servicio de Animalario, Hospital Universitario Virgen Macarena (HUVM), Sevilla, E-41009, Spain
| | - Juan José Casañas
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, Sevilla, E-41009, Spain.,Instituto de Biomedicina de Sevilla, IBIS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla,, Sevilla, E-41013, Spain
| | - María Luz Montesinos
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, Sevilla, E-41009, Spain.,Instituto de Biomedicina de Sevilla, IBIS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla,, Sevilla, E-41013, Spain
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15
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Cerebellar networks and neuropathology of cerebellar developmental disorders. HANDBOOK OF CLINICAL NEUROLOGY 2018; 154:109-128. [PMID: 29903435 DOI: 10.1016/b978-0-444-63956-1.00007-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cerebellar system is a series of axonal projections and synaptic circuits as networks, similar to those of the limbic system and those subserving the propagation and spread of seizures. Three principal cerebellar networks are identified and cerebellar disease often affects components of the networks other than just the cerebellar cortex. Contemporary developmental neuropathology of the cerebellum is best considered in the context of alterations of developmental processes: embryonic segmentation and genetic gradients along the three axes of the neural tube, individual neuronal and glial cell differentiation, migration, synaptogenesis, and myelination. Precisely timed developmental processes may be delayed or precocious rhombencephalosynapsis and pontocerebellar hypoplasia exemplify opposite gradients in the horizontal axis. Chiari II malformation may be reconsidered as a disorder of segmentation rather than simply due to mechanical forces upon normally developing hindbrain structures. Cellular nodules in the roof of the fourth ventricle are heterotopia of histologically differentiated but architecturally disoriented and disorganized neurons and glial cells; they often are less mature immunocytochemically than similar cells in adjacent normal folia. Cell rests are nodules of undifferentiated neuroepithelial cells. Both are frequent in human fetuses and neonates. Axonal projections from heterotopia to adjacent cerebellar folia or nuclei are few or absent, hence these nodules are clinically silent despite neuronal differentiation.
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16
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Weingarten J, Weingarten M, Wegner M, Volknandt W. APP-A Novel Player within the Presynaptic Active Zone Proteome. Front Mol Neurosci 2017; 10:43. [PMID: 28265241 PMCID: PMC5316543 DOI: 10.3389/fnmol.2017.00043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
The amyloid precursor protein (APP) was discovered in the 1980s as the precursor protein of the amyloid A4 peptide. The amyloid A4 peptide, also known as A-beta (Aβ), is the main constituent of senile plaques implicated in Alzheimer's disease (AD). In association with the amyloid deposits, increasing impairments in learning and memory as well as the degeneration of neurons especially in the hippocampus formation are hallmarks of the pathogenesis of AD. Within the last decades much effort has been expended into understanding the pathogenesis of AD. However, little is known about the physiological role of APP within the central nervous system (CNS). Allocating APP to the proteome of the highly dynamic presynaptic active zone (PAZ) identified APP as a novel player within this neuronal communication and signaling network. The analysis of the hippocampal PAZ proteome derived from APP-mutant mice demonstrates that APP is tightly embedded in the underlying protein network. Strikingly, APP deletion accounts for major dysregulation within the PAZ proteome network. Ca2+-homeostasis, neurotransmitter release and mitochondrial function are affected and resemble the outcome during the pathogenesis of AD. The observed changes in protein abundance that occur in the absence of APP as well as in AD suggest that APP is a structural and functional regulator within the hippocampal PAZ proteome. Within this review article, we intend to introduce APP as an important player within the hippocampal PAZ proteome and to outline the impact of APP deletion on individual PAZ proteome subcommunities.
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Affiliation(s)
- Jens Weingarten
- Institute for Cell Biology and Neuroscience, Biologicum and BMLS, Goethe University Frankfurt am Main, Germany
| | - Melanie Weingarten
- Institute for Cell Biology and Neuroscience, Biologicum and BMLS, Goethe University Frankfurt am Main, Germany
| | - Martin Wegner
- Department of Molecular Bioinformatics, Goethe University Frankfurt am Main, Germany
| | - Walter Volknandt
- Institute for Cell Biology and Neuroscience, Biologicum and BMLS, Goethe University Frankfurt am Main, Germany
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17
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Dzyubenko E, Rozenberg A, Hermann DM, Faissner A. Colocalization of synapse marker proteins evaluated by STED-microscopy reveals patterns of neuronal synapse distribution in vitro. J Neurosci Methods 2016; 273:149-159. [PMID: 27615741 DOI: 10.1016/j.jneumeth.2016.09.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND Quantification of synapses and their morphological analysis are extensively used in network development and connectivity studies, drug screening and other areas of neuroscience. Thus, a number of quantitative approaches were introduced so far. However, most of the available methods are highly tailored to specific applications and have limitations for widespread use. NEW METHOD We present a new plugin for the open-source software ImageJ to provide a modifiable, high-throughput and easy to use method for synaptic puncta analysis. Our approach is based on colocalization of pre- and postsynaptic protein markers. Structurally completed glutamatergic and GABAergic synapses were identified by VGLUT1-PSD95 and VGAT-gephyrin colocalization, respectively. By combining conventional confocal microscopy with stimulated emission depletion (STED) imaging, we propose a method to quantify the number of scaffolding protein clusters, recruited to a single postsynaptic density. RESULTS In a proof-of-concept study, we reveal the differential distribution of glutamatergic and GABAergic synapse density with reference to perineuronal net (PNN) expression. Using super-resolution STED imaging, we demonstrate that postsynaptic puncta of completed synapses are composed of significantly more protein clusters, compared to uncompleted synapses. COMPARISON WITH EXISTING METHODS Our Synapse Counter plugin for ImageJ offers a rapid and unbiased research tool for a broad spectrum of neuroscientists. The proposed method of synaptic protein clusters quantification exploits super-resolution imaging to provide a comprehensive approach to the analysis of postsynaptic density composition. CONCLUSIONS Our results strongly substantiate the benefits of colocalization-based synapse detection.
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Affiliation(s)
- Egor Dzyubenko
- Department of Cell Morphology and Molecular Neurobiology, Ruhr-University Bochum, Germany; International School of Neuroscience (IGSN), Ruhr-University Bochum, Germany
| | - Andrey Rozenberg
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr-University Bochum, Germany
| | - Dirk M Hermann
- Department of Neurology, University Hospital Essen, Germany
| | - Andreas Faissner
- Department of Cell Morphology and Molecular Neurobiology, Ruhr-University Bochum, Germany.
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18
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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.
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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
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19
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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.
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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.
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20
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Laßek M, Weingarten J, Wegner M, Volknandt W. The Amyloid Precursor Protein-A Novel Player within the Molecular Array of Presynaptic Nanomachines. Front Synaptic Neurosci 2016; 7:21. [PMID: 26834621 PMCID: PMC4719097 DOI: 10.3389/fnsyn.2015.00021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/24/2015] [Indexed: 12/27/2022] Open
Abstract
More than 20 years ago the amyloid precursor protein (APP) was identified as the precursor protein of the Aβ peptide, the main component of senile plaques in brains affected by Alzheimer’s disease (AD). The pathophysiology of AD, characterized by a massive loss of synapses, cognitive decline, and behavioral changes was in principle attributed to the accumulation of Aβ. Within the last decades, much effort has gone into understanding the molecular basis of the progression of AD. However, little is known about the actual physiological function of APPs. Allocating APP to the proteome of the structurally and functionally dynamic presynaptic active zone (PAZ) highlights APP as a hitherto unknown player within the setting of the presynapse. The molecular array of presynaptic nanomachines comprising the life cycle of synaptic vesicles, exo- and endocytosis, cytoskeletal rearrangements, and mitochondrial activity provides a balance between structural and functional maintenance and diversity. The generation of genetically designed mouse models further deciphered APP as an essential player in synapse formation and plasticity. Deletion of APP causes an age-dependent phenotype: while younger mice revealed almost no physiological impairments, this condition was changed in the elderly mice. Interestingly, the proteomic composition of neurotransmitter release sites already revealed substantial changes at young age. These changes point to a network that incorporates APP into a cluster of nanomachines. Currently, the underlying mechanism of how APP acts within these machines is still elusive. Within the scope of this review, we shall construct a network of APP interaction partners within the PAZ. Furthermore, we intend to outline how deletion of APP affects this network during space and time leading to impairments in learning and memory. These alterations may provide a molecular link to the pathogenesis of AD and the physiological function of APP in the central nervous system.
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Affiliation(s)
- Melanie Laßek
- Department of Molecular and Cellular Neurobiology, Goethe University Frankfurt Frankfurt am Main, Germany
| | - Jens Weingarten
- Department of Molecular and Cellular Neurobiology, Goethe University Frankfurt Frankfurt am Main, Germany
| | - Martin Wegner
- Department of Molecular Bioinformatics, Goethe University Frankfurt Frankfurt am Main, Germany
| | - Walter Volknandt
- Department of Molecular and Cellular Neurobiology, Goethe University Frankfurt Frankfurt am Main, Germany
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21
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Pazos Obregón F, Papalardo C, Castro S, Guerberoff G, Cantera R. Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach. BMC Genomics 2015; 16:694. [PMID: 26370122 PMCID: PMC4570697 DOI: 10.1186/s12864-015-1888-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 09/01/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Assembly and function of neuronal synapses require the coordinated expression of a yet undetermined set of genes. Although roughly a thousand genes are expected to be important for this function in Drosophila melanogaster, just a few hundreds of them are known so far. RESULTS In this work we trained three learning algorithms to predict a "synaptic function" for genes of Drosophila using data from a whole-body developmental transcriptome published by others. Using statistical and biological criteria to analyze and combine the predictions, we obtained a gene catalogue that is highly enriched in genes of relevance for Drosophila synapse assembly and function but still not recognized as such. CONCLUSIONS The utility of our approach is that it reduces the number of genes to be tested through hypothesis-driven experimentation.
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Affiliation(s)
- Flavio Pazos Obregón
- Departamento de Biología del Neurodesarrollo, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, PC 11600, Montevideo, Uruguay.
| | - Cecilia Papalardo
- Instituto de Matemática y Estadística "Prof. Ing. Rafael Laguardia", Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay.
| | - Sebastián Castro
- Instituto de Matemática y Estadística "Prof. Ing. Rafael Laguardia", Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay.
| | - Gustavo Guerberoff
- Instituto de Matemática y Estadística "Prof. Ing. Rafael Laguardia", Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay.
| | - Rafael Cantera
- Departamento de Biología del Neurodesarrollo, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, PC 11600, Montevideo, Uruguay.
- Zoology Department, Stockholm University, Stockholm, Sweden.
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22
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Ackermann F, Waites CL, Garner CC. Presynaptic active zones in invertebrates and vertebrates. EMBO Rep 2015; 16:923-38. [PMID: 26160654 DOI: 10.15252/embr.201540434] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/19/2015] [Indexed: 11/09/2022] Open
Abstract
The regulated release of neurotransmitter occurs via the fusion of synaptic vesicles (SVs) at specialized regions of the presynaptic membrane called active zones (AZs). These regions are defined by a cytoskeletal matrix assembled at AZs (CAZ), which functions to direct SVs toward docking and fusion sites and supports their maturation into the readily releasable pool. In addition, CAZ proteins localize voltage-gated Ca(2+) channels at SV release sites, bringing the fusion machinery in close proximity to the calcium source. Proteins of the CAZ therefore ensure that vesicle fusion is temporally and spatially organized, allowing for the precise and reliable release of neurotransmitter. Importantly, AZs are highly dynamic structures, supporting presynaptic remodeling, changes in neurotransmitter release efficacy, and thus presynaptic forms of plasticity. In this review, we discuss recent advances in the study of active zones, highlighting how the CAZ molecularly defines sites of neurotransmitter release, endocytic zones, and the integrity of synapses.
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Affiliation(s)
- Frauke Ackermann
- German Center for Neurodegenerative Disease, Charité Medical University, Berlin, Germany
| | - Clarissa L Waites
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Craig C Garner
- German Center for Neurodegenerative Disease, Charité Medical University, Berlin, Germany
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Regional Specializations of the PAZ Proteomes Derived from Mouse Hippocampus, Olfactory Bulb and Cerebellum. Proteomes 2015; 3:74-88. [PMID: 28248263 PMCID: PMC5217373 DOI: 10.3390/proteomes3020074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/05/2015] [Indexed: 11/25/2022] Open
Abstract
Neurotransmitter release as well as structural and functional dynamics at the presynaptic active zone (PAZ) comprising synaptic vesicles attached to the presynaptic plasma membrane are mediated and controlled by its proteinaceous components. Here we describe a novel experimental design to immunopurify the native PAZ-complex from individual mouse brain regions such as olfactory bulb, hippocampus, and cerebellum with high purity that is essential for comparing their proteome composition. Interestingly, quantitative immunodetection demonstrates significant differences in the abundance of prominent calcium-dependent PAZ constituents. Furthermore, we characterized the proteomes of the immunoisolated PAZ derived from the three brain regions by mass spectrometry. The proteomes of the release sites from the respective regions exhibited remarkable differences in the abundance of a large variety of PAZ constituents involved in various functional aspects of the release sites such as calcium homeostasis, synaptic plasticity and neurogenesis. On the one hand, our data support an identical core architecture of the PAZ for all brain regions and, on the other hand, demonstrate that the proteinaceous composition of their presynaptic active zones vary, suggesting that changes in abundance of individual proteins strengthen the ability of the release sites to adapt to specific functional requirements.
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Fernandez-Irigoyen J, Labarga A, Zabaleta A, de Morentin XM, Perez-Valderrama E, Zelaya MV, Santamaria E. Toward defining the anatomo-proteomic puzzle of the human brain: An integrative analysis. Proteomics Clin Appl 2015; 9:796-807. [PMID: 25418211 DOI: 10.1002/prca.201400127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/17/2014] [Accepted: 11/18/2014] [Indexed: 01/18/2023]
Abstract
The human brain is exceedingly complex, constituted by billions of neurons and trillions of synaptic connections that, in turn, define ∼900 neuroanatomical subdivisions in the adult brain (Hawrylycz et al. An anatomically comprehensive atlas of the human brain transcriptome. Nature 2012, 489, 391-399). The human brain transcriptome has revealed specific regional transcriptional signatures that are regulated in a spatiotemporal manner, increasing the complexity of the structural and molecular organization of this organ (Kang et al. Spatio-temporal transcriptome of the human brain. Nature 2011, 478, 483-489). During the last decade, neuroproteomics has emerged as a powerful approach to profile neural proteomes using shotgun-based MS, providing complementary information about protein content and function at a global level. Here, we revise recent proteome profiling studies performed in human brain, with special emphasis on proteome mapping of anatomical macrostructures, specific subcellular compartments, and cerebrospinal fluid. Moreover, we have performed an integrative functional analysis of the protein compilation derived from these large-scale human brain proteomic studies in order to obtain a comprehensive view of human brain biology. Finally, we also discuss the potential contribution of our meta-analysis to the Chromosome-centric Human Proteome Project initiative.
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Affiliation(s)
- Joaquín Fernandez-Irigoyen
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Alberto Labarga
- Bioinformatics Unit, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Aintzane Zabaleta
- Biofunctional Nanomaterials Laboratory, CIC Biomagune, San Sebastian, Spain
| | - Xabier Martínez de Morentin
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Estela Perez-Valderrama
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | | | - Enrique Santamaria
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
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