1
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Li H, Rajani V, Sengar AS, Salter MW. Src dependency of the regulation of LTP by alternative splicing of GRIN1 exon 5. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230236. [PMID: 38853562 DOI: 10.1098/rstb.2023.0236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/11/2024] [Indexed: 06/11/2024] Open
Abstract
Alternative splicing of Grin1 exon 5 regulates induction of long-term potentiation (LTP) at Schaffer collateral-CA1 synapses: LTP in mice lacking the GluN1 exon 5-encoded N1 cassette (GluN1a mice) is significantly increased compared with that in mice compulsorily expressing this exon (GluN1b mice). The mechanism underlying this difference is unknown. Here, we report that blocking the non-receptor tyrosine kinase Src prevents induction of LTP in GluN1a mice but not in GluN1b. We find that activating Src enhances pharmacologically isolated synaptic N-methyl-d-aspartate receptor (NMDAR) currents in GluN1a mice but not in GluN1b. Moreover, we observe that Src activation increases the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor component of Schaffer collateral-evoked excitatory post-synaptic potentials in GluN1a mice, but this increase is prevented by blocking NMDARs. We conclude that at these synapses, NMDARs in GluN1a mice are subject to upregulation by Src that mediates induction of LTP, whereas NMDARs in GluN1b mice are not regulated by Src, leading to Src-resistance of LTP. Thus, we have uncovered that a key regulatory mechanism for synaptic potentiation is gated by differential splicing of exon 5 of Grin1. This article is part of a discussion meeting issue 'Long-term potentiation: 50 years on'.
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Affiliation(s)
- Hongbin Li
- Program in Neurosciences & Mental Health, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada
| | - Vishaal Rajani
- Program in Neurosciences & Mental Health, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada
| | - Ameet S Sengar
- Program in Neurosciences & Mental Health, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada
| | - Michael W Salter
- Program in Neurosciences & Mental Health, The Hospital for Sick Children , Toronto, ON M5G 1X8, Canada
- Department of Physiology, University of Toronto , Toronto, ON M5S 1A8, Canada
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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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van Oostrum M, Blok TM, Giandomenico SL, Tom Dieck S, Tushev G, Fürst N, Langer JD, Schuman EM. The proteomic landscape of synaptic diversity across brain regions and cell types. Cell 2023; 186:5411-5427.e23. [PMID: 37918396 PMCID: PMC10686415 DOI: 10.1016/j.cell.2023.09.028] [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: 02/09/2023] [Revised: 08/18/2023] [Accepted: 09/28/2023] [Indexed: 11/04/2023]
Abstract
Neurons build synaptic contacts using different protein combinations that define the specificity, function, and plasticity potential of synapses; however, the diversity of synaptic proteomes remains largely unexplored. We prepared synaptosomes from 7 different transgenic mouse lines with fluorescently labeled presynaptic terminals. Combining microdissection of 5 different brain regions with fluorescent-activated synaptosome sorting (FASS), we isolated and analyzed the proteomes of 18 different synapse types. We discovered ∼1,800 unique synapse-type-enriched proteins and allocated thousands of proteins to different types of synapses (https://syndive.org/). We identify shared synaptic protein modules and highlight the proteomic hotspots for synapse specialization. We reveal unique and common features of the striatal dopaminergic proteome and discover the proteome signatures that relate to the functional properties of different interneuron classes. This study provides a molecular systems-biology analysis of synapses and a framework to integrate proteomic information for synapse subtypes of interest with cellular or circuit-level experiments.
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Affiliation(s)
- Marc van Oostrum
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Thomas M Blok
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | | | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Nicole Fürst
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
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5
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Tapia-González S, DeFelipe J. Secretagogin as a marker to distinguish between different neuron types in human frontal and temporal cortex. Front Neuroanat 2023; 17:1210502. [PMID: 38020216 PMCID: PMC10646422 DOI: 10.3389/fnana.2023.1210502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/28/2023] [Indexed: 12/01/2023] Open
Abstract
The principal aim of the present work was to chemically characterize the population of neurons labeled for the calcium binding protein secretagogin (SCGN) in the human frontal and temporal cortices (Brodmann's area 10 and 21, respectively). Both cortical regions are involved in many high cognitive functions that are especially well developed (or unique) in humans, but with different functional roles. The pattern of SCGN immunostaining was rather similar in BA10 and BA21, with all the labeled neurons displaying a non-pyramidal morphology (interneurons). Although SCGN cells were present throughout all layers, they were more frequently observed in layers II, III and IV, whereas in layer I they were found only occasionally. We examined the degree of colocalization of SCGN with parvalbumin (PV) and calretinin (CR), as well as with nitric oxide synthase (nNOS; the enzyme responsible for the synthesis of nitric oxide by neurons) by triple immunostaining. We looked for possible similarities or differences in the coexpression patterns of SCGN with PV, CR and nNOS between BA10 and BA21 throughout the different cortical layers (I-VI). The percentage of colocalization was estimated by counting the number of all labeled cells through columns (1,100-1,400 μm wide) across the entire thickness of the cortex (from the pial surface to the white matter) in 50 μm-thick sections. Several hundred neurons were examined in both cortical regions. We found that SCGN cells include multiple neurochemical subtypes, whose abundance varies according to the cortical area and layer. The present results further highlight the regional specialization of cortical neurons and underline the importance of performing additional experiments to characterize the subpopulation of SCGN cells in the human cerebral cortex in greater detail.
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Affiliation(s)
- Silvia Tapia-González
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
- Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Laboratorio de Neurofisiología Celular, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Javier DeFelipe
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
- Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
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6
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Wang L, Pang K, Zhou L, Cebrián-Silla A, González-Granero S, Wang S, Bi Q, White ML, Ho B, Li J, Li T, Perez Y, Huang EJ, Winkler EA, Paredes MF, Kovner R, Sestan N, Pollen AA, Liu P, Li J, Piao X, García-Verdugo JM, Alvarez-Buylla A, Liu Z, Kriegstein AR. A cross-species proteomic map reveals neoteny of human synapse development. Nature 2023; 622:112-119. [PMID: 37704727 PMCID: PMC10576238 DOI: 10.1038/s41586-023-06542-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
The molecular mechanisms and evolutionary changes accompanying synapse development are still poorly understood1,2. Here we generate a cross-species proteomic map of synapse development in the human, macaque and mouse neocortex. By tracking the changes of more than 1,000 postsynaptic density (PSD) proteins from midgestation to young adulthood, we find that PSD maturation in humans separates into three major phases that are dominated by distinct pathways. Cross-species comparisons reveal that human PSDs mature about two to three times slower than those of other species and contain higher levels of Rho guanine nucleotide exchange factors (RhoGEFs) in the perinatal period. Enhancement of RhoGEF signalling in human neurons delays morphological maturation of dendritic spines and functional maturation of synapses, potentially contributing to the neotenic traits of human brain development. In addition, PSD proteins can be divided into four modules that exert stage- and cell-type-specific functions, possibly explaining their differential associations with cognitive functions and diseases. Our proteomic map of synapse development provides a blueprint for studying the molecular basis and evolutionary changes of synapse maturation.
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Affiliation(s)
- Li Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
| | - Kaifang Pang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Li Zhou
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Arantxa Cebrián-Silla
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Susana González-Granero
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia and CIBERNED, Valencia, Spain
| | - Shaohui Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Qiuli Bi
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew L White
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Brandon Ho
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Jiani Li
- Gilead Sciences, Foster City, CA, USA
| | - Tao Li
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Yonatan Perez
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Huang
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Ethan A Winkler
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Mercedes F Paredes
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Rothem Kovner
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Alex A Pollen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Pengyuan Liu
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Jingjing Li
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Xianhua Piao
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Division of Neonatology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Newborn Brain Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - José Manuel García-Verdugo
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia and CIBERNED, Valencia, Spain
| | - Arturo Alvarez-Buylla
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Arnold R Kriegstein
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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7
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Pitcher GM, Garzia L, Morrissy AS, Taylor MD, Salter MW. Synapse-specific diversity of distinct postsynaptic GluN2 subtypes defines transmission strength in spinal lamina I. Front Synaptic Neurosci 2023; 15:1197174. [PMID: 37503309 PMCID: PMC10368998 DOI: 10.3389/fnsyn.2023.1197174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/16/2023] [Indexed: 07/29/2023] Open
Abstract
The unitary postsynaptic response to presynaptic quantal glutamate release is the fundamental basis of excitatory information transfer between neurons. The view, however, of individual glutamatergic synaptic connections in a population as homogenous, fixed-strength units of neural communication is becoming increasingly scrutinized. Here, we used minimal stimulation of individual glutamatergic afferent axons to evoke single synapse resolution postsynaptic responses from central sensory lamina I neurons in an ex vivo adult rat spinal slice preparation. We detected unitary events exhibiting a NMDA receptor component with distinct kinetic properties across synapses conferred by specific GluN2 subunit composition, indicative of GluN2 subtype-based postsynaptic heterogeneity. GluN2A, 2A and 2B, or 2B and 2D synaptic predominance functioned on distinct lamina I neuron types to narrowly, intermediately, or widely tune, respectively, the duration of evoked unitary depolarization events from resting membrane potential, which enabled individual synapses to grade differentially depolarizing steps during temporally patterned afferent input. Our results lead to a model wherein a core locus of proteomic complexity prevails at this central glutamatergic sensory synapse that involves distinct GluN2 subtype configurations. These findings have major implications for subthreshold integrative capacity and transmission strength in spinal lamina I and other CNS regions.
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Affiliation(s)
- Graham M. Pitcher
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Livia Garzia
- Department of Surgery, Faculty of Medicine, McGill University, and Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - A. Sorana Morrissy
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael D. Taylor
- Brain Tumor Program, Texas Medical Centre, Houston, TX, United States
| | - Michael W. Salter
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
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8
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Mercaldo V, Vidimova B, Gastaldo D, Fernández E, Lo AC, Cencelli G, Pedini G, De Rubeis S, Longo F, Klann E, Smit AB, Grant SGN, Achsel T, Bagni C. Altered striatal actin dynamics drives behavioral inflexibility in a mouse model of fragile X syndrome. Neuron 2023; 111:1760-1775.e8. [PMID: 36996810 DOI: 10.1016/j.neuron.2023.03.008] [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: 02/01/2022] [Revised: 12/21/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023]
Abstract
The proteome of glutamatergic synapses is diverse across the mammalian brain and involved in neurodevelopmental disorders (NDDs). Among those is fragile X syndrome (FXS), an NDD caused by the absence of the functional RNA-binding protein FMRP. Here, we demonstrate how the brain region-specific composition of postsynaptic density (PSD) contributes to FXS. In the striatum, the FXS mouse model shows an altered association of the PSD with the actin cytoskeleton, reflecting immature dendritic spine morphology and reduced synaptic actin dynamics. Enhancing actin turnover with constitutively active RAC1 ameliorates these deficits. At the behavioral level, the FXS model displays striatal-driven inflexibility, a typical feature of FXS individuals, which is rescued by exogenous RAC1. Striatal ablation of Fmr1 is sufficient to recapitulate behavioral impairments observed in the FXS model. These results indicate that dysregulation of synaptic actin dynamics in the striatum, a region largely unexplored in FXS, contributes to the manifestation of FXS behavioral phenotypes.
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Affiliation(s)
- Valentina Mercaldo
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Barbora Vidimova
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Denise Gastaldo
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Esperanza Fernández
- VIB & UGent Center for Medical Biotechnology, Universiteit Gent, 9052 Ghent, Belgium
| | - Adrian C Lo
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Giulia Cencelli
- Department of Biomedicine and Prevention, Università degli Studi di Roma "Tor Vergata", 00133 Rome, Italy; Institute of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Giorgia Pedini
- Department of Biomedicine and Prevention, Università degli Studi di Roma "Tor Vergata", 00133 Rome, Italy
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesco Longo
- Center for Neural Science, New York University, New York, NY 10029, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY 10029, USA
| | - August B Smit
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Seth G N Grant
- Center for the Clinical Brain Sciences and Simons Initiatives for the Developing Brain, The University of Edinburgh, Edinburgh EH16 4SB, Scotland
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland.
| | - Claudia Bagni
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland; Department of Biomedicine and Prevention, Università degli Studi di Roma "Tor Vergata", 00133 Rome, Italy.
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9
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Griffiths J, Grant SGN. Synapse pathology in Alzheimer's disease. Semin Cell Dev Biol 2023; 139:13-23. [PMID: 35690535 DOI: 10.1016/j.semcdb.2022.05.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/12/2022] [Accepted: 05/27/2022] [Indexed: 12/31/2022]
Abstract
Synapse loss and damage are central features of Alzheimer's disease (AD) and contribute to the onset and progression of its behavioural and physiological features. Here we review the literature describing synapse pathology in AD, from what we have learned from microscopy in terms of its impacts on synapse architecture, to the mechanistic role of Aβ, tau and glial cells, mitochondrial dysfunction, and the link with AD risk genes. We consider the emerging view that synapse pathology may operate at a further level, that of synapse diversity, and discuss the prospects for leveraging new synaptome mapping methods to comprehensively understand the molecular properties of vulnerable and resilient synapses. Uncovering AD impacts on brain synapse diversity should inform therapeutic approaches targeted at preserving or replenishing lost and damaged synapses and aid the interpretation of clinical imaging approaches that aim to measure synapse damage.
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Affiliation(s)
- Jessica Griffiths
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Dementia Research Institute at Imperial College, Department of Brain Sciences, Imperial College London, London W12 0NN, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
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10
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Scaduto P, Lauterborn JC, Cox CD, Fracassi A, Zeppillo T, Gutierrez BA, Keene CD, Crane PK, Mukherjee S, Russell WK, Taglialatela G, Limon A. Functional excitatory to inhibitory synaptic imbalance and loss of cognitive performance in people with Alzheimer's disease neuropathologic change. Acta Neuropathol 2023; 145:303-324. [PMID: 36538112 PMCID: PMC9925531 DOI: 10.1007/s00401-022-02526-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/12/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Individuals at distinct stages of Alzheimer's disease (AD) show abnormal electroencephalographic activity, which has been linked to network hyperexcitability and cognitive decline. However, whether pro-excitatory changes at the synaptic level are observed in brain areas affected early in AD, and if they are emergent in MCI, is not clearly known. Equally important, it is not known whether global synaptic E/I imbalances correlate with the severity of cognitive impairment in the continuum of AD. Measuring the amplitude of ion currents of human excitatory and inhibitory synaptic receptors microtransplanted from the hippocampus and temporal cortex of cognitively normal, mildly cognitively impaired and AD individuals into surrogate cells, we found regional differences in pro-excitatory shifts of the excitatory to inhibitory (E/I) current ratio that correlates positively with toxic proteins and degree of pathology, and impinges negatively on cognitive performance scores. Using these data with electrophysiologically anchored analysis of the synapto-proteome in the same individuals, we identified a group of proteins sustaining synaptic function and those related to synaptic toxicity. We also found an uncoupling between the function and expression of proteins for GABAergic signaling in the temporal cortex underlying larger E/I and worse cognitive performance. Further analysis of transcriptomic and in situ hybridization datasets from an independent cohort across the continuum of AD confirm regional differences in pro-excitatory shifts of the E/I balance that correlate negatively with the most recent calibrated composite scores for memory, executive function, language and visuospatial abilities, as well as overall cognitive performance. These findings indicate that early shifts of E/I balance may contribute to loss of cognitive capabilities in the continuum of AD clinical syndrome.
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Affiliation(s)
- Pietro Scaduto
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Julie C Lauterborn
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, CA, USA
| | - Conor D Cox
- Department of Anatomy and Neurobiology, University of California Irvine, Irvine, CA, USA
| | - Anna Fracassi
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Tommaso Zeppillo
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Berenice A Gutierrez
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, USA
| | - Giulio Taglialatela
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Agenor Limon
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch at Galveston, Galveston, TX, USA.
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11
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Moroz LL, Romanova DY. Alternative neural systems: What is a neuron? (Ctenophores, sponges and placozoans). Front Cell Dev Biol 2022; 10:1071961. [PMID: 36619868 PMCID: PMC9816575 DOI: 10.3389/fcell.2022.1071961] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
How to make a neuron, a synapse, and a neural circuit? Is there only one 'design' for a neural architecture with a universally shared genomic blueprint across species? The brief answer is "No." Four early divergent lineages from the nerveless common ancestor of all animals independently evolved distinct neuroid-type integrative systems. One of these is a subset of neural nets in comb jellies with unique synapses; the second lineage is the well-known Cnidaria + Bilateria; the two others are non-synaptic neuroid systems in sponges and placozoans. By integrating scRNA-seq and microscopy data, we revise the definition of neurons as synaptically-coupled polarized and highly heterogenous secretory cells at the top of behavioral hierarchies with learning capabilities. This physiological (not phylogenetic) definition separates 'true' neurons from non-synaptically and gap junction-coupled integrative systems executing more stereotyped behaviors. Growing evidence supports the hypothesis of multiple origins of neurons and synapses. Thus, many non-bilaterian and bilaterian neuronal classes, circuits or systems are considered functional rather than genetic categories, composed of non-homologous cell types. In summary, little-explored examples of convergent neuronal evolution in representatives of early branching metazoans provide conceptually novel microanatomical and physiological architectures of behavioral controls in animals with prospects of neuro-engineering and synthetic biology.
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Affiliation(s)
- Leonid L. Moroz
- Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, United States,Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, United States,*Correspondence: Leonid L. Moroz, ; Daria Y. Romanova,
| | - Daria Y. Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, 5A Butlerova, Moscow, Russia,*Correspondence: Leonid L. Moroz, ; Daria Y. Romanova,
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12
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Rayaprolu S, Bitarafan S, Santiago JV, Betarbet R, Sunna S, Cheng L, Xiao H, Nelson RS, Kumar P, Bagchi P, Duong DM, Goettemoeller AM, Oláh VJ, Rowan M, Levey AI, Wood LB, Seyfried NT, Rangaraju S. Cell type-specific biotin labeling in vivo resolves regional neuronal and astrocyte proteomic differences in mouse brain. Nat Commun 2022; 13:2927. [PMID: 35614064 PMCID: PMC9132937 DOI: 10.1038/s41467-022-30623-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 05/06/2022] [Indexed: 01/19/2023] Open
Abstract
Proteomic profiling of brain cell types using isolation-based strategies pose limitations in resolving cellular phenotypes representative of their native state. We describe a mouse line for cell type-specific expression of biotin ligase TurboID, for in vivo biotinylation of proteins. Using adenoviral and transgenic approaches to label neurons, we show robust protein biotinylation in neuronal soma and axons throughout the brain, allowing quantitation of over 2000 neuron-derived proteins spanning synaptic proteins, transporters, ion channels and disease-relevant druggable targets. Next, we contrast Camk2a-neuron and Aldh1l1-astrocyte proteomes and identify brain region-specific proteomic differences within both cell types, some of which might potentially underlie the selective vulnerability to neurological diseases. Leveraging the cellular specificity of proteomic labeling, we apply an antibody-based approach to uncover differences in neuron and astrocyte-derived signaling phospho-proteins and cytokines. This approach will facilitate the characterization of cell-type specific proteomes in a diverse number of tissues under both physiological and pathological states.
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Affiliation(s)
- Sruti Rayaprolu
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Sara Bitarafan
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Juliet V Santiago
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Ranjita Betarbet
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Sydney Sunna
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Lihong Cheng
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Hailian Xiao
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Ruth S Nelson
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Prateek Kumar
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Duc M Duong
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | | | - Viktor János Oláh
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Matt Rowan
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Allan I Levey
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Levi B Wood
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, 30322, USA.
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
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13
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Miski M, Keömley-Horváth BM, Rákóczi Megyeriné D, Csikász-Nagy A, Gáspári Z. Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach. PLoS Comput Biol 2022; 18:e1009758. [PMID: 35041658 PMCID: PMC8797218 DOI: 10.1371/journal.pcbi.1009758] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 01/28/2022] [Accepted: 12/15/2021] [Indexed: 11/18/2022] Open
Abstract
The postsynaptic density (PSD) is a dense protein network playing a key role in information processing during learning and memory, and is also indicated in a number of neurological disorders. Efforts to characterize its detailed molecular organization are encumbered by the large variability of the abundance of its constituent proteins both spatially, in different brain areas, and temporally, during development, circadian rhythm, and also in response to various stimuli. In this study we ran large-scale stochastic simulations of protein binding events to predict the presence and distribution of PSD complexes. We simulated the interactions of seven major PSD proteins (NMDAR, AMPAR, PSD-95, SynGAP, GKAP, Shank3, Homer1) based on previously published, experimentally determined protein abundance data from 22 different brain areas and 42 patients (altogether 524 different simulations). Our results demonstrate that the relative ratio of the emerging protein complexes can be sensitive to even subtle changes in protein abundances and thus explicit simulations are invaluable to understand the relationships between protein availability and complex formation. Our observations are compatible with a scenario where larger supercomplexes are formed from available smaller binary and ternary associations of PSD proteins. Specifically, Homer1 and Shank3 self-association reactions substantially promote the emergence of very large protein complexes. The described simulations represent a first approximation to assess PSD complex abundance, and as such, use significant simplifications. Therefore, their direct biological relevance might be limited but we believe that the major qualitative findings can contribute to the understanding of the molecular features of the postsynapse. Chemical and electrical synapses connect neurons in the brain. In chemical synapses the information is sent via molecules from one neuron (presynaptic one) to the other neuron (postsynaptic one). The messenger molecule called neurotransmitter is released from the presynaptic neuron’s active zone and binds to receptor molecules sitting on the postsynaptic neuron’s cell surface. This part of the postsynaptic neuron is the dendrite. Inside the dendrite there is an electron dense region full of proteins binding to each other forming large protein complexes. These complexes make sure that the receptor molecules are on the right place usually in front of the active zone. The protein dense region of the postsynaptic cell in the dendrites is called the postsynaptic density. We have performed extensive simulations on the formation of postsynaptic protein complexes using a well-defined set of proteins and a large number of publicly available input data sets on protein abundance. We used a simulator implementing the Gillespie algorithm to simulate binding and unbinding events proteins. We found that the relationship between single protein and protein complex abundances can be non-trivial, since similar complex distributions can emerge from distinct relative protein abundances and quite different protein complexes can be formed from almost similar initial protein abundances. Our results are compatible with the idea that the association-dissociation of smaller subcomplexes lead to the formation of large supercomplexes. The emergence of supercomplexes is largely facilitated by the self-association of Homer1 and Shank3 proteins. Our results are qualitatively in agreement with the formation of the experimentally observed ‘nanodomains’ in the postsynaptic density.
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Affiliation(s)
- Marcell Miski
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Bence Márk Keömley-Horváth
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
- Cytocast Ltd., Vecsés, Hungary
| | - Dorina Rákóczi Megyeriné
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Attila Csikász-Nagy
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
- Cytocast Ltd., Vecsés, Hungary
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
- * E-mail: (AC-N); (ZG)
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
- * E-mail: (AC-N); (ZG)
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14
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Sabaie H, Mazaheri Moghaddam M, Mazaheri Moghaddam M, Amirinejad N, Asadi MR, Daneshmandpour Y, Hussen BM, Taheri M, Rezazadeh M. Long non-coding RNA-associated competing endogenous RNA axes in the olfactory epithelium in schizophrenia: a bioinformatics analysis. Sci Rep 2021; 11:24497. [PMID: 34969953 PMCID: PMC8718521 DOI: 10.1038/s41598-021-04326-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
Abstract
The etiology of schizophrenia (SCZ), as a serious mental illness, is unknown. The significance of genetics in SCZ pathophysiology is yet unknown, and newly identified mechanisms involved in the regulation of gene transcription may be helpful in determining how these changes affect SCZ development and progression. In the current work, we used a bioinformatics approach to describe the role of long non-coding RNA (lncRNA)-associated competing endogenous RNAs (ceRNAs) in the olfactory epithelium (OE) samples in order to better understand the molecular regulatory processes implicated in SCZ disorders in living individuals. The Gene Expression Omnibus database was used to obtain the OE microarray dataset (GSE73129) from SCZ sufferers and control subjects, which contained information about both lncRNAs and mRNAs. The limma package of R software was used to identify the differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs). RNA interaction pairs were discovered using the Human MicroRNA Disease Database, DIANA-LncBase, and miRTarBase databases. In this study, the Pearson correlation coefficient was utilized to find positive correlations between DEmRNAs and DElncRNAs in the ceRNA network. Eventually, lncRNA-associated ceRNA axes were developed based on co-expression relations and DElncRNA-miRNA-DEmRNA interactions. This work found six potential DElncRNA-miRNA-DEmRNA loops in SCZ pathogenesis, including, SNTG2-AS1/hsa-miR-7-5p/SLC7A5, FLG-AS1/hsa-miR-34a-5p/FOSL1, LINC00960/hsa-miR-34a-5p/FOSL1, AQP4-AS1/hsa-miR-335-5p/FMN2, SOX2-OT/hsa-miR-24-3p/NOS3, and CASC2/hsa-miR-24-3p/NOS3. According to the findings, ceRNAs in OE might be promising research targets for studying SCZ molecular mechanisms. This could be a great opportunity to examine different aspects of neurodevelopment that may have been hampered early in SCZ patients.
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Affiliation(s)
- Hani Sabaie
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Madiheh Mazaheri Moghaddam
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran
| | - Nazanin Amirinejad
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Reza Asadi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Daneshmandpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. .,Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.
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15
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Sabaie H, Moghaddam MM, Moghaddam MM, Ahangar NK, Asadi MR, Hussen BM, Taheri M, Rezazadeh M. Bioinformatics analysis of long non-coding RNA-associated competing endogenous RNA network in schizophrenia. Sci Rep 2021; 11:24413. [PMID: 34952924 PMCID: PMC8709859 DOI: 10.1038/s41598-021-03993-3] [Citation(s) in RCA: 4] [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: 05/23/2021] [Accepted: 12/14/2021] [Indexed: 12/17/2022] Open
Abstract
Schizophrenia (SCZ) is a serious psychiatric condition with a 1% lifetime risk. SCZ is one of the top ten global causes of disabilities. Despite numerous attempts to understand the function of genetic factors in SCZ development, genetic components in SCZ pathophysiology remain unknown. The competing endogenous RNA (ceRNA) network has been demonstrated to be involved in the development of many kinds of diseases. The ceRNA hypothesis states that cross-talks between coding and non-coding RNAs, including long non-coding RNAs (lncRNAs), via miRNA complementary sequences known as miRNA response elements, creates a large regulatory network across the transcriptome. In the present study, we developed a lncRNA-related ceRNA network to elucidate molecular regulatory mechanisms involved in SCZ. Microarray datasets associated with brain regions (GSE53987) and lymphoblasts (LBs) derived from peripheral blood (sample set B from GSE73129) of SCZ patients and control subjects containing information about both mRNAs and lncRNAs were downloaded from the Gene Expression Omnibus database. The GSE53987 comprised 48 brain samples taken from SCZ patients (15 HPC: hippocampus, 15 BA46: Brodmann area 46, 18 STR: striatum) and 55 brain samples taken from control subjects (18 HPC, 19 BA46, 18 STR). The sample set B of GSE73129 comprised 30 LB samples (15 patients with SCZ and 15 controls). Differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) were identified using the limma package of the R software. Using DIANA-LncBase, Human MicroRNA Disease Database (HMDD), and miRTarBase, the lncRNA- associated ceRNA network was generated. Pathway enrichment of DEmRNAs was performed using the Enrichr tool. We developed a protein-protein interaction network of DEmRNAs and identified the top five hub genes by the use of STRING and Cytoscape, respectively. Eventually, the hub genes, DElncRNAs, and predictive miRNAs were chosen to reconstruct the subceRNA networks. Our bioinformatics analysis showed that twelve key DEmRNAs, including BDNF, VEGFA, FGF2, FOS, CD44, SOX2, NRAS, SPARC, ZFP36, FGG, ELAVL1, and STARD13, participate in the ceRNA network in SCZ. We also identified DLX6-AS1, NEAT1, MINCR, LINC01094, DLGAP1-AS1, BABAM2-AS1, PAX8-AS1, ZFHX4-AS1, XIST, and MALAT1 as key DElncRNAs regulating the genes mentioned above. Furthermore, expression of 15 DEmRNAs (e.g., ADM and HLA-DRB1) and one DElncRNA (XIST) were changed in both the brain and LB, suggesting that they could be regarded as candidates for future biomarker studies. The study indicated that ceRNAs could be research candidates for investigating SCZ molecular pathways.
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Affiliation(s)
- Hani Sabaie
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Madiheh Mazaheri Moghaddam
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran
| | | | - Noora Karim Ahangar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Asadi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Mohammad Taheri
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Rezazadeh
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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16
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Curran OE, Qiu Z, Smith C, Grant SGN. A single-synapse resolution survey of PSD95-positive synapses in twenty human brain regions. Eur J Neurosci 2021; 54:6864-6881. [PMID: 32492218 PMCID: PMC7615673 DOI: 10.1111/ejn.14846] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/24/2022]
Abstract
Mapping the molecular composition of individual excitatory synapses across the mouse brain reveals high synapse diversity with each brain region showing a distinct composition of synapse types. As a first step towards systematic mapping of synapse diversity across the human brain, we have labelled and imaged synapses expressing the excitatory synapse protein PSD95 in twenty human brain regions, including 13 neocortical, two subcortical, one hippocampal, one cerebellar and three brainstem regions, in four phenotypically normal individuals. We quantified the number, size and intensity of individual synaptic puncta and compared their regional distributions. We found that each region showed a distinct signature of synaptic puncta parameters. Comparison of brain regions showed that cortical and hippocampal structures are similar, and distinct from those of cerebellum and brainstem. Comparison of synapse parameters from human and mouse brain revealed conservation of parameters, hierarchical organization of brain regions and network architecture. This work illustrates the feasibility of generating a systematic single-synapse resolution atlas of the human brain, a potentially significant resource in studies of brain health and disease.
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Affiliation(s)
- Olimpia E Curran
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Zhen Qiu
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Colin Smith
- Academic Neuropathology, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, Edinburgh, UK
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17
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A unified resource and configurable model of the synapse proteome and its role in disease. Sci Rep 2021; 11:9967. [PMID: 33976238 PMCID: PMC8113277 DOI: 10.1038/s41598-021-88945-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Genes encoding synaptic proteins are highly associated with neuronal disorders many of which show clinical co-morbidity. We integrated 58 published synaptic proteomic datasets that describe over 8000 proteins and combined them with direct protein-protein interactions and functional metadata to build a network resource that reveals the shared and unique protein components that underpin multiple disorders. All the data are provided in a flexible and accessible format to encourage custom use.
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18
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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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19
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Jamjoom AAB, Rhodes J, Andrews PJD, Grant SGN. The synapse in traumatic brain injury. Brain 2021; 144:18-31. [PMID: 33186462 PMCID: PMC7880663 DOI: 10.1093/brain/awaa321] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Traumatic brain injury (TBI) is a leading cause of death and disability worldwide and is a risk factor for dementia later in life. Research into the pathophysiology of TBI has focused on the impact of injury on the neuron. However, recent advances have shown that TBI has a major impact on synapse structure and function through a combination of the immediate mechanical insult and the ensuing secondary injury processes, leading to synapse loss. In this review, we highlight the role of the synapse in TBI pathophysiology with a focus on the confluence of multiple secondary injury processes including excitotoxicity, inflammation and oxidative stress. The primary insult triggers a cascade of events in each of these secondary processes and we discuss the complex interplay that occurs at the synapse. We also examine how the synapse is impacted by traumatic axonal injury and the role it may play in the spread of tau after TBI. We propose that astrocytes play a crucial role by mediating both synapse loss and recovery. Finally, we highlight recent developments in the field including synapse molecular imaging, fluid biomarkers and therapeutics. In particular, we discuss advances in our understanding of synapse diversity and suggest that the new technology of synaptome mapping may prove useful in identifying synapses that are vulnerable or resistant to TBI.
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Affiliation(s)
- Aimun A B Jamjoom
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Jonathan Rhodes
- Anaesthesia, Critical Care and Pain Medicine, University of Edinburgh, Edinburgh EH16 4SA, UK
| | - Peter J D Andrews
- Anaesthesia, Critical Care and Pain Medicine, University of Edinburgh, Edinburgh EH16 4SA, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4SB, UK
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
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20
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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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21
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Proteomic Characterization of Synaptosomes from Human Substantia Nigra Indicates Altered Mitochondrial Translation in Parkinson's Disease. Cells 2020; 9:cells9122580. [PMID: 33276480 PMCID: PMC7761546 DOI: 10.3390/cells9122580] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/17/2020] [Accepted: 11/24/2020] [Indexed: 12/25/2022] Open
Abstract
The pathological hallmark of Parkinson's disease (PD) is the loss of neuromelanin-containing dopaminergic neurons within the substantia nigra pars compacta (SNpc). Additionally, numerous studies indicate an altered synaptic function during disease progression. To gain new insights into the molecular processes underlying the alteration of synaptic function in PD, a proteomic study was performed. Therefore, synaptosomes were isolated by density gradient centrifugation from SNpc tissue of individuals at advanced PD stages (N = 5) as well as control subjects free of pathology (N = 5) followed by mass spectrometry-based analysis. In total, 362 proteins were identified and assigned to the synaptosomal core proteome. This core proteome comprised all proteins expressed within the synapses without regard to data analysis software, gender, age, or disease. The differential analysis between control subjects and PD cases revealed that CD9 antigen was overrepresented and fourteen proteins, among them Thymidine kinase 2 (TK2), mitochondrial, 39S ribosomal protein L37, neurolysin, and Methionine-tRNA ligase (MARS2) were underrepresented in PD suggesting an alteration in mitochondrial translation within synaptosomes.
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22
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Gulyássy P, Puska G, Györffy BA, Todorov-Völgyi K, Juhász G, Drahos L, Kékesi KA. Proteomic comparison of different synaptosome preparation procedures. Amino Acids 2020; 52:1529-1543. [PMID: 33211194 PMCID: PMC7695668 DOI: 10.1007/s00726-020-02912-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 11/05/2020] [Indexed: 01/10/2023]
Abstract
Synaptosomes are frequently used research objects in neurobiology studies focusing on synaptic transmission as they mimic several aspects of the physiological synaptic functions. They contain the whole apparatus for neurotransmission, the presynaptic nerve ending with synaptic vesicles, synaptic mitochondria and often a segment of the postsynaptic membrane along with the postsynaptic density is attached to its outer surface. As being artificial functional organelles, synaptosomes are viable for several hours, retain their activity, membrane potential, and capable to store, release, and reuptake neurotransmitters. Synaptosomes are ideal subjects for proteomic analysis. The recently available separation and protein detection techniques can cope with the reduced complexity of the organelle and enable the simultaneous qualitative and quantitative analysis of thousands of proteins shaping the structural and functional characteristics of the synapse. Synaptosomes are formed during the homogenization of nervous tissue in the isoosmotic milieu and can be isolated from the homogenate by various approaches. Each enrichment method has its own benefits and drawbacks and there is not a single method that is optimal for all research purposes. For a proper proteomic experiment, it is desirable to preserve the native synaptic structure during the isolation procedure and keep the degree of contamination from other organelles or cell types as low as possible. In this article, we examined five synaptosome isolation methods from a proteomic point of view by the means of electron microscopy, Western blot, and liquid chromatography-mass spectrometry to compare their efficiency in the isolation of synaptosomes and depletion of contaminating subcellular structures. In our study, the different isolation procedures led to a largely overlapping pool of proteins with a fairly similar distribution of presynaptic, active zone, synaptic vesicle, and postsynaptic proteins; however, discrete differences were noticeable in individual postsynaptic proteins and in the number of identified transmembrane proteins. Much pronounced variance was observed in the degree of contamination with mitochondrial and glial structures. Therefore, we suggest that in selecting the appropriate isolation method for any neuroproteomics experiment carried out on synaptosomes, the degree and sort/source of contamination should be considered as a primary aspect.
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Affiliation(s)
- Péter Gulyássy
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary.
| | - Gina Puska
- Department of Anatomy, Cell and Development Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,Department of Ecology, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary.,MTA-ELTE NAP Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Balázs A Györffy
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,ELTE-NAP Neuroimmunology Research Group, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Katalin Todorov-Völgyi
- MTA-ELTE NAP Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Gábor Juhász
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary.,Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - László Drahos
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary.,MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, 1117, Hungary
| | - Katalin Adrienna Kékesi
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,Department of Physiology and Neurobiology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
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23
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Ageta-Ishihara N, Kinoshita M. Developmental and postdevelopmental roles of septins in the brain. Neurosci Res 2020; 170:6-12. [PMID: 33159992 DOI: 10.1016/j.neures.2020.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 11/25/2022]
Abstract
Morphogenetic processes during brain development and postdevelopmental remodeling of neural architecture depend on the exquisite interplay between the microtubule- and actin-based cytoskeletal systems. Accumulation of evidence indicates cooperative roles of another cytoskeletal system composed of the septin family. Here we overview experimental findings on mammalian septins and their hypothetical roles in the proliferation of neural progenitor cells, neurite development, synapse formation and regulations. The diverse, mostly unexpected phenotypes obtained from gain- and loss-of-function mutants point to unknown molecular network to be elucidated, which may underlie pathogenetic processes of infectious diseases and neuropsychiatric disorders in humans.
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Affiliation(s)
- Natsumi Ageta-Ishihara
- Division of Biological Science, Nagoya University Graduate School of Science, Furo, Chikusa, Nagoya 464-8602, Japan.
| | - Makoto Kinoshita
- Division of Biological Science, Nagoya University Graduate School of Science, Furo, Chikusa, Nagoya 464-8602, Japan.
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24
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van Oostrum M, Campbell B, Seng C, Müller M, Tom Dieck S, Hammer J, Pedrioli PGA, Földy C, Tyagarajan SK, Wollscheid B. Surfaceome dynamics reveal proteostasis-independent reorganization of neuronal surface proteins during development and synaptic plasticity. Nat Commun 2020; 11:4990. [PMID: 33020478 PMCID: PMC7536423 DOI: 10.1038/s41467-020-18494-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 08/24/2020] [Indexed: 12/27/2022] Open
Abstract
Neurons are highly compartmentalized cells with tightly controlled subcellular protein organization. While brain transcriptome, connectome and global proteome maps are being generated, system-wide analysis of temporal protein dynamics at the subcellular level are currently lacking. Here, we perform a temporally-resolved surfaceome analysis of primary neuron cultures and reveal dynamic surface protein clusters that reflect the functional requirements during distinct stages of neuronal development. Direct comparison of surface and total protein pools during development and homeostatic synaptic scaling demonstrates system-wide proteostasis-independent remodeling of the neuronal surface, illustrating widespread regulation on the level of surface trafficking. Finally, quantitative analysis of the neuronal surface during chemical long-term potentiation (cLTP) reveals fast externalization of diverse classes of surface proteins beyond the AMPA receptor, providing avenues to investigate the requirement of exocytosis for LTP. Our resource (neurosurfaceome.ethz.ch) highlights the importance of subcellular resolution for systems-level understanding of cellular processes. Cell surface proteins contribute to neuronal development and activity-dependent synaptic plasticity. Here, the authors perform a time-resolved surfaceome analysis of developing primary neurons and in response to homeostatic synaptic scaling and chemical long-term potentiation (cLTP), revealing surface proteome remodeling largely independent of global proteostasis.
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Affiliation(s)
- Marc van Oostrum
- Neuroscience Center Zurich, Zurich, Switzerland.,Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Benjamin Campbell
- Neuroscience Center Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Charlotte Seng
- Neuroscience Center Zurich, Zurich, Switzerland.,Laboratory of Neural Connectivity, Faculties of Medicine and Natural Sciences, Brain Research Institute, University of Zurich, Zürich, 8057, Switzerland
| | - Maik Müller
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | | | - Jacqueline Hammer
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland
| | - Patrick G A Pedrioli
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Csaba Földy
- Neuroscience Center Zurich, Zurich, Switzerland.,Laboratory of Neural Connectivity, Faculties of Medicine and Natural Sciences, Brain Research Institute, University of Zurich, Zürich, 8057, Switzerland
| | - Shiva K Tyagarajan
- Neuroscience Center Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Neuroscience Center Zurich, Zurich, Switzerland. .,Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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25
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Grant SGN, Fransén E. The Synapse Diversity Dilemma: Molecular Heterogeneity Confounds Studies of Synapse Function. Front Synaptic Neurosci 2020; 12:590403. [PMID: 33132891 PMCID: PMC7561708 DOI: 10.3389/fnsyn.2020.590403] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/15/2020] [Indexed: 11/24/2022] Open
Abstract
Recent studies have shown an unexpectedly high degree of synapse diversity arising from molecular and morphological differences among individual synapses. Diverse synapse types are spatially distributed within individual dendrites, between different neurons, and across and between brain regions, producing the synaptome architecture of the brain. The spatial organization of synapse heterogeneity is important because the physiological activation of heterogeneous excitatory synapses produces a non-uniform spatial output of synaptic potentials, which confounds the interpretation of measurements obtained from population-averaging electrodes, optrodes and biochemical methods that lack single-synapse resolution. Population-averaging measurements cannot distinguish between changes in the composition of populations of synapses and changing synaptic physiology. Here we consider the implications of synapse diversity and its organization into synaptome architecture for studies of synapse physiology, plasticity, development and behavior, and for the interpretation of phenotypes arising from pharmacological and genetic perturbations. We conclude that prevailing models based on population-averaging measurements need reconsideration and that single-synapse resolution physiological recording methods are required to confirm or refute the major synaptic models of behavior.
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Affiliation(s)
- Seth G N Grant
- Genes to Cognition Programme, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Erik Fransén
- Department of Computational Science and Technology, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
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26
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Shen K, Zeppillo T, Limon A. Regional transcriptome analysis of AMPA and GABA A receptor subunit expression generates E/I signatures of the human brain. Sci Rep 2020; 10:11352. [PMID: 32647210 PMCID: PMC7347860 DOI: 10.1038/s41598-020-68165-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/08/2020] [Indexed: 11/09/2022] Open
Abstract
Theoretical and experimental work has demonstrated that excitatory (E) and inhibitory (I) currents within cortical circuits stabilize to a balanced state. This E/I balance, observed from single neuron to network levels, has a fundamental role in proper brain function and its impairment has been linked to numerous brain disorders. Over recent years, large amount of microarray and RNA-Sequencing datasets have been collected, however few studies have made use of these resources for exploring the balance of global gene expression levels between excitatory AMPA receptors (AMPARs) and inhibitory GABAA receptors. Here, we analyzed the relative relationships between these receptors to generate a basic transcriptional marker of E/I ratio. Using publicly available data from the Allen Brain Institute, we generated whole brain and regional signatures of AMPAR subunit gene expression in healthy human brains as well as the transcriptional E/I (tE/I) ratio. Then we refined the tE/I ratio to cell-type signatures in the mouse brain using data from the Gene Expression Omnibus. Lastly, we applied our workflow to developmental data from the Allen Brain Institute and revealed spatially and temporally controlled changes in the tE/I ratio during the embryonic and early postnatal stages that ultimately lead to the tE/I balance in adults.
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Affiliation(s)
- Kevin Shen
- Gladstone Institute of Neurological Disease, University of California, San Francisco, USA
| | - Tommaso Zeppillo
- Department of Life Sciences, B.R.A.I.N., Centre for Neuroscience, University of Trieste, Trieste, Italy.,Department of Neurology, Mitchell Center for Neurodegenerative Diseases, School of Medicine, University of Texas Medical Branch, 10.138B. Medical Research Building, Galveston, TX, 77555, USA
| | - Agenor Limon
- Department of Neurology, Mitchell Center for Neurodegenerative Diseases, School of Medicine, University of Texas Medical Branch, 10.138B. Medical Research Building, Galveston, TX, 77555, USA.
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27
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Loaiza CD, Duhan N, Lister M, Kaundal R. In silico prediction of host-pathogen protein interactions in melioidosis pathogen Burkholderia pseudomallei and human reveals novel virulence factors and their targets. Brief Bioinform 2020; 22:5842243. [PMID: 32444871 DOI: 10.1093/bib/bbz162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/13/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022] Open
Abstract
The aerobic, Gram-negative motile bacillus, Burkholderia pseudomallei is a facultative intracellular bacterium causing melioidosis, a critical disease of public health importance, which is widely endemic in the tropics and subtropical regions of the world. Melioidosis is associated with high case fatality rates in animals and humans; even with treatment, its mortality is 20-50%. It also infects plants and is designated as a biothreat agent. B. pseudomallei is pathogenic due to its ability to invade, resist factors in serum and survive intracellularly. Despite its importance, to date only a few effector proteins have been functionally characterized, and there is not much information regarding the host-pathogen protein-protein interactions (PPI) of this system, which are important to studying infection mechanisms and thereby develop prevention measures. We explored two computational approaches, the homology-based interolog and the domain-based method, to predict genome-scale host-pathogen interactions (HPIs) between two different strains of B. pseudomallei (prototypical, and highly virulent) and human. In total, 76 335 common HPIs (between the two strains) were predicted involving 8264 human and 1753 B. pseudomallei proteins. Among the unique PPIs, 14 131 non-redundant HPIs were found to be unique between the prototypical strain and human, compared to 3043 non-redundant HPIs between the highly virulent strain and human. The protein hubs analysis showed that most B. pseudomallei proteins formed a hub with human dnaK complex proteins associated with tuberculosis, a disease similar in symptoms to melioidosis. In addition, drug-binding and carbohydrate-binding mechanisms were found overrepresented within the host-pathogen network, and metabolic pathways were frequently activated according to the pathway enrichment. Subcellular localization analysis showed that most of the pathogen proteins are targeting human proteins inside cytoplasm and nucleus. We also discovered the host targets of the drug-related pathogen proteins and proteins that form T3SS and T6SS in B. pseudomallei. Additionally, a comparison between the unique PPI patterns present in the prototypical and highly virulent strains was performed. The current study is the first report on developing a genome-scale host-pathogen protein interaction networks between the human and B. pseudomallei, a critical biothreat agent. We have identified novel virulence factors and their interacting partners in the human proteome. These PPIs can be further validated by high-throughput experiments and may give new insights on how B. pseudomallei interacts with its host, which will help medical researchers in developing better prevention measures.
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Affiliation(s)
- Cristian D Loaiza
- Center for Integrated BioSystems/Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, USA
| | - Naveen Duhan
- Center for Integrated BioSystems/Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, USA
| | - Matthew Lister
- Bioinformatics Facility, Center for Integrated BioSystems, Utah State University, USA
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate/Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322 USA
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28
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Xu M, Wang H, Wang J, Burhan D, Shang R, Wang P, Zhou Y, Li R, Liang B, Evert K, Utpatel K, Xu Z, Song X, Che L, Calvisi DF, Wang B, Chen X, Zeng Y, Chen X. mTORC2 Signaling Is Necessary for Timely Liver Regeneration after Partial Hepatectomy. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:817-829. [PMID: 32035060 DOI: 10.1016/j.ajpath.2019.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
Liver regeneration is a fundamental biological process required for sustaining body homeostasis and restoring liver function after injury. Emerging evidence demonstrates that cytokines, growth factors, and multiple signaling pathways contribute to liver regeneration. Mammalian target of rapamycin complex 2 (mTORC2) regulates cell metabolism, proliferation and survival. The major substrates for mTORC2 are the AGC family members of kinases, including AKT, SGK, and PKC-α. We investigated the functional roles of mTORC2 during liver regeneration. Partial hepatectomy (PHx) was performed in liver-specific Rictor (the pivotal unit of mTORC2 complex) knockout (RictorLKO) and wild-type (Rictorfl/fl) mice. Rictor-deficient mice were found to be more intolerant to PHx and displayed higher mortality after PHx. Mechanistically, loss of Rictor resulted in decreased Akt phosphorylation, leading to a delay in hepatocyte proliferation and lipid droplets formation along liver regeneration. Overall, these results indicate an essential role of the mTORC2 signaling pathway during liver regeneration.
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Affiliation(s)
- Meng Xu
- Department of General Surgery, The Second Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, PR China; Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California
| | - Haichuan Wang
- Department of Liver Surgery, Liver Transplantation Division, West China Hospital, Sichuan University, Chengdu, PR China; Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California; Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, PR China; Department of General Surgery, The Second Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, PR China
| | - Jingxiao Wang
- Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California; School of Life Sciences, Beijing University of Chinese Medicine, Beijing, PR China
| | - Deviana Burhan
- Department of Medicine, Liver Center, University of California, San Francisco, California
| | - Runze Shang
- Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California; Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Military Medical University, Xi'an, PR China
| | - Pan Wang
- Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California; Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, Beijing, PR China
| | - Yi Zhou
- Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California; Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, PR China
| | - Rong Li
- Department of Anesthesiology, The Second Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, PR China
| | - Bingyong Liang
- Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California; Hepatic Surgery Center, Department of Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Katja Evert
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Kirsten Utpatel
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Zhong Xu
- Department of Gastroenterology, Guizhou Provincial People's Hospital, Medical College of Guizhou University, Guiyang, PR China
| | - Xinhua Song
- Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California
| | - Li Che
- Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California
| | - Diego F Calvisi
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Bruce Wang
- Department of Medicine, Liver Center, University of California, San Francisco, California
| | - Xi Chen
- Department of General Surgery, The Second Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, PR China
| | - Yong Zeng
- Department of Liver Surgery, Liver Transplantation Division, West China Hospital, Sichuan University, Chengdu, PR China; Laboratory of Liver Surgery, West China Hospital, Sichuan University, Chengdu, PR China.
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences, Liver Center, University of California, San Francisco, California.
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29
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Abstract
Emerging evidence indicates that liquid-liquid phase separation, the formation of a condensed molecular assembly within another diluted aqueous solution, is a means for cells to organize highly condensed biological assemblies (also known as biological condensates or membraneless compartments) with very broad functions and regulatory properties in different subcellular regions. Molecular machineries dictating synaptic transmissions in both presynaptic boutons and postsynaptic densities of neuronal synapses may be such biological condensates. Here we review recent developments showing how phase separation can build dense synaptic molecular clusters, highlight unique features of such condensed clusters in the context of synaptic development and signaling, discuss how aberrant phase-separation-mediated synaptic assembly formation may contribute to dysfunctional signaling in psychiatric disorders, and present some challenges and opportunities of phase separation in synaptic biology.
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30
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Proteomic Analysis of Brain Region and Sex-Specific Synaptic Protein Expression in the Adult Mouse Brain. Cells 2020; 9:cells9020313. [PMID: 32012899 PMCID: PMC7072627 DOI: 10.3390/cells9020313] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/19/2022] Open
Abstract
Genetic disruption of synaptic proteins results in a whole variety of human neuropsychiatric disorders including intellectual disability, schizophrenia or autism spectrum disorder (ASD). In a wide range of these so-called synaptopathies a sex bias in prevalence and clinical course has been reported. Using an unbiased proteomic approach, we analyzed the proteome at the interaction site of the pre- and postsynaptic compartment, in the prefrontal cortex, hippocampus, striatum and cerebellum of male and female adult C57BL/6J mice. We were able to reveal a specific repertoire of synaptic proteins in different brain areas as it has been implied before. Additionally, we found a region-specific set of novel synaptic proteins differentially expressed between male and female individuals including the strong ASD candidates DDX3X, KMT2C, MYH10 and SET. Being the first comprehensive analysis of brain region-specific synaptic proteomes from male and female mice, our study provides crucial information on sex-specific differences in the molecular anatomy of the synapse. Our efforts should serve as a neurobiological framework to better understand the influence of sex on synapse biology in both health and disease.
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31
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Abstract
One of the fundamental questions in neuroscience is how brain activity relates to conscious experience. Even though self-consciousness is considered an emergent property of the brain network, a quantum physics-based theory assigns a momentum of consciousness to the single neuron level. In this work, we present a brain self theory from an evolutionary biological perspective by analogy with the immune self. In this scheme, perinatal reactivity to self inputs would guide the selection of neocortical neurons within the subplate, similarly to T lymphocytes in the thymus. Such self-driven neuronal selection would enable effective discrimination of external inputs and avoid harmful "autoreactive" responses. Multiple experimental and clinical evidences for this model are provided. Based on this self tenet, we outline the postulates of the so-called autophrenic diseases, to then make the case for schizophrenia, an archetypic disease with rupture of the self. Implications of this model are discussed, along with potential experimental verification.
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Affiliation(s)
- Silvia Sánchez-Ramón
- Department of Clinical Immunology, IML and IdISSC, Hospital Clínico San Carlos, Madrid, Spain.,Department of Immunology, ENT and Ophthalmology, Complutense University School of Medicine, Madrid, Spain
| | - Florence Faure
- INSERM U932, PSL Research University, Institut Curie, Paris, France
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32
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Grant SGN. Synapse diversity and synaptome architecture in human genetic disorders. Hum Mol Genet 2019; 28:R219-R225. [PMID: 31348488 PMCID: PMC6872429 DOI: 10.1093/hmg/ddz178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 12/03/2022] Open
Abstract
Over 130 brain diseases are caused by mutations that disrupt genes encoding the proteome of excitatory synapses. These include neurological and psychiatric disorders with early and late onset such as autism, schizophrenia and depression and many other rarer conditions. The proteome of synapses is highly complex with over 1000 conserved proteins which are differentially expressed generating a vast, potentially unlimited, number of synapse types. The diversity of synapses and their location in the brain are described by the synaptome. A recent study has mapped the synaptome across the mouse brain, revealing that synapse diversity is distributed into an anatomical architecture observed at scales from individual dendrites to the whole systems level. The synaptome architecture is built from the hierarchical expression and assembly of proteins into complexes and supercomplexes which are distributed into different synapses. Mutations in synapse proteins change the synaptome architecture leading to behavioral phenotypes. Mutations in the mechanisms regulating the hierarchical assembly of the synaptome, including transcription and proteostasis, may also change synapse diversity and synaptome architecture. The logic of synaptome hierarchical assembly provides a mechanistic framework that explains how diverse genetic disorders can converge on synapses in different brain circuits to produce behavioral phenotypes.
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Affiliation(s)
- Seth G N Grant
- Centre for Clinical Brain Science, Edinburgh University, Edinburgh, UK
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33
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Bernard-Gauthier V, Mossine AV, Knight A, Patnaik D, Zhao WN, Cheng C, Krishnan HS, Xuan LL, Chindavong PS, Reis SA, Chen JM, Shao X, Stauff J, Arteaga J, Sherman P, Salem N, Bonsall D, Amaral B, Varlow C, Wells L, Martarello L, Patel S, Liang SH, Kurumbail RG, Haggarty SJ, Scott PJH, Vasdev N. Structural Basis for Achieving GSK-3β Inhibition with High Potency, Selectivity, and Brain Exposure for Positron Emission Tomography Imaging and Drug Discovery. J Med Chem 2019; 62:9600-9617. [PMID: 31535859 PMCID: PMC6883410 DOI: 10.1021/acs.jmedchem.9b01030] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Using structure-guided design, several cell based assays, and microdosed positron emission tomography (PET) imaging, we identified a series of highly potent, selective, and brain-penetrant oxazole-4-carboxamide-based inhibitors of glycogen synthase kinase-3 (GSK-3). An isotopologue of our first-generation lead, [3H]PF-367, demonstrates selective and specific target engagement in vitro, irrespective of the activation state. We discovered substantial ubiquitous GSK-3-specific radioligand binding in Tg2576 Alzheimer's disease (AD), suggesting application for these compounds in AD diagnosis and identified [11C]OCM-44 as our lead GSK-3 radiotracer, with optimized brain uptake by PET imaging in nonhuman primates. GSK-3β-isozyme selectivity was assessed to reveal OCM-51, the most potent (IC50 = 0.030 nM) and selective (>10-fold GSK-3β/GSK-3α) GSK-3β inhibitor known to date. Inhibition of CRMP2T514 and tau phosphorylation, as well as favorable therapeutic window against WNT/β-catenin signaling activation, was observed in cells.
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Affiliation(s)
- Vadim Bernard-Gauthier
- Azrieli Centre for Neuro-Radiochemistry, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
- Department of Psychiatry/Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 1R8, Canada
- Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital and Department of Radiology, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Andrew V. Mossine
- Division of Nuclear Medicine, Department of Radiology, The University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Ashley Knight
- Azrieli Centre for Neuro-Radiochemistry, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
- Department of Psychiatry/Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 1R8, Canada
- Eisai AiM Institute, Boston, Massachusetts 01810, United States
| | - Debasis Patnaik
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Chialin Cheng
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Hema S. Krishnan
- Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital and Department of Radiology, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Lucius L. Xuan
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Peter S. Chindavong
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Surya A. Reis
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jinshan Michael Chen
- Pfizer Worldwide Research and Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Xia Shao
- Division of Nuclear Medicine, Department of Radiology, The University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Jenelle Stauff
- Division of Nuclear Medicine, Department of Radiology, The University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Janna Arteaga
- Division of Nuclear Medicine, Department of Radiology, The University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Phillip Sherman
- Division of Nuclear Medicine, Department of Radiology, The University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Nicolas Salem
- Biogen, Research and Early Development Imaging, Cambridge, Massachusetts 02142, United States
| | | | - Brenda Amaral
- Biogen, Research and Early Development Imaging, Cambridge, Massachusetts 02142, United States
| | - Cassis Varlow
- Azrieli Centre for Neuro-Radiochemistry, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
| | | | - Laurent Martarello
- Biogen, Research and Early Development Imaging, Cambridge, Massachusetts 02142, United States
| | - Shil Patel
- Eisai AiM Institute, Boston, Massachusetts 01810, United States
| | - Steven H. Liang
- Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital and Department of Radiology, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ravi G. Kurumbail
- Pfizer Worldwide Research and Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Peter J. H. Scott
- Division of Nuclear Medicine, Department of Radiology, The University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
- The Interdepartmental Program in Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Neil Vasdev
- Azrieli Centre for Neuro-Radiochemistry, Research Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
- Department of Psychiatry/Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 1R8, Canada
- Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital and Department of Radiology, Harvard Medical School, Boston, Massachusetts 02114, United States
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34
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Zhu F, Collins MO, Harmse J, Choudhary JS, Grant SGN, Komiyama NH. Cell-type-specific visualisation and biochemical isolation of endogenous synaptic proteins in mice. Eur J Neurosci 2019; 51:793-805. [PMID: 31621109 PMCID: PMC7079123 DOI: 10.1111/ejn.14597] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/07/2019] [Accepted: 10/08/2019] [Indexed: 01/01/2023]
Abstract
In recent years, the remarkable molecular complexity of synapses has been revealed, with over 1,000 proteins identified in the synapse proteome. Although it is known that different receptors and other synaptic proteins are present in different types of neurons, the extent of synapse diversity across the brain is largely unknown. This is mainly due to the limitations of current techniques. Here, we report an efficient method for the purification of synaptic protein complexes, fusing a high‐affinity tag to endogenous PSD95 in specific cell types. We also developed a strategy, which enables the visualisation of endogenous PSD95 with fluorescent‐protein tag in Cre‐recombinase‐expressing cells. We demonstrate the feasibility of proteomic analysis of synaptic protein complexes and visualisation of these in specific cell types. We find that the composition of PSD95 complexes purified from specific cell types differs from those extracted from tissues with diverse cellular composition. The results suggest that there might be differential interactions in the PSD95 complexes in different brain regions. We have detected differentially interacting proteins by comparing data sets from the whole hippocampus and the CA3 subfield of the hippocampus. Therefore, these novel conditional PSD95 tagging lines will not only serve as powerful tools for precisely dissecting synapse diversity in specific brain regions and subsets of neuronal cells, but also provide an opportunity to better understand brain region‐ and cell‐type‐specific alterations associated with various psychiatric/neurological diseases. These newly developed conditional gene tagging methods can be applied to many different synaptic proteins and will facilitate research on the molecular complexity of synapses.
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Affiliation(s)
- Fei Zhu
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark O Collins
- Department of Biomedical Science, The University of Sheffield, Sheffield, UK
| | - Johan Harmse
- The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Jyoti S Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,The Wellcome Trust Sanger Institute, Cambridge, UK.,Simons Initiative for the Developing Brain (SIDB), University of Edinburgh, Edinburgh, UK
| | - Noboru H Komiyama
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain (SIDB), University of Edinburgh, Edinburgh, UK.,The Patrick Wild Centre for Research into Autism, Fragile X Syndrome and Intellectual Disabilities, University of Edinburgh, Edinburgh, UK
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35
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Fallah H, Azari I, Neishabouri SM, Oskooei VK, Taheri M, Ghafouri-Fard S. Sex-specific up-regulation of lncRNAs in peripheral blood of patients with schizophrenia. Sci Rep 2019; 9:12737. [PMID: 31484957 PMCID: PMC6726592 DOI: 10.1038/s41598-019-49265-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023] Open
Abstract
Schizophrenia as a common disabling psychiatric disorder has been associated with dysregulation of several genes and pathways among them are those being regulated by long non-coding RNAs (lncRNAs). Based on the acknowledged roles of lncRNAs in neurodevelopment, in the current study, we assessed expression of six lncRNAs namely HOXA-AS2, Linc-ROR, MALAT1, MEG3, SPRY4-IT1 and UCA1 in peripheral blood of 60 patients with schizophrenia and 60 healthy subjects. HOXA-AS2, Linc-ROR, MEG3, SPRY4-IT1 and UCA1 levels were significantly higher in total patients compared with total controls. However, when evaluating expression of genes in sex-based subgroups, the differences in the expression of these lncRNAs were significant only among females. Assessment of partial correlation between expression of lncRNAs and age of study participants after controlling the effect of sex, revealed significant correlations for HOXA-AS2, MALAT1 and UCA1 in both patients and controls. Besides, expressions of Linc-ROR and SPRY4-IT1 were correlated with age only in patients. Significant pairwise correlations were recognized between expression levels of lncRNAs in both patients with schizophrenia and controls. Based on the area under curve (AUC) values, SPRY4-IT1 had the best performance in differentiation of female patients with schizophrenia from female controls (AUC = 0.85, P < 0.0001). Combination of Linc-ROR, MEG3, SPRY4-IT1 and UCA1 expression levels could differentiate female patients with 95.2% sensitivity, 76.9% specificity and diagnostic power of 0.88 (P < 0.0001). The current study suggests the presence of a sex-based dysregulation of lncRNAs in patients with schizophrenia and their possible application as diagnostic biomarkers.
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Affiliation(s)
- Hamid Fallah
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Iman Azari
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Vahid Kholghi Oskooei
- Department of Laboratory Sciences, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Neuroscience Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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36
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Network Analysis of a Membrane-Enriched Brain Proteome across Stages of Alzheimer's Disease. Proteomes 2019; 7:proteomes7030030. [PMID: 31461916 PMCID: PMC6789842 DOI: 10.3390/proteomes7030030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 12/12/2022] Open
Abstract
Previous systems-based proteomic approaches have characterized alterations in protein co-expression networks of unfractionated asymptomatic (AsymAD) and symptomatic Alzheimer’s disease (AD) brains. However, it remains unclear how sample fractionation and sub-proteomic analysis influences the organization of these protein networks and their relationship to clinicopathological traits of disease. In this proof-of-concept study, we performed a systems-based sub-proteomic analysis of membrane-enriched post-mortem brain samples from pathology-free control, AsymAD, and AD brains (n = 6 per group). Label-free mass spectrometry based on peptide ion intensity was used to quantify the 18 membrane-enriched fractions. Differential expression and weighted protein co-expression network analysis (WPCNA) were then used to identify and characterize modules of co-expressed proteins most significantly altered between the groups. We identified a total of 27 modules of co-expressed membrane-associated proteins. In contrast to the unfractionated proteome, these networks did not map strongly to cell-type specific markers. Instead, these modules were principally organized by their associations with a wide variety of membrane-bound compartments and organelles. Of these, the mitochondrion was associated with the greatest number of modules, followed by modules linked to the cell surface compartment. In addition, we resolved networks with strong associations to the endoplasmic reticulum, Golgi apparatus, and other membrane-bound organelles. A total of 14 of the 27 modules demonstrated significant correlations with clinical and pathological AD phenotypes. These results revealed that the proteins within individual compartments feature a heterogeneous array of AD-associated expression patterns, particularly during the preclinical stages of disease. In conclusion, this systems-based analysis of the membrane-associated AsymAD brain proteome yielded a unique network organization highly linked to cellular compartmentalization. Further study of this membrane-associated proteome may reveal novel insight into the complex pathways governing the earliest stages of disease.
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37
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Koopmans F, van Nierop P, Andres-Alonso M, Byrnes A, Cijsouw T, Coba MP, Cornelisse LN, Farrell RJ, Goldschmidt HL, Howrigan DP, Hussain NK, Imig C, de Jong APH, Jung H, Kohansalnodehi M, Kramarz B, Lipstein N, Lovering RC, MacGillavry H, Mariano V, Mi H, Ninov M, Osumi-Sutherland D, Pielot R, Smalla KH, Tang H, Tashman K, Toonen RFG, Verpelli C, Reig-Viader R, Watanabe K, van Weering J, Achsel T, Ashrafi G, Asi N, Brown TC, De Camilli P, Feuermann M, Foulger RE, Gaudet P, Joglekar A, Kanellopoulos A, Malenka R, Nicoll RA, Pulido C, de Juan-Sanz J, Sheng M, Südhof TC, Tilgner HU, Bagni C, Bayés À, Biederer T, Brose N, Chua JJE, Dieterich DC, Gundelfinger ED, Hoogenraad C, Huganir RL, Jahn R, Kaeser PS, Kim E, Kreutz MR, McPherson PS, Neale BM, O'Connor V, Posthuma D, Ryan TA, Sala C, Feng G, Hyman SE, Thomas PD, Smit AB, Verhage M. SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron 2019; 103:217-234.e4. [PMID: 31171447 DOI: 10.1016/j.neuron.2019.05.002] [Citation(s) in RCA: 395] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/02/2019] [Accepted: 04/30/2019] [Indexed: 12/23/2022]
Abstract
Synapses are fundamental information-processing units of the brain, and synaptic dysregulation is central to many brain disorders ("synaptopathies"). However, systematic annotation of synaptic genes and ontology of synaptic processes are currently lacking. We established SynGO, an interactive knowledge base that accumulates available research about synapse biology using Gene Ontology (GO) annotations to novel ontology terms: 87 synaptic locations and 179 synaptic processes. SynGO annotations are exclusively based on published, expert-curated evidence. Using 2,922 annotations for 1,112 genes, we show that synaptic genes are exceptionally well conserved and less tolerant to mutations than other genes. Many SynGO terms are significantly overrepresented among gene variations associated with intelligence, educational attainment, ADHD, autism, and bipolar disorder and among de novo variants associated with neurodevelopmental disorders, including schizophrenia. SynGO is a public, universal reference for synapse research and an online analysis platform for interpretation of large-scale -omics data (https://syngoportal.org and http://geneontology.org).
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Affiliation(s)
- Frank Koopmans
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands; Department of Molecular and Cellular Neurobiology, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Pim van Nierop
- Department of Molecular and Cellular Neurobiology, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Maria Andres-Alonso
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; Leibniz Group "Dendritic Organelles and Synaptic Function," ZMNH, University MC, Hamburg, 20251, Germany
| | - Andrea Byrnes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tony Cijsouw
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Marcelo P Coba
- Zilkha Neurogenetic Institute and Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90333, USA
| | - L Niels Cornelisse
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Ryan J Farrell
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hana L Goldschmidt
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel P Howrigan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Natasha K Hussain
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Cordelia Imig
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Arthur P H de Jong
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Hwajin Jung
- Center for Synaptic Brain Dysfunctions, IBS, and Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | - Mahdokht Kohansalnodehi
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Barbara Kramarz
- Functional Gene Annotation, Institute of Cardiovascular Science, UCL, London WC1E 6JF, UK
| | - Noa Lipstein
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Ruth C Lovering
- Functional Gene Annotation, Institute of Cardiovascular Science, UCL, London WC1E 6JF, UK
| | - Harold MacGillavry
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Vittoria Mariano
- Department of Fundamental Neurosciences, University of Lausanne, 1006 Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Huaiyu Mi
- Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Momchil Ninov
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Rainer Pielot
- Leibniz Institute for Neurobiology, CBBS and Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Karl-Heinz Smalla
- Leibniz Institute for Neurobiology, CBBS and Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Haiming Tang
- Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Katherine Tashman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruud F G Toonen
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Chiara Verpelli
- CNR Neuroscience Institute Milan and Department of Biotechnology and Translational Medicine, University of Milan, 20129 Milan, Italy
| | - Rita Reig-Viader
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, 08025 Barcelona, Spain; Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Vallès, Spain
| | - Kyoko Watanabe
- Department Complex Trait Genetics, CNCR, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands; Department of Clinical Genetics, UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Jan van Weering
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, University of Lausanne, 1006 Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Ghazaleh Ashrafi
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nimra Asi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tyler C Brown
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pietro De Camilli
- Departments of Neuroscience and Cell Biology, HHMI, Kavli Institute for Neuroscience, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Marc Feuermann
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Rebecca E Foulger
- Functional Gene Annotation, Institute of Cardiovascular Science, UCL, London WC1E 6JF, UK
| | - Pascale Gaudet
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Anoushka Joglekar
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Alexandros Kanellopoulos
- Department of Fundamental Neurosciences, University of Lausanne, 1006 Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Robert Malenka
- Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Roger A Nicoll
- Departments of Cellular and Molecular Pharmacology and Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Camila Pulido
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jaime de Juan-Sanz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Morgan Sheng
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Hagen U Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, 1006 Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Àlex Bayés
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, 08025 Barcelona, Spain; Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Vallès, Spain
| | - Thomas Biederer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - John Jia En Chua
- Department of Physiology, Yong Loo Lin School of Medicine and Neurobiology/Ageing Program, Life Sciences Institute, National University of Singapore and Institute of Molecular and Cell Biology, A(∗)STAR, Singapore, Singapore
| | - Daniela C Dieterich
- Leibniz Institute for Neurobiology, CBBS and Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Eckart D Gundelfinger
- Leibniz Institute for Neurobiology, CBBS and Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Casper Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Richard L Huganir
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Reinhard Jahn
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Pascal S Kaeser
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, IBS, and Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; Leibniz Group "Dendritic Organelles and Synaptic Function," ZMNH, University MC, Hamburg, 20251, Germany
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Ben M Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vincent O'Connor
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Danielle Posthuma
- Department Complex Trait Genetics, CNCR, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands; Department of Clinical Genetics, UMC Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Timothy A Ryan
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Carlo Sala
- CNR Neuroscience Institute Milan and Department of Biotechnology and Translational Medicine, University of Milan, 20129 Milan, Italy
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven E Hyman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands.
| | - Matthijs Verhage
- Department of Functional Genomics, CNCR, VU University and UMC Amsterdam, 1081 HV Amsterdam, the Netherlands.
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Wilson RS, Rauniyar N, Sakaue F, Lam TT, Williams KR, Nairn AC. Development of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD). Proteomes 2019; 7:12. [PMID: 30986977 PMCID: PMC6630806 DOI: 10.3390/proteomes7020012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 02/07/2023] Open
Abstract
The postsynaptic density (PSD) is a structural, electron-dense region of excitatory glutamatergic synapses, which is involved in a variety of cellular and signaling processes in neurons. The PSD is comprised of a large network of proteins, many of which have been implicated in a wide variety of neuropsychiatric disorders. Biochemical fractionation combined with mass spectrometry analyses have enabled an in-depth understanding of the protein composition of the PSD. However, the PSD composition may change rapidly in response to stimuli, and robust and reproducible methods to thoroughly quantify changes in protein abundance are warranted. Here, we report on the development of two types of targeted mass spectrometry-based assays for quantitation of PSD-enriched proteins. In total, we quantified 50 PSD proteins in a targeted, parallel reaction monitoring (PRM) assay using heavy-labeled, synthetic internal peptide standards and identified and quantified over 2100 proteins through a pre-determined spectral library using a data-independent acquisition (DIA) approach in PSD fractions isolated from mouse cortical brain tissue.
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Affiliation(s)
- Rashaun S Wilson
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- W.M Keck Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06511, USA.
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | | | - Fumika Sakaue
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Tokyo 113-8519, Japan.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- W.M Keck Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06511, USA.
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
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The Structural Model: a theory linking connections, plasticity, pathology, development and evolution of the cerebral cortex. Brain Struct Funct 2019; 224:985-1008. [PMID: 30739157 PMCID: PMC6500485 DOI: 10.1007/s00429-019-01841-9] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/29/2019] [Indexed: 12/21/2022]
Abstract
The classical theory of cortical systematic variation has been independently described in reptiles, monotremes, marsupials and placental mammals, including primates, suggesting a common bauplan in the evolution of the cortex. The Structural Model is based on the systematic variation of the cortex and is a platform for advancing testable hypotheses about cortical organization and function across species, including humans. The Structural Model captures the overall laminar structure of areas by dividing the cortical architectonic continuum into discrete categories (cortical types), which can be used to test hypotheses about cortical organization. By type, the phylogenetically ancient limbic cortices-which form a ring at the base of the cerebral hemisphere-are agranular if they lack layer IV, or dysgranular if they have an incipient granular layer IV. Beyond the dysgranular areas, eulaminate type cortices have six layers. The number and laminar elaboration of eulaminate areas differ depending on species or cortical system within a species. The construct of cortical type retains the topology of the systematic variation of the cortex and forms the basis for a predictive Structural Model, which has successfully linked cortical variation to the laminar pattern and strength of cortical connections, the continuum of plasticity and stability of areas, the regularities in the distribution of classical and novel markers, and the preferential vulnerability of limbic areas to neurodegenerative and psychiatric diseases. The origin of cortical types has been recently traced to cortical development, and helps explain the variability of diseases with an onset in ontogeny.
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Grant SGN. The Synaptomic Theory of Behavior and Brain Disease. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2019; 83:45-56. [PMID: 30886054 DOI: 10.1101/sqb.2018.83.037887] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The purpose of this article is to outline a new molecular and synaptic theory of behavior called the "synaptomic theory," named because it is centered on the synaptome-the complement of synapses in the brain. Synaptomic theory posits that synapses are structures of high molecular complexity and vast diversity that are observable in maps of the brain and that these synaptome maps are fundamental to behavior. Synaptome maps are a means of writing or storing information that can be retrieved by the patterns of activity that stimulate synapses. Synaptome maps have the capacity to store large amounts of information, including multiple representations within the same map. The dynamic properties of synapses allow synaptome maps to store dynamic sequences of representations that could serve to program behavioral sequences. Synaptome maps are genetically programmed and experience-dependent, thereby storing innate and learned behaviors, respectively. Although learning occurs by modification of the synapse proteome, it does not require long-term potentiation (LTP) of synaptic weight or growth of new synapses, and the theory predicts that LTP modulates information recall. The spatial architecture of synaptome maps arise from an underlying molecular hierarchy linking the genome to the supramolecular assembly of proteins into complexes and supercomplexes. This molecular hierarchy can explain how genome evolution results in the behavioral repertoire of the organism. Mutations disrupting this molecular hierarchy change the architecture of synaptome maps, potentially accounting for the behavioral phenotypes associated with neurological and psychiatric disorders.
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Affiliation(s)
- Seth G N Grant
- Genes to Cognition Program, Centre for Clinical Brain Sciences, Edinburgh University, Edinburgh BioQuarter, Edinburgh EH16 4SB, United Kingdom
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41
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Fernández-Irigoyen J, Corrales F, Santamaría E. The Human Brain Proteome Project: Biological and Technological Challenges. Methods Mol Biol 2019; 2044:3-23. [PMID: 31432403 DOI: 10.1007/978-1-4939-9706-0_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Brain proteomics has become a method of choice that allows zooming-in where neuropathophysiological alterations are taking place, detecting protein mediators that might eventually be measured in cerebrospinal fluid (CSF) as potential neuropathologically derived biomarkers. Following this hypothesis, mass spectrometry-based neuroproteomics has emerged as a powerful approach to profile neural proteomes derived from brain structures and CSF in order to map the extensive protein catalog of the human brain. This chapter provides a historical perspective on the Human Brain Proteome Project (HBPP), some recommendation to the experimental design in neuroproteomic projects, and a brief description of relevant technological and computational innovations that are emerging in the neurobiology field thanks to the proteomics community. Importantly, this chapter highlights recent discoveries from the biology- and disease-oriented branch of the HBPP (B/D-HBPP) focused on spatiotemporal proteomic characterizations of mouse models of neurodegenerative diseases, elucidation of proteostatic networks in different types of dementia, the characterization of unresolved clinical phenotypes, and the discovery of novel biomarker candidates in CSF.
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Affiliation(s)
- Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory,, Proteored-ISCIII, CIBERehd, Madrid, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
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Cijsouw T, Ramsey AM, Lam TT, Carbone BE, Blanpied TA, Biederer T. Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins. Proteomes 2018; 6:proteomes6040048. [PMID: 30487426 PMCID: PMC6313906 DOI: 10.3390/proteomes6040048] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/15/2018] [Accepted: 11/18/2018] [Indexed: 12/21/2022] Open
Abstract
Synapses are specialized neuronal cell-cell contacts that underlie network communication in the mammalian brain. Across neuronal populations and circuits, a diverse set of synapses is utilized, and they differ in their molecular composition to enable heterogenous connectivity patterns and functions. In addition to pre- and post-synaptic specializations, the synaptic cleft is now understood to be an integral compartment of synapses that contributes to their structural and functional organization. Aiming to map the cleft proteome, this study applied a peroxidase-mediated proximity labeling approach and used the excitatory synaptic cell adhesion protein SynCAM 1 fused to horseradish peroxidase (HRP) as a reporter in cultured cortical neurons. This reporter marked excitatory synapses as measured by confocal microcopy and was targeted to the edge zone of the synaptic cleft as determined using 3D dSTORM super-resolution imaging. Proximity labeling with a membrane-impermeant biotin-phenol compound restricted labeling to the cell surface, and Label-Free Quantitation (LFQ) mass spectrometry combined with ratiometric HRP tagging of membrane vs. synaptic surface proteins was used to identify the proteomic content of excitatory clefts. Novel cleft candidates were identified, and Receptor-type tyrosine-protein phosphatase zeta was selected and successfully validated. This study supports the robust applicability of peroxidase-mediated proximity labeling for synaptic cleft proteomics and its potential for understanding synapse heterogeneity in health and changes in diseases such as psychiatric disorders and addiction.
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Affiliation(s)
- Tony Cijsouw
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - Austin M Ramsey
- Department of Physiology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- W.M. Keck Biotechnology Resource Laboratory, Yale University School of Medicine, 300 George Street, New Haven, CT 06511, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Beatrice E Carbone
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - Thomas A Blanpied
- Department of Physiology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Thomas Biederer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA.
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43
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McLachlan F, Sires AM, Abbott CM. The role of translation elongation factor eEF1 subunits in neurodevelopmental disorders. Hum Mutat 2018; 40:131-141. [PMID: 30370994 DOI: 10.1002/humu.23677] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/16/2018] [Accepted: 10/23/2018] [Indexed: 11/06/2022]
Abstract
The multi-subunit eEF1 complex plays a crucial role in de novo protein synthesis. The central functional component of the complex is eEF1A, which occurs as two independently encoded variants with reciprocal expression patterns: whilst eEF1A1 is widely expressed, eEF1A2 is found only in neurons and muscle. Heterozygous mutations in the gene encoding eEF1A2, EEF1A2, have recently been shown to cause epilepsy, autism, and intellectual disability. The remaining subunits of the eEF1 complex, eEF1Bα, eEF1Bδ, eEF1Bγ, and valyl-tRNA synthetase (VARS), together form the GTP exchange factor for eEF1A and are ubiquitously expressed, in keeping with their housekeeping role. However, mutations in the genes encoding these subunits EEF1B2 (eEF1Bα), EEF1D (eEF1Bδ), and VARS (valyl-tRNA synthetase) have also now been identified as causes of neurodevelopmental disorders. In this review, we describe the mutations identified so far in comparison with the degree of normal variation in each gene, and the predicted consequences of the mutations on the functions of the proteins and their isoforms. We discuss the likely effects of the mutations in the context of the role of protein synthesis in neuronal development.
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Affiliation(s)
- Fiona McLachlan
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Anna Martinez Sires
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Catherine M Abbott
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
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44
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Zwart R, Mazzo F, Sher E. Microtransplantation of human brain receptors into oocytes to tackle key questions in drug discovery. Drug Discov Today 2018; 24:533-543. [PMID: 30395928 DOI: 10.1016/j.drudis.2018.10.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/18/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
Abstract
It is important in drug discovery to demonstrate that activity of novel drugs found by screening on recombinant receptors translates to activity on native human receptors in brain areas affected by disease. In this review, we summarise the development and use of the microtransplantation technique. Native receptors are reconstituted from human brain tissues into oocytes from the frog Xenopus laevis where they can be functionally assessed. Oocytes microtransplanted with hippocampal tissue from an epileptic patient were used to demonstrate that new antiepileptic agents act on receptors in diseased tissue. Furthermore, frozen post-mortem human tissues were used to show that drugs are active on receptors in brain areas associated with a disease; but not in areas associated with side effects.
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Affiliation(s)
- Ruud Zwart
- Eli Lilly, Lilly Research Centre, Erl Wood Manor, Sunninghill Road, Windlesham, GU20 6PH, UK.
| | - Francesca Mazzo
- Eli Lilly, Lilly Research Centre, Erl Wood Manor, Sunninghill Road, Windlesham, GU20 6PH, UK
| | - Emanuele Sher
- Eli Lilly, Lilly Research Centre, Erl Wood Manor, Sunninghill Road, Windlesham, GU20 6PH, UK
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45
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Bayés À. Setting the stage for a role of the postsynaptic proteome in inherited neurometabolic disorders. J Inherit Metab Dis 2018; 41:1093-1101. [PMID: 30132229 PMCID: PMC6326985 DOI: 10.1007/s10545-018-0240-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/26/2018] [Accepted: 08/02/2018] [Indexed: 12/14/2022]
Abstract
Neurotransmitter diseases are a well-defined group of metabolic conditions caused, in most instances, by genes specifically expressed in the presynaptic button. Better understanding of presynaptic molecular physiology, both in normal and pathological conditions, should help develop therapeutical strategies. The clinical relevance of the presynapse in inherited metabolic disorders is in glaring contrast with that of the postsynaptic component, which so far does not seem to play a relevant role in these disorders. This is somewhat surprising, as postsynaptic proteins are known to be involved in many nervous system diseases, particularly in neurodevelopmental and psychiatric disorders. The goal of this article is to explore if defects in the sophisticated postsynaptic machinery could also have a role in neurometabolic disorders.
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Affiliation(s)
- Àlex Bayés
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), C/Sant Antoni M. Claret, 167, 08025, Barcelona, Spain.
- Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain.
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46
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Zhu F, Cizeron M, Qiu Z, Benavides-Piccione R, Kopanitsa MV, Skene NG, Koniaris B, DeFelipe J, Fransén E, Komiyama NH, Grant SGN. Architecture of the Mouse Brain Synaptome. Neuron 2018; 99:781-799.e10. [PMID: 30078578 PMCID: PMC6117470 DOI: 10.1016/j.neuron.2018.07.007] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 06/22/2018] [Accepted: 07/03/2018] [Indexed: 12/11/2022]
Abstract
Synapses are found in vast numbers in the brain and contain complex proteomes. We developed genetic labeling and imaging methods to examine synaptic proteins in individual excitatory synapses across all regions of the mouse brain. Synapse catalogs were generated from the molecular and morphological features of a billion synapses. Each synapse subtype showed a unique anatomical distribution, and each brain region showed a distinct signature of synapse subtypes. Whole-brain synaptome cartography revealed spatial architecture from dendritic to global systems levels and previously unknown anatomical features. Synaptome mapping of circuits showed correspondence between synapse diversity and structural and functional connectomes. Behaviorally relevant patterns of neuronal activity trigger spatiotemporal postsynaptic responses sensitive to the structure of synaptome maps. Areas controlling higher cognitive function contain the greatest synapse diversity, and mutations causing cognitive disorders reorganized synaptome maps. Synaptome technology and resources have wide-ranging application in studies of the normal and diseased brain.
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Affiliation(s)
- Fei Zhu
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Mélissa Cizeron
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Institut NeuroMyoGène, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5310, INSERM U-1217, 69008 Lyon, France
| | - Zhen Qiu
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Ruth Benavides-Piccione
- Instituto Cajal (CSIC) 28002 Madrid, Centro de Tecnología Biomédica (UPM) 28223 Madrid; CIBERNED, ISCIII, 28031 Madrid, Spain
| | - Maksym V Kopanitsa
- Synome Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK; UK Dementia Research Institute, Imperial College London, London W12 0NN, UK
| | - Nathan G Skene
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK; Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Babis Koniaris
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Javier DeFelipe
- Instituto Cajal (CSIC) 28002 Madrid, Centro de Tecnología Biomédica (UPM) 28223 Madrid; CIBERNED, ISCIII, 28031 Madrid, Spain
| | - Erik Fransén
- Department of Computational Science and Technology, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Noboru H Komiyama
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Seth G N Grant
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
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47
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Roy M, Sorokina O, McLean C, Tapia-González S, DeFelipe J, Armstrong JD, Grant SGN. Regional Diversity in the Postsynaptic Proteome of the Mouse Brain. Proteomes 2018; 6:proteomes6030031. [PMID: 30071621 PMCID: PMC6161190 DOI: 10.3390/proteomes6030031] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 12/14/2022] Open
Abstract
The proteome of the postsynaptic terminal of excitatory synapses comprises over one thousand proteins in vertebrate species and plays a central role in behavior and brain disease. The brain is organized into anatomically distinct regions and whether the synapse proteome differs across these regions is poorly understood. Postsynaptic proteomes were isolated from seven forebrain and hindbrain regions in mice and their composition determined using proteomic mass spectrometry. Seventy-four percent of proteins showed differential expression and each region displayed a unique compositional signature. These signatures correlated with the anatomical divisions of the brain and their embryological origins. Biochemical pathways controlling plasticity and disease, protein interaction networks and individual proteins involved with cognition all showed differential regional expression. Combining proteomic and connectomic data shows that interconnected regions have specific proteome signatures. Diversity in synapse proteome composition is key feature of mouse and human brain structure.
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Affiliation(s)
- Marcia Roy
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
| | - Oksana Sorokina
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.
| | - Colin McLean
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK.
| | - Silvia Tapia-González
- Departamento de Neurobiología Funcional y de Sistemas, Instituto Cajal (CSIC), Ave. Doctor Arce 37, 28002 Madrid and Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica (UPM), 28223 Pozuelo de Alarcón, Madrid, Spain.
| | - Javier DeFelipe
- Departamento de Neurobiología Funcional y de Sistemas, Instituto Cajal (CSIC), Ave. Doctor Arce 37, 28002 Madrid and Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica (UPM), 28223 Pozuelo de Alarcón, Madrid, Spain.
| | | | - Seth G N Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
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48
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Scholtens LH, van den Heuvel MP. Multimodal Connectomics in Psychiatry: Bridging Scales From Micro to Macro. BIOLOGICAL PSYCHIATRY: COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2018; 3:767-776. [PMID: 29779726 DOI: 10.1016/j.bpsc.2018.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 01/21/2023]
Abstract
The human brain is a highly complex system, with a large variety of microscale cellular morphologies and macroscale global properties. Working at multiple scales, it forms an efficient system for processing and integration of multimodal information. Studies have repeatedly demonstrated strong associations between modalities of both microscales and macroscales of brain organization. These consistent observations point toward potential common organization principles where regions with a microscale architecture supportive of a larger computational load have more and stronger connections in the brain network on the macroscale. Conversely, disruptions observed on one organizational scale could modulate the other. First neuropsychiatric micro-macro comparisons in, among other conditions, Alzheimer's disease and schizophrenia, have, for example, shown overlapping alterations across both scales. We give an overview of recent findings on associations between microscale and macroscale organization observed in the healthy brain, followed by a summary of microscale and macroscale findings reported in the context of brain disorders. We conclude with suggestions for future multiscale connectome comparisons linking multiple scales and modalities of organization and suggest how such comparisons could contribute to a more complete fundamental understanding of brain organization and associated disease-related alterations.
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Affiliation(s)
- Lianne H Scholtens
- Connectome Lab, Department of Complex Traits Genetics, Center for Neurogenomics and Cognitive Research, VU Amsterdam, Amsterdam, The Netherlands
| | - Martijn P van den Heuvel
- Connectome Lab, Department of Complex Traits Genetics, Center for Neurogenomics and Cognitive Research, VU Amsterdam, Amsterdam, The Netherlands; Department of Clinical Genetics, VU University Medical Center, Amsterdam Neuroscience, Amsterdam, The Netherlands.
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49
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Gibbons A, Udawela M, Dean B. Non-Coding RNA as Novel Players in the Pathophysiology of Schizophrenia. Noncoding RNA 2018; 4:E11. [PMID: 29657307 PMCID: PMC6027250 DOI: 10.3390/ncrna4020011] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 03/29/2018] [Accepted: 04/06/2018] [Indexed: 12/22/2022] Open
Abstract
Schizophrenia is associated with diverse changes in the brain's transcriptome and proteome. Underlying these changes is the complex dysregulation of gene expression and protein production that varies both spatially across brain regions and temporally with the progression of the illness. The growing body of literature showing changes in non-coding RNA in individuals with schizophrenia offers new insights into the mechanisms causing this dysregulation. A large number of studies have reported that the expression of microRNA (miRNA) is altered in the brains of individuals with schizophrenia. This evidence is complemented by findings that single nucleotide polymorphisms (SNPs) in miRNA host gene sequences can confer an increased risk of developing the disorder. Additionally, recent evidence suggests the expression of other non-coding RNAs, such as small nucleolar RNA and long non-coding RNA, may also be affected in schizophrenia. Understanding how these changes in non-coding RNAs contribute to the development and progression of schizophrenia offers potential avenues for the better treatment and diagnosis of the disorder. This review will focus on the evidence supporting the involvement of non-coding RNA in schizophrenia and its therapeutic potential.
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Affiliation(s)
- Andrew Gibbons
- The Florey Institute for Neuroscience and Mental Health, 30 Royal Parade, Parkville, VIC 3052, Australia.
- The Department of Psychiatry, the University of Melbourne, Parkville, Victoria, Australia.
| | - Madhara Udawela
- The Florey Institute for Neuroscience and Mental Health, 30 Royal Parade, Parkville, VIC 3052, Australia.
| | - Brian Dean
- The Florey Institute for Neuroscience and Mental Health, 30 Royal Parade, Parkville, VIC 3052, Australia.
- The Centre for Mental Health, Swinburne University of Technology, Hawthorn, Victoria, Australia.
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50
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Suchowerska AK, Fok S, Stefen H, Gunning PW, Hardeman EC, Power J, Fath T. Developmental Profiling of Tropomyosin Expression in Mouse Brain Reveals Tpm4.2 as the Major Post-synaptic Tropomyosin in the Mature Brain. Front Cell Neurosci 2017; 11:421. [PMID: 29311841 PMCID: PMC5743921 DOI: 10.3389/fncel.2017.00421] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/14/2017] [Indexed: 12/14/2022] Open
Abstract
Nerve cell connections, formed in the developing brain of mammals, undergo a well-programmed process of maturation with changes in their molecular composition over time. The major structural element at the post-synaptic specialization is the actin cytoskeleton, which is composed of different populations of functionally distinct actin filaments. Previous studies, using ultrastructural and light imaging techniques have established the presence of different actin filament populations at the post-synaptic site. However, it remains unknown, how these different actin filament populations are defined and how their molecular composition changes over time. In the present study, we have characterized changes in a core component of actin filaments, the tropomyosin (Tpm) family of actin-associated proteins from embryonal stage to the adult stage. Using biochemical fractionation of mouse brain tissue, we identified the tropomyosin Tpm4.2 as the major post-synaptic Tpm. Furthermore, we found age-related differences in the composition of Tpms at the post-synaptic compartment. Our findings will help to guide future studies that aim to define the functional properties of actin filaments at different developmental stages in the mammalian brain.
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Affiliation(s)
- Alexandra K Suchowerska
- Neurodegeneration and Repair Unit, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sandra Fok
- Neurodegeneration and Repair Unit, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Holly Stefen
- Neurodegeneration and Repair Unit, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,Neuron Culture Core Facility, University of New South Wales, SydneyNSW, Australia
| | - Peter W Gunning
- Cellular and Genetic Medicine Unit, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Edna C Hardeman
- Cellular and Genetic Medicine Unit, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - John Power
- Translational Neuroscience Facility, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Thomas Fath
- Neurodegeneration and Repair Unit, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,Neuron Culture Core Facility, University of New South Wales, SydneyNSW, Australia
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