101
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Affiliation(s)
- Kristina D Micheva
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Richard J Weinberg
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen J Smith
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA. .,Allen Institute for Brain Science, Seattle, WA, USA
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102
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Cizeron M, Qiu Z, Koniaris B, Gokhale R, Komiyama NH, Fransén E, Grant SGN. A brainwide atlas of synapses across the mouse life span. Science 2020; 369:270-275. [PMID: 32527927 PMCID: PMC7115813 DOI: 10.1126/science.aba3163] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 05/19/2020] [Indexed: 01/03/2023]
Abstract
Synapses connect neurons together to form the circuits of the brain, and their molecular composition controls innate and learned behavior. We analyzed the molecular and morphological diversity of 5 billion excitatory synapses at single-synapse resolution across the mouse brain from birth to old age. A continuum of changes alters synapse composition in all brain regions across the life span. Expansion in synapse diversity produces differentiation of brain regions until early adulthood, and compositional changes cause dedifferentiation in old age. The spatiotemporal synaptome architecture of the brain potentially accounts for life-span transitions in intellectual ability, memory, and susceptibility to behavioral disorders.
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Affiliation(s)
- 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
| | - Babis Koniaris
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
- School of Computing, Edinburgh Napier University, Edinburgh EH10 5DT, UK
| | - Ragini Gokhale
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Noboru H Komiyama
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Erik Fransén
- Department of Computational Science and Technology, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
- Science for Life Laboratory, KTH Royal Institute of Technology, SE-171 65 Solna, Sweden
| | - Seth G N Grant
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
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103
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Friedman R. Measurements of neuronal morphological variation across the rat neocortex. Neurosci Lett 2020; 734:135077. [PMID: 32485285 DOI: 10.1016/j.neulet.2020.135077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/20/2020] [Indexed: 11/16/2022]
Abstract
Neuron morphology is highly variable across the mammalian brain. It is thought that these attributes of neuronal cell shape, such as soma surface area and branching frequency, are determined by biological function and information processing. In this study, a large data set of neurons across the rat neocortex were clustered by their anatomical characters for evidence of distinctiveness among neocortical regions and the somatosensory layers. This data set of neuronal morphologies was compiled from 31 different lab sources with a validation procedure so that data records are potentially comparable across research studies. With this large set of heterogeneous data and by clustering analysis, this study shows that neuronal morphological traits overlap among neocortical and somatosensory regions. In the context of past neuroanatomical studies, this result is not congruent with tissue level analysis and strongly suggests further sampling of neuronal data to lessen the effect of confounding factors, such as the influence of different methodologies from use of heterogeneous samples of neuronal data.
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Affiliation(s)
- Robert Friedman
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States.
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104
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Nanostructural Diversity of Synapses in the Mammalian Spinal Cord. Sci Rep 2020; 10:8189. [PMID: 32424125 PMCID: PMC7235094 DOI: 10.1038/s41598-020-64874-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/21/2020] [Indexed: 11/25/2022] Open
Abstract
Functionally distinct synapses exhibit diverse and complex organisation at molecular and nanoscale levels. Synaptic diversity may be dependent on developmental stage, anatomical locus and the neural circuit within which synapses reside. Furthermore, astrocytes, which align with pre and post-synaptic structures to form ‘tripartite synapses’, can modulate neural circuits and impact on synaptic organisation. In this study, we aimed to determine which factors impact the diversity of excitatory synapses throughout the lumbar spinal cord. We used PSD95-eGFP mice, to visualise excitatory postsynaptic densities (PSDs) using high-resolution and super-resolution microscopy. We reveal a detailed and quantitative map of the features of excitatory synapses in the lumbar spinal cord, detailing synaptic diversity that is dependent on developmental stage, anatomical region and whether associated with VGLUT1 or VGLUT2 terminals. We report that PSDs are nanostructurally distinct between spinal laminae and across age groups. PSDs receiving VGLUT1 inputs also show enhanced nanostructural complexity compared with those receiving VGLUT2 inputs, suggesting pathway-specific diversity. Finally, we show that PSDs exhibit greater nanostructural complexity when part of tripartite synapses, and we provide evidence that astrocytic activation enhances PSD95 expression. Taken together, these results provide novel insights into the regulation and diversification of synapses across functionally distinct spinal regions and advance our general understanding of the ‘rules’ governing synaptic nanostructural organisation.
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105
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Abstract
The NMDA subtype of ionotropic glutamate receptor is a sophisticated integrator and transducer of information. NMDAR-mediated signals control diverse processes across the life course, including synaptogenesis and synaptic plasticity, as well as contribute to excitotoxic processes in neurological disorders. At the basic biophysical level, the NMDAR is a coincidence detector, requiring the co-presence of agonist, co-agonist, and membrane depolarization in order to open. However, the NMDAR is not merely a conduit for ions to flow through; it is linked on the cytoplasmic side to a large network of signaling and scaffolding proteins, primarily via the C-terminal domain of NMDAR GluN2 subunits. These physical interactions help to organize the signaling cascades downstream of NMDAR activation. Notably, the NMDAR does not come in a single form: the subunit composition of the NMDAR, particularly the GluN2 subunit subtype (GluN2A-D), influences the biophysical properties of the channel. Moreover, a growing number of studies have illuminated the extent to which GluN2 C-terminal interactions vary according to GluN2 subtype and how this impacts on the processes that NMDAR activity controls. We will review recent advances, controversies, and outstanding questions in this active area of research.
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Affiliation(s)
- Giles Hardingham
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK.,Centre for Discovery Brain Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh, EH8 9XD, UK
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106
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Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Syst 2020; 10:333-350.e14. [PMID: 32325033 PMCID: PMC7938770 DOI: 10.1016/j.cels.2020.03.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/25/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022]
Abstract
Connectivity webs mediate the unique biology of the mammalian brain. Yet, while cell circuit maps are increasingly available, knowledge of their underlying molecular networks remains limited. Here, we applied multi-dimensional biochemical fractionation with mass spectrometry and machine learning to survey endogenous macromolecules across the adult mouse brain. We defined a global "interactome" comprising over one thousand multi-protein complexes. These include hundreds of brain-selective assemblies that have distinct physical and functional attributes, show regional and cell-type specificity, and have links to core neurological processes and disorders. Using reciprocal pull-downs and a transgenic model, we validated a putative 28-member RNA-binding protein complex associated with amyotrophic lateral sclerosis, suggesting a coordinated function in alternative splicing in disease progression. This brain interaction map (BraInMap) resource facilitates mechanistic exploration of the unique molecular machinery driving core cellular processes of the central nervous system. It is publicly available and can be explored here https://www.bu.edu/dbin/cnsb/mousebrain/.
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Affiliation(s)
- Reza Pourhaghighi
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Peter E A Ash
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Sadhna Phanse
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Regina, Regina, SK, Canada; Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Florian Goebels
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Lucas Z M Hu
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Siwei Chen
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Yingying Zhang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Shayne D Wierbowski
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Samantha Boudeau
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | | | - Ramy H Malty
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Edyta Malolepsza
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Kalliopi Tsafou
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Aparna Nathan
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Graham Cromar
- Program in Molecular Medicine, Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Hongbo Guo
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ali Al Abdullatif
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Daniel J Apicco
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Lindsay A Becker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Ahmed Youssef
- Program in Bioinformatics, Boston University, Boston, MA, USA; Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Ryan Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Pierre C Havugimana
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA; Departments of Biochemistry and Biology, Boston University, Boston, MA, USA
| | - Carl A White
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS, Milan, Italy
| | - Camron D Bryant
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - John Parkinson
- Program in Molecular Medicine, Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Kasper Lage
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Haiyuan Yu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Gary D Bader
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Benjamin Wolozin
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA; Department of Neurology, Boston University School of Medicine, Boston, MA, USA; Program in Neuroscience, Boston University, Boston, MA, USA.
| | - Andrew Emili
- Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Program in Bioinformatics, Boston University, Boston, MA, USA; Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, MA, USA; Departments of Biochemistry and Biology, Boston University, Boston, MA, USA.
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107
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Similar Microglial Cell Densities across Brain Structures and Mammalian Species: Implications for Brain Tissue Function. J Neurosci 2020; 40:4622-4643. [PMID: 32253358 DOI: 10.1523/jneurosci.2339-19.2020] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/10/2019] [Accepted: 01/05/2020] [Indexed: 12/30/2022] Open
Abstract
Microglial cells play essential volume-related actions in the brain that contribute to the maturation and plasticity of neural circuits that ultimately shape behavior. Microglia can thus be expected to have similar cell sizes and even distribution both across brain structures and across species with different brain sizes. To test this hypothesis, we determined microglial cell densities (the inverse of cell size) using immunocytochemistry to Iba1 in samples of free cell nuclei prepared with the isotropic fractionator from brain structures of 33 mammalian species belonging to males and females of five different clades. We found that microglial cells constitute ∼7% of non-neuronal cells in different brain structures as well as in the whole brain of all mammalian species examined. Further, they vary little in cell density compared with neuronal cell densities within the cerebral cortex, across brain structures, across species within the same clade, and across mammalian clades. As a consequence, we find that one microglial cell services as few as one and as many as 100 neurons in different brain regions and species, depending on the local neuronal density. We thus conclude that the addition of microglial cells to mammalian brains is governed by mechanisms that constrain the size of these cells and have remained conserved over 200 million years of mammalian evolution. We discuss the probable consequences of such constrained size for brain function in health and disease.SIGNIFICANCE STATEMENT Microglial cells are resident macrophages of the CNS, with key functions in recycling synapses and maintaining the local environment in health and disease. We find that microglial cells occur in similar densities in the brains of different species and in the different structures of each individual brain, which indicates that these cells maintain a similar average size in mammalian evolution, suggesting in turn that the volume monitored by each microglial cell remains constant across mammals. Because the density of neurons is highly variable across the same brain structures and species, our finding implies that microglia-dependent functional recovery may be particularly difficult in those brain structures and species with high neuronal densities and therefore fewer microglial cells per neuron.
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108
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Moradi K, Ascoli GA. A comprehensive knowledge base of synaptic electrophysiology in the rodent hippocampal formation. Hippocampus 2020; 30:314-331. [PMID: 31472001 DOI: 10.1101/632760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/16/2019] [Accepted: 08/06/2019] [Indexed: 05/25/2023]
Abstract
The cellular and synaptic architecture of the rodent hippocampus has been described in thousands of peer-reviewed publications. However, no human- or machine-readable public catalog of synaptic electrophysiology data exists for this or any other neural system. Harnessing state-of-the-art information technology, we have developed a cloud-based toolset for identifying empirical evidence from the scientific literature pertaining to synaptic electrophysiology, for extracting the experimental data of interest, and for linking each entry to relevant text or figure excerpts. Mining more than 1,200 published journal articles, we have identified eight different signal modalities quantified by 90 different methods to measure synaptic amplitude, kinetics, and plasticity in hippocampal neurons. We have designed a data structure that both reflects the differences and maintains the existing relations among experimental modalities. Moreover, we mapped every annotated experiment to identified potential connections, that is, specific pairs of presynaptic and postsynaptic neuron types. To this aim, we leveraged Hippocampome.org, an open-access knowledge base of morphologically, electrophysiologically, and molecularly characterized neuron types in the rodent hippocampal formation. Specifically, we have implemented a computational pipeline to systematically translate neuron type properties into formal queries in order to find all compatible potential connections. With this system, we have collected nearly 40,000 synaptic data entities covering 88% of the 3,120 potential connections in Hippocampome.org. Correcting membrane potentials with respect to liquid junction potentials significantly reduced the difference between theoretical and experimental reversal potentials, thereby enabling the accurate conversion of all synaptic amplitudes to conductance. This data set allows for large-scale hypothesis testing of the general rules governing synaptic signals. To illustrate these applications, we confirmed several expected correlations between synaptic measurements and their covariates while suggesting previously unreported ones. We release all data open-source at Hippocampome.org in order to further research across disciplines.
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Affiliation(s)
- Keivan Moradi
- Neuroscience Program, Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia
| | - Giorgio A Ascoli
- Neuroscience Program, Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia
- Bioengineering Department, Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia
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109
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Moradi K, Ascoli GA. A comprehensive knowledge base of synaptic electrophysiology in the rodent hippocampal formation. Hippocampus 2020; 30:314-331. [PMID: 31472001 PMCID: PMC7875289 DOI: 10.1002/hipo.23148] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/16/2019] [Accepted: 08/06/2019] [Indexed: 01/14/2023]
Abstract
The cellular and synaptic architecture of the rodent hippocampus has been described in thousands of peer-reviewed publications. However, no human- or machine-readable public catalog of synaptic electrophysiology data exists for this or any other neural system. Harnessing state-of-the-art information technology, we have developed a cloud-based toolset for identifying empirical evidence from the scientific literature pertaining to synaptic electrophysiology, for extracting the experimental data of interest, and for linking each entry to relevant text or figure excerpts. Mining more than 1,200 published journal articles, we have identified eight different signal modalities quantified by 90 different methods to measure synaptic amplitude, kinetics, and plasticity in hippocampal neurons. We have designed a data structure that both reflects the differences and maintains the existing relations among experimental modalities. Moreover, we mapped every annotated experiment to identified potential connections, that is, specific pairs of presynaptic and postsynaptic neuron types. To this aim, we leveraged Hippocampome.org, an open-access knowledge base of morphologically, electrophysiologically, and molecularly characterized neuron types in the rodent hippocampal formation. Specifically, we have implemented a computational pipeline to systematically translate neuron type properties into formal queries in order to find all compatible potential connections. With this system, we have collected nearly 40,000 synaptic data entities covering 88% of the 3,120 potential connections in Hippocampome.org. Correcting membrane potentials with respect to liquid junction potentials significantly reduced the difference between theoretical and experimental reversal potentials, thereby enabling the accurate conversion of all synaptic amplitudes to conductance. This data set allows for large-scale hypothesis testing of the general rules governing synaptic signals. To illustrate these applications, we confirmed several expected correlations between synaptic measurements and their covariates while suggesting previously unreported ones. We release all data open-source at Hippocampome.org in order to further research across disciplines.
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Affiliation(s)
- Keivan Moradi
- Neuroscience Program, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA (USA)
| | - Giorgio A. Ascoli
- Neuroscience Program, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA (USA)
- Bioengineering Department, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA (USA)
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110
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111
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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: 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: 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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112
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Locating the engram: Should we look for plastic synapses or information-storing molecules? Neurobiol Learn Mem 2020; 169:107164. [PMID: 31945459 DOI: 10.1016/j.nlm.2020.107164] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/18/2019] [Accepted: 01/10/2020] [Indexed: 12/12/2022]
Abstract
Karl Lashley began the search for the engram nearly seventy years ago. In the time since, much has been learned but divisions remain. In the contemporary neurobiology of learning and memory, two profoundly different conceptions contend: the associative/connectionist (A/C) conception and the computational/representational (C/R) conception. Both theories ground themselves in the belief that the mind is emergent from the properties and processes of a material brain. Where these theories differ is in their description of what the neurobiological substrate of memory is and where it resides in the brain. The A/C theory of memory emphasizes the need to distinguish memory cognition from the memory engram and postulates that memory cognition is an emergent property of patterned neural activity routed through engram circuits. In this model, learning re-organizes synapse association strengths to guide future neural activity. Importantly, the version of the A/C theory advocated for here contends that synaptic change is not symbolic and, despite normally being necessary, is not sufficient for memory cognition. Instead, synaptic change provides the capacity and a blueprint for reinstating symbolic patterns of neural activity. Unlike the A/C theory, which posits that memory emerges at the circuit level, the C/R conception suggests that memory manifests at the level of intracellular molecular structures. In C/R theory, these intracellular structures are information-conveying and have properties compatible with the view that brain computation utilizes a read/write memory, functionally similar to that in a computer. New research has energized both sides and highlighted the need for new discussion. Both theories, the key questions each theory has yet to resolve and several potential paths forward are presented here.
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113
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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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114
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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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Tiam1 is Critical for Glutamatergic Synapse Structure and Function in the Hippocampus. J Neurosci 2019; 39:9306-9315. [PMID: 31597723 DOI: 10.1523/jneurosci.1566-19.2019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 02/06/2023] Open
Abstract
Mounting evidence suggests numerous glutamatergic synapse subtypes exist in the brain, and that these subtypes are likely defined by unique molecular regulatory mechanisms. Recent work has identified substantial divergence of molecular composition between commonly studied Schaffer collateral synapses and perforant path-dentate gyrus (DG) synapses of the hippocampus. However, little is known about the molecular mechanisms that may confer unique properties to perforant path-DG synapses. Here we investigate whether the RhoGEF (Rho guanine-nucleotide exchange factor) protein Tiam1 plays a unique role in the regulation of glutamatergic synapses in dentate granule neurons using a combination of molecular, electrophysiological, and imaging approaches in rat entorhino-hippocampal slices of both sexes. We find that inhibition of Tiam1 function in dentate granule neurons reduces synaptic AMPA receptor function and causes dendritic spines to adopt an elongated filopodia-like morphology. We also find that Tiam1's support of perforant path-DG synapse function is dependent on its GEF domain and identify a potential role for the auto-inhibitory PH domain of Tiam1 in regulating Tiam1 function at these synapses. In marked contrast, reduced Tiam1 expression in CA1 pyramidal neurons produced no effect on glutamatergic synapse development. Together, these data identify a critical role for Tiam1 in the hippocampus and reveal a unique Tiam1-mediated molecular program of glutamatergic synapse regulation in dentate granule neurons.SIGNIFICANCE STATEMENT Several lines of evidence independently point to the molecular diversity of glutamatergic synapses in the brain. Rho guanine-nucleotide exchange factor (RhoGEF) proteins as powerful modulators of glutamatergic synapse function have also become increasingly appreciated in recent years. Here we investigate the synaptic regulatory role of the RhoGEF protein Tiam1, whose expression appears to be remarkably enriched in granule neurons of the dentate gyrus. We find that Tiam1 plays a critical role in the development of glutamatergic perforant path-dentate gyrus synapses, but not in commonly studied in Schaffer collateral-CA1 synapses. Together, these data reveal a unique RhoGEF-mediated molecular program of glutamatergic synapse regulation in dentate granule neurons.
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Noguchi J, Nagaoka A, Hayama T, Ucar H, Yagishita S, Takahashi N, Kasai H. Bidirectional in vivo structural dendritic spine plasticity revealed by two-photon glutamate uncaging in the mouse neocortex. Sci Rep 2019; 9:13922. [PMID: 31558759 PMCID: PMC6763442 DOI: 10.1038/s41598-019-50445-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/11/2019] [Indexed: 11/18/2022] Open
Abstract
Most excitatory synapses in the brain form on dendritic spines. Two-photon uncaging of glutamate is widely utilized to characterize the structural plasticity of dendritic spines in brain slice preparations in vitro. In the present study, glutamate uncaging was used to investigate spine plasticity, for the first time, in vivo. A caged glutamate compound was applied to the surface of the mouse visual cortex in vivo, revealing the successful induction of spine enlargement by repetitive two-photon uncaging in a magnesium free solution. Notably, this induction occurred in a smaller fraction of spines in the neocortex in vivo (22%) than in hippocampal slices (95%). Once induced, the time course and mean long-term enlargement amplitudes were similar to those found in hippocampal slices. However, low-frequency (1–2 Hz) glutamate uncaging in the presence of magnesium caused spine shrinkage in a similar fraction (35%) of spines as in hippocampal slices, though spread to neighboring spines occurred less frequently than it did in hippocampal slices. Thus, the structural plasticity may occur similarly in the neocortex in vivo as in hippocampal slices, although it happened less frequently in our experimental conditions.
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Affiliation(s)
- Jun Noguchi
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, 187-8502, Japan. .,Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Akira Nagaoka
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tatsuya Hayama
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hasan Ucar
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.,International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Sho Yagishita
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.,International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Noriko Takahashi
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Department of Physiology, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Haruo Kasai
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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118
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Marhounová L, Kotrschal A, Kverková K, Kolm N, Němec P. Artificial selection on brain size leads to matching changes in overall number of neurons. Evolution 2019; 73:2003-2012. [PMID: 31339177 PMCID: PMC6772110 DOI: 10.1111/evo.13805] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/16/2022]
Abstract
Neurons are the basic computational units of the brain, but brain size is the predominant surrogate measure of brain functional capacity in comparative and cognitive neuroscience. This approach is based on the assumption that larger brains harbor higher numbers of neurons and their connections, and therefore have a higher information-processing capacity. However, recent studies have shown that brain mass may be less strongly correlated with neuron counts than previously thought. Till now, no experimental test has been conducted to examine the relationship between evolutionary changes in brain size and the number of brain neurons. Here, we provide such a test by comparing neuron number in artificial selection lines of female guppies (Poecilia reticulata) with >15% difference in relative brain mass and numerous previously demonstrated cognitive differences. Using the isotropic fractionator, we demonstrate that large-brained females have a higher overall number of neurons than small-brained females, but similar neuronal densities. Importantly, this difference holds also for the telencephalon, a key region for cognition. Our study provides the first direct experimental evidence that selection for brain mass leads to matching changes in number of neurons and shows that brain size evolution is intimately linked to the evolution of neuron number and cognition.
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Affiliation(s)
- Lucie Marhounová
- Department of Zoology, Faculty of ScienceCharles University12844PragueCzech Republic
| | - Alexander Kotrschal
- Behavioural Ecology GroupDepartment of Animal Sciences6708wdWageningenNetherlands
- Department of Zoology/EthologyStockholm University10691StockholmSweden
| | - Kristina Kverková
- Department of Zoology, Faculty of ScienceCharles University12844PragueCzech Republic
| | - Niclas Kolm
- Department of Zoology/EthologyStockholm University10691StockholmSweden
| | - Pavel Němec
- Department of Zoology, Faculty of ScienceCharles University12844PragueCzech Republic
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119
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Abstract
The NMDA subtype of ionotropic glutamate receptor is a sophisticated integrator and transducer of information. NMDAR-mediated signals control diverse processes across the life course, including synaptogenesis and synaptic plasticity, as well as contribute to excitotoxic processes in neurological disorders. At the basic biophysical level, the NMDAR is a coincidence detector, requiring the co-presence of agonist, co-agonist, and membrane depolarization in order to open. However, the NMDAR is not merely a conduit for ions to flow through; it is linked on the cytoplasmic side to a large network of signaling and scaffolding proteins, primarily via the C-terminal domain of NMDAR GluN2 subunits. These physical interactions help to organize the signaling cascades downstream of NMDAR activation. Notably, the NMDAR does not come in a single form: the subunit composition of the NMDAR, particularly the GluN2 subunit subtype (GluN2A–D), influences the biophysical properties of the channel. Moreover, a growing number of studies have illuminated the extent to which GluN2 C-terminal interactions vary according to GluN2 subtype and how this impacts on the processes that NMDAR activity controls. We will review recent advances, controversies, and outstanding questions in this active area of research.
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Affiliation(s)
- Giles Hardingham
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, UK.,Centre for Discovery Brain Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh, EH8 9XD, UK
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120
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Zheng T, Feng Z, Wang X, Jiang T, Jin R, Zhao P, Luo T, Gong H, Luo Q, Yuan J. Review of micro-optical sectioning tomography (MOST): technology and applications for whole-brain optical imaging [Invited]. BIOMEDICAL OPTICS EXPRESS 2019; 10:4075-4096. [PMID: 31452996 PMCID: PMC6701528 DOI: 10.1364/boe.10.004075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/20/2019] [Accepted: 06/25/2019] [Indexed: 05/14/2023]
Abstract
Elucidating connectivity and functionality at the whole-brain level is one of the most challenging research goals in neuroscience. Various whole-brain optical imaging technologies with submicron lateral resolution have been developed to reveal the fine structures of brain-wide neural and vascular networks at the mesoscopic level. Among them, micro-optical sectioning tomography (MOST) is attracting increasing attention, as a variety of technological variations and solutions tailored toward different biological applications have been optimized. Here, we summarize the recent development of MOST technology in whole-brain imaging and anticipate future improvements.
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Affiliation(s)
- Ting Zheng
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Equal contribution
| | - Zhao Feng
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Equal contribution
| | - Xiaojun Wang
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tao Jiang
- HUST–Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, Jiangsu 215000, China
| | - Rui Jin
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Peilin Zhao
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ting Luo
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Hui Gong
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- HUST–Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, Jiangsu 215000, China
| | - Qingming Luo
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- HUST–Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, Jiangsu 215000, China
| | - Jing Yuan
- Collaborative Innovation Center for Biomedical Engineering, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- HUST–Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, Jiangsu 215000, China
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121
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Koutsoumpa A, Papatheodoropoulos C. Short-term dynamics of input and output of CA1 network greatly differ between the dorsal and ventral rat hippocampus. BMC Neurosci 2019; 20:35. [PMID: 31331291 PMCID: PMC6647178 DOI: 10.1186/s12868-019-0517-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
Background The functional heterogeneity of the hippocampus along its longitudinal axis at the level of behavior is an established concept; however, the neurobiological mechanisms are still unknown. Diversifications in the functioning of intrinsic hippocampal circuitry including short-term dynamics of synaptic inputs and neuronal output, that are important determinants of information processing in the brain, may profoundly contribute to functional specializations along the hippocampus. The objectives of the present study were the examination of the role of the GABAA receptor-mediated inhibition, the μ-opioid receptors and the effect of stimulation intensity on the dynamics of both synaptic input and neuronal output of CA1 region in the dorsal and ventral hippocampus. We used recordings of field potentials from adult rat hippocampal slices evoked by brief repetitive activation of Schaffer collaterals. Results We find that the local CA1 circuit of the dorsal hippocampus presents a remarkably increased dynamic range of frequency-dependent short-term changes in both input and output, ranging from strong facilitation to intense depression at low and high stimulation frequencies respectively. Furthermore, the input–output relationship in the dorsal CA1 circuit is profoundly influenced by frequency and time of presynaptic activation. Strikingly, the ventral hippocampus responds mostly with depression, displaying a rather monotonous input–output relationship over frequency and time. Partial blockade of GABAA receptor-mediated transmission (by 5 μM picrotoxin) profoundly influences input and output dynamics in the dorsal hippocampus but affected only the neuronal output in the ventral hippocampus. M-opioid receptors control short-term dynamics of input and output in the dorsal hippocampus but they play no role in the ventral hippocampus. Conclusion The results demonstrate that information processing by CA1 local network is highly diversified between the dorsal and ventral hippocampus. Transient detection of incoming patterns of activity and frequency-dependent sustained signaling of amplified neuronal information may be assigned to the ventral and dorsal hippocampal circuitry respectively. This disparity should have profound implications for the functional roles ascribed to distinct segments along the long axis of the hippocampus. Electronic supplementary material The online version of this article (10.1186/s12868-019-0517-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andriana Koutsoumpa
- Laboratory of Neurophysiology, Department of Medicine, University of Patras, 26504, Rion, Greece.,Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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122
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Letellier M, Levet F, Thoumine O, Goda Y. Differential role of pre- and postsynaptic neurons in the activity-dependent control of synaptic strengths across dendrites. PLoS Biol 2019; 17:e2006223. [PMID: 31166943 PMCID: PMC6576792 DOI: 10.1371/journal.pbio.2006223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/17/2019] [Accepted: 05/17/2019] [Indexed: 01/07/2023] Open
Abstract
Neurons receive a large number of active synaptic inputs from their many presynaptic partners across their dendritic tree. However, little is known about how the strengths of individual synapses are controlled in balance with other synapses to effectively encode information while maintaining network homeostasis. This is in part due to the difficulty in assessing the activity of individual synapses with identified afferent and efferent connections for a synapse population in the brain. Here, to gain insights into the basic cellular rules that drive the activity-dependent spatial distribution of pre- and postsynaptic strengths across incoming axons and dendrites, we combine patch-clamp recordings with live-cell imaging of hippocampal pyramidal neurons in dissociated cultures and organotypic slices. Under basal conditions, both pre- and postsynaptic strengths cluster on single dendritic branches according to the identity of the presynaptic neurons, thus highlighting the ability of single dendritic branches to exhibit input specificity. Stimulating a single presynaptic neuron induces input-specific and dendritic branchwise spatial clustering of presynaptic strengths, which accompanies a widespread multiplicative scaling of postsynaptic strengths in dissociated cultures and heterosynaptic plasticity at distant synapses in organotypic slices. Our study provides evidence for a potential homeostatic mechanism by which the rapid changes in global or distant postsynaptic strengths compensate for input-specific presynaptic plasticity.
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Affiliation(s)
- Mathieu Letellier
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France
- * E-mail: (ML); (YG)
| | - Florian Levet
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France
- Bordeaux Imaging Center, University of Bordeaux, Bordeaux, France
- Bordeaux Imaging Center, CNRS UMS 3420, Bordeaux, France
- Bordeaux Imaging Center, INSERM US04, Bordeaux, France
| | - Olivier Thoumine
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France
| | - Yukiko Goda
- RIKEN Center for Brain Science, Wako, Saitama, Japan
- * E-mail: (ML); (YG)
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123
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A blueprint of septin expression in human tissues. Funct Integr Genomics 2019; 19:787-797. [PMID: 31089837 DOI: 10.1007/s10142-019-00690-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/29/2022]
Abstract
Septins are GTP-binding proteins that polymerize to form filaments involved in several important biological processes. In human, 13 distinct septins genes are classified in four groups. Filaments formed by septins are complex and usually involve members of each group in specific positions. Expression data from GTEx database, a publicly available expression database with thousands of samples derived from multiple human tissues, was used to evaluate the expression of septins. The brain is noticeably a hotspot for septin expression where few genes contribute to a large portion of septin transcript pool. Co-expression data between septins suggests two predominant specific complexes in brain tissues and one filament in other tissues. SEPT3 and SEPT5 are two genes highly expressed in the brain and with a strong co-expression in all brain tissues. Additional analysis shows that the expression of these two genes is highly variable between individuals, but significantly dependent on the individual's age. Age-dependent decrease of expression from those two septins involved in synapses reinforces their possible link with cognitive decay and neurodegenerative diseases associated with aging. Analysis of enrichment of Gene Ontology terms from lists of genes consistently co-expressed with septins suggests participation in diverse biological processes, pointing out some novel roles for septins. Interestingly, we observed strong consistency of some of these terms with experimentally described roles of septins. Coordination of septins expression with genes involved in DNA repair and cell cycle control may provide insights for previously described links between septins and cancer.
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124
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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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125
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Zhang Q, Lee WCA, Paul DL, Ginty DD. Multiplexed peroxidase-based electron microscopy labeling enables simultaneous visualization of multiple cell types. Nat Neurosci 2019; 22:828-839. [PMID: 30886406 PMCID: PMC6555422 DOI: 10.1038/s41593-019-0358-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/07/2019] [Indexed: 01/06/2023]
Abstract
Electron microscopy (EM) is a powerful tool for circuit mapping, but identifying specific cell types in EM datasets remains a major challenge. Here we describe a technique enabling simultaneous visualization of multiple, genetically identified neuronal populations so that synaptic interactions between them can be unequivocally defined. We present 15 AAV constructs and six mouse reporter lines for multiplexed EM labeling in the mammalian nervous system. These reporters feature dAPEX2, which exhibits dramatically improved signal compared to previously described ascorbate peroxidases. By targeting this enhanced peroxidase to different subcellular compartments, multiple orthogonal reporters can be simultaneously visualized and distinguished under EM using a protocol compatible with existing EM pipelines. Proof-of-principle double and triple EM labeling experiments demonstrated synaptic connections between primary afferents, descending cortical inputs, and inhibitory interneurons in the spinal cord dorsal horn. Our multiplexed peroxidase-based EM labeling system should therefore greatly facilitate analysis of connectivity in the nervous system.
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Affiliation(s)
- Qiyu Zhang
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Wei-Chung A Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - David L Paul
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | - David D Ginty
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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Zhang H, Zou Y, Lei H. Regional metabolic differences in rat prefrontal cortex measured with in vivo 1 H-MRS correlate with regional histochemical differences. NMR IN BIOMEDICINE 2019; 32:e4024. [PMID: 30376204 DOI: 10.1002/nbm.4024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
Many neurological/psychiatric disorders are associated with metabolic abnormalities in the brain observable with in vivo proton MRS (1 H-MRS). The underlying molecular/cellular mechanisms and functional correlations of such metabolic alterations, however, are yet to be understood fully. The rodent prefrontal cortex (PFC) is comprised of multiple sub-regions with distinctive cytoarchitecture and functions, providing a good model system to study the correlations among cerebral metabolism, regional cytoarchitecture and connectivity. In this study, the metabolic profiles in two voxels containing mainly the medial PFC (mPFC) and posterior part of the cingulate cortex (pCG), respectively, were measured with single-voxel in vivo 1 H-MRS in adult male rats. The levels of glutamine synthetase and glutamatergic synaptic proteins, including vesicular glutamate transporter 1, vesicular glutamate transporter 2 (VGLUT2) and post-synaptic density protein 95 (PSD95), as well as the density of astrocytes, in these two regions were also compared semi-quantitatively. It was shown that, relative to the pCG voxel, the mPFC voxel had significantly higher N-acetyl aspartate, glutamate (Glu), glutamine (Gln), Glx (Glu + Gln), myo-inositol and taurine levels. The VGLUT2/PSD95 levels and astrocyte density were also higher in the mPFC voxel than in the pCG voxel. Taken together, these results indicated that regional metabolic variations in the PFC of the adult male rat may reflect regional differences in the density of astrocytes and glutamatergic terminals associated with subcortical projections. The study provided a link between the Glu concentration measured with localized in vivo 1 H-MRS and regional glutamatergic activities/connections in the rat PFC.
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Affiliation(s)
- Hui Zhang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yijuan Zou
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Hao Lei
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
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127
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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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128
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Grant SGN. Synapse molecular complexity and the plasticity behaviour problem. Brain Neurosci Adv 2018; 2:2398212818810685. [PMID: 32166154 PMCID: PMC7058196 DOI: 10.1177/2398212818810685] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Indexed: 01/06/2023] Open
Abstract
Synapses are the hallmark of brain complexity and have long been thought of as simple connectors between neurons. We are now in an era in which we know the full complement of synapse proteins and this has created an existential crisis because the molecular complexity far exceeds the requirements of most simple models of synaptic function. Studies of the organisation of proteome complexity and its evolution provide surprising new insights that challenge existing dogma and promote the development of new theories about the origins and role of synapses in behaviour. The postsynaptic proteome of excitatory synapses is a structure with high molecular complexity and sophisticated computational properties that is disrupted in over 130 brain diseases. A key goal of 21st-century neuroscience is to develop comprehensive molecular datasets on the brain and develop theories that explain the molecular basis of behaviour.
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Affiliation(s)
- Seth G N Grant
- Genes to Cognition Programme, Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
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129
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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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