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Jones G, Akter Y, Shifflett V, Hruska M. Nanoscale analysis of functionally diverse glutamatergic synapses in the neocortex reveals input and layer-specific organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592008. [PMID: 38746319 PMCID: PMC11092571 DOI: 10.1101/2024.05.01.592008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Discovery of synaptic nanostructures suggests a molecular logic for the flexibility of synaptic function. We still have little understanding of how functionally diverse synapses in the brain organize their nanoarchitecture due to challenges associated with super-resolution imaging in complex brain tissue. Here, we characterized single-domain camelid nanobodies for the 3D quantitative multiplex imaging of synaptic nano-organization in 6 µm brain cryosections using STED nanoscopy. We focused on thalamocortical (TC) and corticocortical (CC) synapses along the apical-basal axis of layer 5 pyramidal neurons as models of functionally diverse glutamatergic synapses in the brain. Spines receiving TC input were larger than CC spines in all layers examined. However, TC synapses on apical and basal dendrites conformed to different organizational principles. TC afferents on apical dendrites frequently contacted spines with multiple aligned PSD-95/Bassoon nanomodules, which are larger. TC spines on basal dendrites contained mostly one aligned PSD-95/Bassoon nanocluster. However, PSD-95 nanoclusters were larger and scaled with spine volume. The nano-organization of CC synapses did not change across cortical layers. These results highlight striking nanoscale diversity of functionally distinct glutamatergic synapses, relying on afferent input and sub-cellular localization of individual synaptic connections.
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2
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Roig Adam A, Martínez-López JA, van der Spek SJF, Sullivan PF, Smit AB, Verhage M, Hjerling-Leffler J. Transcriptional diversity in specific synaptic gene sets discriminates cortical neuronal identity. Biol Direct 2023; 18:22. [PMID: 37161421 PMCID: PMC10170694 DOI: 10.1186/s13062-023-00372-y] [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: 03/02/2023] [Accepted: 04/05/2023] [Indexed: 05/11/2023] Open
Abstract
Synapse diversity has been described from different perspectives, ranging from the specific neurotransmitters released, to their diverse biophysical properties and proteome profiles. However, synapse diversity at the transcriptional level has not been systematically identified across all synapse populations in the brain. To quantify and identify specific synaptic features of neuronal cell types we combined the SynGO (Synaptic Gene Ontology) database with single-cell RNA sequencing data of the mouse neocortex. We show that cell types can be discriminated by synaptic genes alone with the same power as all genes. The cell type discriminatory power is not equally distributed across synaptic genes as we could identify functional categories and synaptic compartments with greater cell type specific expression. Synaptic genes, and specific SynGO categories, belonged to three different types of gene modules: gradient expression over all cell types, gradient expression in selected cell types and cell class- or type-specific profiles. This data provides a deeper understanding of synapse diversity in the neocortex and identifies potential markers to selectively identify synapses from specific neuronal populations.
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Affiliation(s)
- Amparo Roig Adam
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
- Present Address: Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - José A. Martínez-López
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Sophie J. F. van der Spek
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264 USA
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Matthijs Verhage
- Present Address: Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Functional Genomics Section, Department of Human Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Amsterdam University Medical Center (UMC), De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Jens Hjerling-Leffler
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
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3
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Complex regulation of Gephyrin splicing is a determinant of inhibitory postsynaptic diversity. Nat Commun 2022; 13:3507. [PMID: 35717442 PMCID: PMC9206673 DOI: 10.1038/s41467-022-31264-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/10/2022] [Indexed: 01/05/2023] Open
Abstract
Gephyrin (GPHN) regulates the clustering of postsynaptic components at inhibitory synapses and is involved in pathophysiology of neuropsychiatric disorders. Here, we uncover an extensive diversity of GPHN transcripts that are tightly controlled by splicing during mouse and human brain development. Proteomic analysis reveals at least a hundred isoforms of GPHN incorporated at inhibitory Glycine and gamma-aminobutyric acid A receptors containing synapses. They exhibit different localization and postsynaptic clustering properties, and altering the expression level of one isoform is sufficient to affect the number, size, and density of inhibitory synapses in cerebellar Purkinje cells. Furthermore, we discovered that splicing defects reported in neuropsychiatric disorders are carried by multiple alternative GPHN transcripts, demonstrating the need for a thorough analysis of the GPHN transcriptome in patients. Overall, we show that alternative splicing of GPHN is an important genetic variation to consider in neurological diseases and a determinant of the diversity of postsynaptic inhibitory synapses. The protein gephyrin is involved in organizing synapses. Here, the authors show how different transcripts of gephyrin form and regulate inhibitory synapses.
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4
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Kim HY, Um JW, Ko J. Proper synaptic adhesion signaling in the control of neural circuit architecture and brain function. Prog Neurobiol 2021; 200:101983. [PMID: 33422662 DOI: 10.1016/j.pneurobio.2020.101983] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/23/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022]
Abstract
Trans-synaptic cell-adhesion molecules are critical for governing various stages of synapse development and specifying neural circuit properties via the formation of multifarious signaling pathways. Recent studies have pinpointed the putative roles of trans-synaptic cell-adhesion molecules in mediating various cognitive functions. Here, we review the literature on the roles of a diverse group of central synaptic organizers, including neurexins (Nrxns), leukocyte common antigen-related receptor protein tyrosine phosphatases (LAR-RPTPs), and their associated binding proteins, in regulating properties of specific type of synapses and neural circuits. In addition, we highlight the findings that aberrant synaptic adhesion signaling leads to alterations in the structures, transmission, and plasticity of specific synapses across diverse brain areas. These results seem to suggest that proper trans-synaptic signaling pathways by Nrxns, LAR-RPTPs, and their interacting network is likely to constitute central molecular complexes that form the basis for cognitive functions, and that these complexes are heterogeneously and complexly disrupted in many neuropsychiatric and neurodevelopmental disorders.
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Affiliation(s)
- Hee Young Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, South Korea
| | - Ji Won Um
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, South Korea; Core Protein Resources Center, DGIST, Daegu, 42988, South Korea.
| | - Jaewon Ko
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, South Korea.
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5
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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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6
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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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7
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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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8
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Abstract
Cerebral organoids are an emerging cutting-edge technology to model human brain
development and neurodevelopmental disorders, for which mouse models exhibit significant
limitations. In the human brain, synaptic connections define neural circuits, and synaptic
deficits account for various neurodevelopmental disorders. Thus, harnessing the full power
of cerebral organoids for human brain modeling requires the ability to visualize and
analyze synapses in cerebral organoids. Previously, we devised an optimized method to
generate human cerebral organoids, and showed that optimal organoids express mature-neuron
markers, including synaptic proteins and neurotransmitter receptors and transporters.
Here, we give evidence for synaptogenesis in cerebral organoids, via microscopical
visualization of synapses. We also describe multiple approaches to quantitatively analyze
synapses in cerebral organoids. Collectively, our work provides sufficient evidence for
the possibility of modeling synaptogenesis and synaptic disorders in cerebral organoids,
and may help advance the use of cerebral organoids in molecular neuroscience and studies
of neurodevelopmental disorders such as autism.
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Affiliation(s)
- Abraam M Yakoub
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark Sadek
- Department of Pharmaceutical Biotechnology, University of Illinois College of Pharmacy, Chicago, IL, USA.,Department of Research and Development, Akorn Pharmaceuticals, Vernon Hills, IL, USA
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9
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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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10
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Sossin WS. Memory Synapses Are Defined by Distinct Molecular Complexes: A Proposal. Front Synaptic Neurosci 2018; 10:5. [PMID: 29695960 PMCID: PMC5904272 DOI: 10.3389/fnsyn.2018.00005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/26/2018] [Indexed: 12/17/2022] Open
Abstract
Synapses are diverse in form and function. While there are strong evidential and theoretical reasons for believing that memories are stored at synapses, the concept of a specialized “memory synapse” is rarely discussed. Here, we review the evidence that memories are stored at the synapse and consider the opposing possibilities. We argue that if memories are stored in an active fashion at synapses, then these memory synapses must have distinct molecular complexes that distinguish them from other synapses. In particular, examples from Aplysia sensory-motor neuron synapses and synapses on defined engram neurons in rodent models are discussed. Specific hypotheses for molecular complexes that define memory synapses are presented, including persistently active kinases, transmitter receptor complexes and trans-synaptic adhesion proteins.
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Affiliation(s)
- Wayne S Sossin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
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11
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The Purkinje cell as a model of synaptogenesis and synaptic specificity. Brain Res Bull 2016; 129:12-17. [PMID: 27721030 DOI: 10.1016/j.brainresbull.2016.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 01/03/2023]
Abstract
Since the groundbreaking work of Ramon y Cajal, the cerebellar Purkinje cell has always represented an ideal model for studying the organization, development and function of synaptic circuits. Purkinje cells receive distinct types of glutamatergic and GABAergic synapses, each characterized by exquisite sub-cellular and molecular specificity. The formation and refinement of these connections results from a temporally-regulated sequence of events that involves molecular interactions between distinct sets of secreted and surface proteins, as well as activity-dependent competition between converging inputs. Insights into the mechanisms controlling synaptic specificity in Purkinje cells may help understand synapse development also in other brain regions and disclose circuit abnormalities that underlie neurodevelopmental disorders.
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12
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Merlo L, Cimino F, Angileri FF, La Torre D, Conti A, Cardali SM, Saija A, Germanò A. Alteration in synaptic junction proteins following traumatic brain injury. J Neurotrauma 2015; 31:1375-85. [PMID: 24661152 DOI: 10.1089/neu.2014.3385] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Extensive research and scientific efforts have been focused on the elucidation of the pathobiology of cellular and axonal damage following traumatic brain injury (TBI). Conversely, few studies have specifically addressed the issue of synaptic dysfunction. Synaptic junction proteins may be involved in post-TBI alterations, leading to synaptic loss or disrupted plasticity. A Synapse Protein Database on synapse ontology identified 109 domains implicated in synaptic activities and over 5000 proteins, but few of these demonstrated to play a role in the synaptic dysfunction after TBI. These proteins are involved in neuroplasticity and neuromodulation and, most importantly, may be used as novel neuronal markers of TBI for specific intervention.
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Affiliation(s)
- Lucia Merlo
- 1 Department of Neurosciences, University of Messina , Messina, Italy
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13
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Automated analysis of a diverse synapse population. PLoS Comput Biol 2013; 9:e1002976. [PMID: 23555213 PMCID: PMC3610606 DOI: 10.1371/journal.pcbi.1002976] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 01/21/2013] [Indexed: 12/22/2022] Open
Abstract
Synapses of the mammalian central nervous system are highly diverse in function and molecular composition. Synapse diversity per se may be critical to brain function, since memory and homeostatic mechanisms are thought to be rooted primarily in activity-dependent plastic changes in specific subsets of individual synapses. Unfortunately, the measurement of synapse diversity has been restricted by the limitations of methods capable of measuring synapse properties at the level of individual synapses. Array tomography is a new high-resolution, high-throughput proteomic imaging method that has the potential to advance the measurement of unit-level synapse diversity across large and diverse synapse populations. Here we present an automated feature extraction and classification algorithm designed to quantify synapses from high-dimensional array tomographic data too voluminous for manual analysis. We demonstrate the use of this method to quantify laminar distributions of synapses in mouse somatosensory cortex and validate the classification process by detecting the presence of known but uncommon proteomic profiles. Such classification and quantification will be highly useful in identifying specific subpopulations of synapses exhibiting plasticity in response to perturbations from the environment or the sensory periphery. Synaptic connections are fundamental to every aspect of brain function. There is growing recognition that individual synapses are the key sites of the functional plasticity that allows brain circuits to store and retrieve memories and to adapt to changing demands and environments. There is also a growing consensus that many neurological, psychiatric, neurodevelopmental and neurodegenerative disorders may be best understood at the level of specific, proteomically-defined synapse subsets. Here, we introduce and validate computational analysis tools designed to complement array tomography, a new high-resolution proteomic imaging method, to enable the analysis of diverse synapse populations of unprecedentedly large size at the single-synapse level. We expect these new single-synapse classification and analysis tools to substantially advance the search for the specific physical traces, or engrams, of specific memories in the brains synaptic circuits. We also expect these same tools to be useful for identifying the specific subsets of synapses that are impacted by the various synaptically-rooted afflictions of the brain.
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14
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Sassoè-Pognetto M, Frola E, Pregno G, Briatore F, Patrizi A. Understanding the molecular diversity of GABAergic synapses. Front Cell Neurosci 2011; 5:4. [PMID: 21713106 PMCID: PMC3112311 DOI: 10.3389/fncel.2011.00004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 05/23/2011] [Indexed: 01/17/2023] Open
Abstract
GABAergic synapses exhibit a high degree of subcellular and molecular specialization, which contrasts with their apparent simplicity in ultrastructural appearance. Indeed, when observed in the electron microscope, GABAergic synapses fit in the symmetric, or Gray’s type II category, being characterized by a relatively simple postsynaptic specialization. The inhibitory postsynaptic density cannot be readily isolated, and progress in understanding its molecular composition has lagged behind that of excitatory synapses. However, recent studies have brought significant progress in the identification of new synaptic proteins, revealing an unexpected complexity in the molecular machinery that regulates GABAergic synaptogenesis. In this article, we provide an overview of the molecular diversity of GABAergic synapses, and we consider how synapse specificity may be encoded by selective trans-synaptic interactions between pre- and postsynaptic adhesion molecules and secreted factors that reside in the synaptic cleft. We also discuss the importance of developing cataloguing tools that could be used to decipher the molecular diversity of synapses and to predict alterations of inhibitory transmission in the course of neurological diseases.
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Affiliation(s)
- Marco Sassoè-Pognetto
- Department of Anatomy, Pharmacology and Forensic Medicine, University of Turin Torino, Italy
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15
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Micheva KD, Busse B, Weiler NC, O'Rourke N, Smith SJ. Single-synapse analysis of a diverse synapse population: proteomic imaging methods and markers. Neuron 2010; 68:639-53. [PMID: 21092855 PMCID: PMC2995697 DOI: 10.1016/j.neuron.2010.09.024] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2010] [Indexed: 12/23/2022]
Abstract
A lack of methods for measuring the protein compositions of individual synapses in situ has so far hindered the exploration and exploitation of synapse molecular diversity. Here, we describe the use of array tomography, a new high-resolution proteomic imaging method, to determine the composition of glutamate and GABA synapses in somatosensory cortex of Line-H-YFP Thy-1 transgenic mice. We find that virtually all synapses are recognized by antibodies to the presynaptic phosphoprotein synapsin I, while antibodies to 16 other synaptic proteins discriminate among 4 subtypes of glutamatergic synapses and GABAergic synapses. Cell-specific YFP expression in the YFP-H mouse line allows synapses to be assigned to specific presynaptic and postsynaptic partners and reveals that a subpopulation of spines on layer 5 pyramidal cells receives both VGluT1-subtype glutamatergic and GABAergic synaptic inputs. These results establish a means for the high-throughput acquisition of proteomic data from individual cortical synapses in situ.
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Affiliation(s)
- Kristina D Micheva
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.
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16
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Sassoè-Pognetto M. Molecular and functional heterogeneity of neural circuits: an example from the olfactory bulb. ACTA ACUST UNITED AC 2010; 66:35-42. [PMID: 20600309 DOI: 10.1016/j.brainresrev.2010.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 06/14/2010] [Indexed: 01/11/2023]
Abstract
In 1875 Camillo Golgi published his classical description of the olfactory bulb, which contained the first images of neurons visualized with the "black reaction". This new staining method opened the way for structural investigations of the nervous tissue, that culminated in the extraordinary neuroanatomical work of Ramón y Cajal and the formulation of the neuron doctrine. Later developments in neurochemical techniques have revealed an astonishing diversity of neural circuits at the molecular level. This essay reflects on the physiological importance of the molecular heterogeneity of synaptic connections. Dendrodendritic circuits of the olfactory bulb will serve as a case for illustrating the relation between molecular composition and functional properties. Specifically, I will consider how the differential expression of GABA(A) receptor subtypes shapes dendrodendritic inhibition and influences olfactory bulb network activities. A concept emerging from recent investigations is that the molecular diversity of GABAergic systems supports neural circuit operations under an extensive range of behavior-dependent network states. Considering the great molecular diversity of synaptic connections, it is useful to reflect on the importance of high-resolution immunohistochemical analyses as a tool for investigating the structural and functional architecture of neural circuits.
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Affiliation(s)
- Marco Sassoè-Pognetto
- Department of Anatomy, Pharmacology and Forensic Medicine, and National Institute of Neuroscience, University of Torino, Torino, Italy.
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Neuroproteomics: understanding the molecular organization and complexity of the brain. Nat Rev Neurosci 2009; 10:635-46. [DOI: 10.1038/nrn2701] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Circuit reconstruction tools today. Curr Opin Neurobiol 2007; 17:601-8. [PMID: 18082394 DOI: 10.1016/j.conb.2007.11.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 10/17/2007] [Accepted: 11/03/2007] [Indexed: 11/22/2022]
Abstract
To understand how a brain processes information, we must understand the structure of its neural circuits-especially circuit interconnection topologies and the cell and synapse molecular architectures that determine circuit-signaling dynamics. Our information on these key aspects of neural circuit structure has remained incomplete and fragmentary, however, because of limitations of the best available imaging methods. Now, new transgenic tool mice and new image acquisition tools appear poised to permit very significant advances in our abilities to reconstruct circuit connection topologies and molecular architectures.
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