1
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Bonthron C, Burley S, Broadhead MJ, Metodieva V, Grant SGN, Chandran S, Miles GB. Excitatory to inhibitory synaptic ratios are unchanged at presymptomatic stages in multiple models of ALS. PLoS One 2024; 19:e0306423. [PMID: 39088455 PMCID: PMC11293752 DOI: 10.1371/journal.pone.0306423] [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: 02/22/2024] [Accepted: 06/17/2024] [Indexed: 08/03/2024] Open
Abstract
Hyperexcitability of motor neurons and spinal cord motor circuitry has been widely reported in the early stages of Amyotrophic Lateral Sclerosis (ALS). Changes in the relative amount of excitatory to inhibitory inputs onto a neuron (E:I synaptic ratio), possibly through a developmental shift in synapse formation in favour of excitatory transmission, could underlie pathological hyperexcitability. Given that astrocytes play a major role in early synaptogenesis and are implicated in ALS pathogenesis, their potential contribution to disease mechanisms involving synaptic imbalances and subsequent hyperexcitability is also of great interest. In order to assess E:I ratios in ALS, we utilised a novel primary spinal neuron / astrocyte co-culture system, derived from neonatal mice, in which synapses are formed in vitro. Using multiple ALS mouse models we found that no combination of astrocyte or neuron genotype produced alterations in E:I synaptic ratios assessed using pre- and post-synaptic anatomical markers. Similarly, we observed that ephrin-B1, a major contact-dependent astrocytic synaptogenic protein, was not differentially expressed by ALS primary astrocytes. Further to this, analysis of E:I ratios across the entire grey matter of the lumbar spinal cord in young (post-natal day 16-19) ALS mice revealed no differences versus controls. Finally, analysis in co-cultures of human iPSC-derived motor neurons and astrocytes harbouring the pathogenic C9orf72 hexanucleotide repeat expansion showed no evidence of a bias toward excitatory versus inhibitory synapse formation. We therefore conclude, utilising multiple ALS models, that we do not observe significant changes in the relative abundance of excitatory versus inhibitory synapses as would be expected if imbalances in synaptic inputs contribute to early hyperexcitability.
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Affiliation(s)
- Calum Bonthron
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, United Kingdom
| | - Sarah Burley
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Matthew J. Broadhead
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, United Kingdom
| | - Vanya Metodieva
- School of Biology, University of St Andrews, St Andrews, United Kingdom
- Centre of Biophotonics, University of St Andrews, St Andrews, United Kingdom
| | - Seth G. N. Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Siddharthan Chandran
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- UK Dementia Research Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, United Kingdom
- Patrick Wild Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Gareth B. Miles
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, United Kingdom
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2
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Koukaroudi D, Qiu Z, Fransén E, Gokhale R, Bulovaite E, Komiyama NH, Seibt J, Grant SGN. Sleep maintains excitatory synapse diversity in the cortex and hippocampus. Curr Biol 2024:S0960-9822(24)00935-7. [PMID: 39096907 DOI: 10.1016/j.cub.2024.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/17/2024] [Accepted: 07/05/2024] [Indexed: 08/05/2024]
Abstract
Insufficient sleep is a global problem with serious consequences for cognition and mental health.1 Synapses play a central role in many aspects of cognition, including the crucial function of memory consolidation during sleep.2 Interference with the normal expression or function of synapse proteins is a cause of cognitive, mood, and other behavioral problems in over 130 brain disorders.3 Sleep deprivation (SD) has also been reported to alter synapse protein composition and synapse number, although with conflicting results.4,5,6,7 In our study, we conducted synaptome mapping of excitatory synapses in 125 regions of the mouse brain and found that sleep deprivation selectively reduces synapse diversity in the cortex and in the CA1 region of the hippocampus. Sleep deprivation targeted specific types and subtypes of excitatory synapses while maintaining total synapse density (synapse number/area). Synapse subtypes with longer protein lifetimes exhibited resilience to sleep deprivation, similar to observations in aging and genetic perturbations. Moreover, the altered synaptome architecture affected the responses to neural oscillations, suggesting that sleep plays a vital role in preserving cognitive function by maintaining the brain's synaptome architecture.
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Affiliation(s)
- Dimitra Koukaroudi
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Zhen Qiu
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4HN, 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, 171 65 Solna, Sweden
| | - Ragini Gokhale
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Edita Bulovaite
- 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; The Patrick Wild Centre for Research into Autism, Fragile X Syndrome & Intellectual Disabilities, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK; Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Julie Seibt
- Surrey Sleep Research Centre, School of Biosciences, University of Surrey, Guildford, Surrey GU2 7XP, UK
| | - 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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3
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Rao S, Liang F, Herring BE. RhoGEF Tiam2 Regulates Glutamatergic Synaptic Transmission in Hippocampal CA1 Pyramidal Neurons. eNeuro 2024; 11:ENEURO.0500-21.2024. [PMID: 38871458 PMCID: PMC11262554 DOI: 10.1523/eneuro.0500-21.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/29/2024] [Accepted: 05/23/2024] [Indexed: 06/15/2024] Open
Abstract
Glutamatergic synapses exhibit significant molecular diversity, but circuit-specific mechanisms that underlie synaptic regulation are not well characterized. Prior reports show that Rho-guanine nucleotide exchange factor (RhoGEF) Tiam1 regulates perforant path→dentate gyrus granule neuron synapses. In the present study, we report Tiam1's homolog Tiam2 is implicated in glutamatergic neurotransmission in CA1 pyramidal neurons. We find that Tiam2 regulates evoked excitatory glutamatergic currents via a postsynaptic mechanism mediated by the catalytic Dbl-homology domain. Overall, we present evidence for RhoGEF Tiam2's role in glutamatergic synapse function at Schaffer collateral→CA1 pyramidal neuron synapses.
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Affiliation(s)
- Sadhna Rao
- Department of Biological Sciences, Neurobiology Section, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California 90089
| | - Feng Liang
- Department of Biological Sciences, Neurobiology Section, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California 90089
| | - Bruce E Herring
- Department of Biological Sciences, Neurobiology Section, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California 90089
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4
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Metzbower SR, Levy AD, Dharmasri PA, Anderson MC, Blanpied TA. Distinct SAP102 and PSD-95 Nano-organization Defines Multiple Types of Synaptic Scaffold Protein Domains at Single Synapses. J Neurosci 2024; 44:e1715232024. [PMID: 38777601 PMCID: PMC11211720 DOI: 10.1523/jneurosci.1715-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
MAGUK scaffold proteins play a central role in maintaining and modulating synaptic signaling, providing a framework to retain and position receptors, signaling molecules, and other synaptic components. In particular, the MAGUKs SAP102 and PSD-95 are essential for synaptic function at distinct developmental timepoints and perform both overlapping and unique roles. While their similar structures allow for common binding partners, SAP102 is expressed earlier in synapse development and is required for synaptogenesis, whereas PSD-95 expression peaks later and is associated with synapse maturation. PSD-95 and other key synaptic proteins organize into subsynaptic nanodomains that have a significant impact on synaptic transmission, but the nanoscale organization of SAP102 is unknown. How SAP102 is organized within the synapse, and how it relates spatially to PSD-95 on a nanometer scale, could underlie its unique functions and impact how SAP102 scaffolds synaptic proteins. Here we used DNA-PAINT super-resolution microscopy to measure SAP102 nano-organization and its spatial relationship to PSD-95 at individual synapses in mixed-sex rat cultured neurons. We found that like PSD-95, SAP102 accumulates in high-density subsynaptic nanoclusters (NCs). However, SAP102 NCs were smaller and denser than PSD-95 NCs across development. Additionally, only a subset of SAP102 NCs co-organized with PSD-95, revealing MAGUK nanodomains within individual synapses containing either one or both proteins. These MAGUK nanodomain types had distinct NC properties and were differentially enriched with the presynaptic release protein Munc13-1. This organization into both shared and distinct subsynaptic nanodomains may underlie the ability of SAP102 and PSD-95 to perform both common and unique synaptic functions.
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Affiliation(s)
- Sarah R Metzbower
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Aaron D Levy
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Poorna A Dharmasri
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Michael C Anderson
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Thomas A Blanpied
- Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, Maryland 21201
- University of Maryland Medicine Institute for Neuroscience Discovery, University of Maryland School of Medicine, Baltimore, Maryland 21201
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5
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Kaizuka T, Takumi T. Alteration of synaptic protein composition during developmental synapse maturation. Eur J Neurosci 2024; 59:2894-2914. [PMID: 38571321 DOI: 10.1111/ejn.16304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 01/02/2024] [Accepted: 02/07/2024] [Indexed: 04/05/2024]
Abstract
The postsynaptic density (PSD) is a collection of specialized proteins assembled beneath the postsynaptic membrane of dendritic spines. The PSD proteome comprises ~1000 proteins, including neurotransmitter receptors, scaffolding proteins and signalling enzymes. Many of these proteins have essential roles in synaptic function and plasticity. During brain development, changes are observed in synapse density and in the stability and shape of spines, reflecting the underlying molecular maturation of synapses. Synaptic protein composition changes in terms of protein abundance and the assembly of protein complexes, supercomplexes and the physical organization of the PSD. Here, we summarize the developmental alterations of postsynaptic protein composition during synapse maturation. We describe major PSD proteins involved in postsynaptic signalling that regulates synaptic plasticity and discuss the effect of altered expression of these proteins during development. We consider the abnormality of synaptic profiles and synaptic protein composition in the brain in neurodevelopmental disorders such as autism spectrum disorders. We also explain differences in synapse development between rodents and primates in terms of synaptic profiles and protein composition. Finally, we introduce recent findings related to synaptic diversity and nanoarchitecture and discuss their impact on future research. Synaptic protein composition can be considered a major determinant and marker of synapse maturation in normality and disease.
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Affiliation(s)
- Takeshi Kaizuka
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Toru Takumi
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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6
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Granato A, Phillips WA, Schulz JM, Suzuki M, Larkum ME. Dysfunctions of cellular context-sensitivity in neurodevelopmental learning disabilities. Neurosci Biobehav Rev 2024; 161:105688. [PMID: 38670298 DOI: 10.1016/j.neubiorev.2024.105688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 04/28/2024]
Abstract
Pyramidal neurons have a pivotal role in the cognitive capabilities of neocortex. Though they have been predominantly modeled as integrate-and-fire point processors, many of them have another point of input integration in their apical dendrites that is central to mechanisms endowing them with the sensitivity to context that underlies basic cognitive capabilities. Here we review evidence implicating impairments of those mechanisms in three major neurodevelopmental disabilities, fragile X, Down syndrome, and fetal alcohol spectrum disorders. Multiple dysfunctions of the mechanisms by which pyramidal cells are sensitive to context are found to be implicated in all three syndromes. Further deciphering of these cellular mechanisms would lead to the understanding of and therapies for learning disabilities beyond any that are currently available.
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Affiliation(s)
- Alberto Granato
- Dept. of Veterinary Sciences. University of Turin, Grugliasco, Turin 10095, Italy.
| | - William A Phillips
- Psychology, Faculty of Natural Sciences, University of Stirling, Scotland FK9 4LA, UK
| | - Jan M Schulz
- Roche Pharma Research & Early Development, Neuroscience & Rare Diseases Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Mototaka Suzuki
- Dept. of Cognitive and Systems Neuroscience, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1098 XH, the Netherlands
| | - Matthew E Larkum
- Neurocure Center for Excellence, Charité Universitätsmedizin Berlin, Berlin 10117, Germany; Institute of Biology, Humboldt University Berlin, Berlin, Germany
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7
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Noguchi J, Watanabe S, Oga T, Isoda R, Nakagaki K, Sakai K, Sumida K, Hoshino K, Saito K, Miyawaki I, Sugano E, Tomita H, Mizukami H, Watakabe A, Yamamori T, Ichinohe N. Altered projection-specific synaptic remodeling and its modification by oxytocin in an idiopathic autism marmoset model. Commun Biol 2024; 7:642. [PMID: 38802535 PMCID: PMC11130163 DOI: 10.1038/s42003-024-06345-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
Alterations in the experience-dependent and autonomous elaboration of neural circuits are assumed to underlie autism spectrum disorder (ASD), though it is unclear what synaptic traits are responsible. Here, utilizing a valproic acid-induced ASD marmoset model, which shares common molecular features with idiopathic ASD, we investigate changes in the structural dynamics of tuft dendrites of upper-layer pyramidal neurons and adjacent axons in the dorsomedial prefrontal cortex through two-photon microscopy. In model marmosets, dendritic spine turnover is upregulated, and spines are generated in clusters and survived more often than in control marmosets. Presynaptic boutons in local axons, but not in commissural long-range axons, demonstrate hyperdynamic turnover in model marmosets, suggesting alterations in projection-specific plasticity. Intriguingly, nasal oxytocin administration attenuates clustered spine emergence in model marmosets. Enhanced clustered spine generation, possibly unique to certain presynaptic partners, may be associated with ASD and be a potential therapeutic target.
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Affiliation(s)
- Jun Noguchi
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan.
| | - Satoshi Watanabe
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Tomofumi Oga
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Risa Isoda
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Keiko Nakagaki
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Kazuhisa Sakai
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Kayo Sumida
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., Osaka, Japan
| | - Kohei Hoshino
- Preclinical Research Laboratories, Sumitomo Pharma Co., Ltd., Osaka, Japan
| | - Koichi Saito
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., Osaka, Japan
| | - Izuru Miyawaki
- Preclinical Research Laboratories, Sumitomo Pharma Co., Ltd., Osaka, Japan
| | - Eriko Sugano
- Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, Morioka, Japan
| | - Hiroshi Tomita
- Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, Morioka, Japan
| | - Hiroaki Mizukami
- Division of Genetic Therapeutics, Jichi Medical University, Shimotsuke, Japan
| | - Akiya Watakabe
- Laboratory for Molecular Analysis of Higher Brain Function, Center for Brain Science, RIKEN, Wako, Japan
| | - Tetsuo Yamamori
- Laboratory for Molecular Analysis of Higher Brain Function, Center for Brain Science, RIKEN, Wako, Japan
- Laboratory for Haptic Perception and Cognitive Physiology, Center for Brain Science, RIKEN, Wako, Japan
- Department of Marmoset Biology and Medicine, CIEM, Kawasaki, Japan
| | - Noritaka Ichinohe
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan.
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8
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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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9
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Bonifazi G, Luchena C, Gaminde-Blasco A, Ortiz-Sanz C, Capetillo-Zarate E, Matute C, Alberdi E, De Pittà M. A nonlinear meccano for Alzheimer's emergence by amyloid β-mediated glutamatergic hyperactivity. Neurobiol Dis 2024; 194:106473. [PMID: 38493903 DOI: 10.1016/j.nbd.2024.106473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/10/2024] [Accepted: 03/10/2024] [Indexed: 03/19/2024] Open
Abstract
The pathophysiological process of Alzheimer's disease (AD) is believed to begin many years before the formal diagnosis of AD dementia. This protracted preclinical phase offers a crucial window for potential therapeutic interventions, yet its comprehensive characterization remains elusive. Accumulating evidence suggests that amyloid-β (Aβ) may mediate neuronal hyperactivity in circuit dysfunction in the early stages of AD. At the same time, neural activity can also facilitate Aβ accumulation through intricate feed-forward interactions, complicating elucidating the conditions governing Aβ-dependent hyperactivity and its diagnostic utility. In this study, we use biophysical modeling to shed light on such conditions. Our analysis reveals that the inherently nonlinear nature of the underlying molecular interactions can give rise to the emergence of various modes of hyperactivity. This diversity in the mechanisms of hyperactivity may ultimately account for a spectrum of AD manifestations.
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Affiliation(s)
- Giulio Bonifazi
- Basque Center for Applied Mathematics, Alameda Mazarredo 14, Bilbao 48009, Bizkaia, Spain; Department of Neurosciences, University of the Basque Country, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Krembil Research Institute, University Health Network, 60 Leonard Ave, Toronto M5T 0S8, ON, Canada
| | - Celia Luchena
- Department of Neurosciences, University of the Basque Country, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Achucarro Basque Center for Neuroscience, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain
| | - Adhara Gaminde-Blasco
- Department of Neurosciences, University of the Basque Country, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Achucarro Basque Center for Neuroscience, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain
| | - Carolina Ortiz-Sanz
- Department of Neurosciences, University of the Basque Country, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Achucarro Basque Center for Neuroscience, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain
| | - Estibaliz Capetillo-Zarate
- Department of Neurosciences, University of the Basque Country, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Achucarro Basque Center for Neuroscience, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain
| | - Carlos Matute
- Department of Neurosciences, University of the Basque Country, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Achucarro Basque Center for Neuroscience, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain
| | - Elena Alberdi
- Department of Neurosciences, University of the Basque Country, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Achucarro Basque Center for Neuroscience, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain
| | - Maurizio De Pittà
- Basque Center for Applied Mathematics, Alameda Mazarredo 14, Bilbao 48009, Bizkaia, Spain; Department of Neurosciences, University of the Basque Country, Barrio Sarriena, s/n, Leioa 48940, Bizkaia, Spain; Krembil Research Institute, University Health Network, 60 Leonard Ave, Toronto M5T 0S8, ON, Canada; Department of Physiology, University of Toronto, 1 King's College Circle, Toronto M5S 1A8, ON, Canada.
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10
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Dummer PD, Lee DI, Hossain S, Wang R, Evard A, Newman G, Ho C, Schneider-Mizell CM, Menon V, Au E. Multidimensional analysis of cortical interneuron synaptic features reveals underlying synaptic heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586340. [PMID: 38659827 PMCID: PMC11042224 DOI: 10.1101/2024.03.22.586340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cortical interneurons represent a diverse set of neuronal subtypes characterized in part by their striking degree of synaptic specificity. However, little is known about the extent of synaptic diversity because of the lack of unbiased methods to extract synaptic features among interneuron subtypes. Here, we develop an approach to aggregate image features from fluorescent confocal images of interneuron synapses and their post-synaptic targets, in order to characterize the heterogeneity of synapses at fine scale. We started by training a model that recognizes pre- and post-synaptic compartments and then determines the target of each genetically-identified interneuron synapse in vitro and in vivo. Our model extracts hundreds of spatial and intensity features from each analyzed synapse, constructing a multidimensional data set, consisting of millions of synapses, which allowed us to perform an unsupervised analysis on this dataset, uncovering novel synaptic subgroups. The subgroups were spatially distributed in a highly structured manner that revealed the local underlying topology of the postsynaptic environment. Dendrite-targeting subgroups were clustered onto subdomains of the dendrite along the proximal to distal axis. Soma-targeting subgroups were enriched onto different postsynaptic cell types. We also find that the two main subclasses of interneurons, basket cells and somatostatin interneurons, utilize distinct strategies to enact inhibitory coverage. Thus, our analysis of multidimensional synaptic features establishes a conceptual framework for studying interneuron synaptic diversity.
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Affiliation(s)
- Patrick D. Dummer
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Dylan I. Lee
- Department of Neurology, Columbia Irving Medical Center, New York NY, 10032
| | - Sakib Hossain
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Runsheng Wang
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Andre Evard
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Gabriel Newman
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Claire Ho
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | | | - Vilas Menon
- Department of Neurology, Columbia Irving Medical Center, New York NY, 10032
| | - Edmund Au
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
- Columbia Translation Neuroscience Initiative Fellow, Columbia Irving Medical Center, New York NY, 10032
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11
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Delhaye M, LeDue J, Robinson K, Xu Q, Zhang Q, Oku S, Zhang P, Craig AM. Adaptation of Magnified Analysis of the Proteome for Excitatory Synaptic Proteins in Varied Samples and Evaluation of Cell Type-Specific Distributions. J Neurosci 2024; 44:e1291232024. [PMID: 38360747 PMCID: PMC10993037 DOI: 10.1523/jneurosci.1291-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024] Open
Abstract
Growing evidence suggests a remarkable diversity and complexity in the molecular composition of synapses, forming the basis for the brain to execute complex behaviors. Hence, there is considerable interest in visualizing the spatial distribution of such molecular diversity at individual synapses within intact brain circuits. Yet this task presents significant technical challenges. Expansion microscopy approaches have revolutionized our view of molecular anatomy. However, their use to study synapse-related questions outside of the labs developing them has been limited. Here we independently adapted a version of Magnified Analysis of the Proteome (MAP) and present a step-by-step protocol for visualizing over 40 synaptic proteins in brain circuits. Surprisingly, our findings show that the advantage of MAP over conventional immunolabeling was primarily due to improved antigen recognition and secondarily physical expansion. Furthermore, we demonstrated the versatile use of MAP in brains perfused with paraformaldehyde or fresh-fixed with formalin and in formalin-fixed paraffin-embedded tissue. These tests expand the potential applications of MAP to combinations with slice electrophysiology or clinical pathology specimens. Using male and female mice expressing YFP-ChR2 exclusively in interneurons, we revealed a distinct composition of AMPA and NMDA receptors and Shank family members at synapses on hippocampal interneurons versus on pyramidal neurons. Quantitative single synapse analyses yielded comprehensive cell type distributions of synaptic proteins and their relationships. These findings exemplify the value of the versatile adapted MAP procedure presented here as an accessible tool for the broad neuroscience community to unravel the complexity of the "synaptome" across brain circuits and disease states.
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Affiliation(s)
- Mathias Delhaye
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Jeffrey LeDue
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Kaylie Robinson
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Qin Xu
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Qian Zhang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Shinichiro Oku
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Peng Zhang
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Ann Marie Craig
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
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12
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Griebel U, Oller DK. From emotional signals to symbols. Front Psychol 2024; 15:1135288. [PMID: 38629043 PMCID: PMC11020113 DOI: 10.3389/fpsyg.2024.1135288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
The quest for the origins of language is a diverse enterprise, where research from a variety of disciplines brings area-specific ideas and area-specific terminology to bear. This variety often results in misunderstandings and misconceptions about communication in various species. In the present paper, we argue for focus on emotional systems as the primary motivators for social signals in animals in general. This focus can help resolve discrepancies of interpretation among different areas of inquiry and can illuminate distinctions among different social signals as well as their phylogenetic origins in animals and especially in humans. We advocate, following Jaak Panksepp, a view wherein the Seeking System, the endogenous tendency to search and explore, is the most fundamental emotional motivation. The Seeking System forms the basis for flexible, voluntary, and exploratory control of motor systems and makes much of learning possible. The relative lack of vocal learning and expression in nonhuman primates contrasted with extensive vocal learning and expression in humans began, we propose, with the evolution in ancient hominins of a necessary foundation for the many subsequent capabilities required for language. That foundation was, according to the reasoning, naturally selected in the form of neurological connections between the Seeking System and mechanisms of glottal/phonatory control. The new connections allowed ancient hominins to develop flexible, endogenous vocal fitness signals produced at very high rates and including large numbers of discrete syllables, recombinable to form syllable combinations with many prosodic variations. The increasing sociality of hominins supported evolution of massive expansion in the utilization of these flexible vocal forms to allow development of words and sentences.
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Affiliation(s)
- Ulrike Griebel
- School of Communication Sciences and Disorders, The University of Memphis, Memphis, TN, United States
- The Institute for Intelligent Systems, University of Memphis, Memphis, TN, United States
- The Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
| | - D. Kimbrough Oller
- School of Communication Sciences and Disorders, The University of Memphis, Memphis, TN, United States
- The Institute for Intelligent Systems, University of Memphis, Memphis, TN, United States
- The Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
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13
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Eteleeb AM, Novotny BC, Tarraga CS, Sohn C, Dhungel E, Brase L, Nallapu A, Buss J, Farias F, Bergmann K, Bradley J, Norton J, Gentsch J, Wang F, Davis AA, Morris JC, Karch CM, Perrin RJ, Benitez BA, Harari O. Brain high-throughput multi-omics data reveal molecular heterogeneity in Alzheimer's disease. PLoS Biol 2024; 22:e3002607. [PMID: 38687811 PMCID: PMC11086901 DOI: 10.1371/journal.pbio.3002607] [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: 09/06/2023] [Revised: 05/10/2024] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Unbiased data-driven omic approaches are revealing the molecular heterogeneity of Alzheimer disease. Here, we used machine learning approaches to integrate high-throughput transcriptomic, proteomic, metabolomic, and lipidomic profiles with clinical and neuropathological data from multiple human AD cohorts. We discovered 4 unique multimodal molecular profiles, one of them showing signs of poor cognitive function, a faster pace of disease progression, shorter survival with the disease, severe neurodegeneration and astrogliosis, and reduced levels of metabolomic profiles. We found this molecular profile to be present in multiple affected cortical regions associated with higher Braak tau scores and significant dysregulation of synapse-related genes, endocytosis, phagosome, and mTOR signaling pathways altered in AD early and late stages. AD cross-omics data integration with transcriptomic data from an SNCA mouse model revealed an overlapping signature. Furthermore, we leveraged single-nuclei RNA-seq data to identify distinct cell-types that most likely mediate molecular profiles. Lastly, we identified that the multimodal clusters uncovered cerebrospinal fluid biomarkers poised to monitor AD progression and possibly cognition. Our cross-omics analyses provide novel critical molecular insights into AD.
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Affiliation(s)
- Abdallah M. Eteleeb
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University, St. Louis, Missouri, United States of America
| | - Brenna C. Novotny
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
| | - Carolina Soriano Tarraga
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
| | - Christopher Sohn
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
| | - Eliza Dhungel
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Logan Brase
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
| | - Aasritha Nallapu
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
| | - Jared Buss
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
| | - Fabiana Farias
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
- NeuroGenomics and Informatics Center, Washington University, St. Louis, Missouri, United States of America
| | - Kristy Bergmann
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
- NeuroGenomics and Informatics Center, Washington University, St. Louis, Missouri, United States of America
| | - Joseph Bradley
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
- NeuroGenomics and Informatics Center, Washington University, St. Louis, Missouri, United States of America
| | - Joanne Norton
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
- NeuroGenomics and Informatics Center, Washington University, St. Louis, Missouri, United States of America
| | - Jen Gentsch
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
- NeuroGenomics and Informatics Center, Washington University, St. Louis, Missouri, United States of America
| | - Fengxian Wang
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
- NeuroGenomics and Informatics Center, Washington University, St. Louis, Missouri, United States of America
| | - Albert A. Davis
- Department of Neurology, Washington University, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University, St. Louis, Missouri, United States of America
| | - John C. Morris
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University, St. Louis, Missouri, United States of America
- Department of Neurology, Washington University, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University, St. Louis, Missouri, United States of America
| | - Celeste M. Karch
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University, St. Louis, Missouri, United States of America
- NeuroGenomics and Informatics Center, Washington University, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University, St. Louis, Missouri, United States of America
| | - Richard J. Perrin
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University, St. Louis, Missouri, United States of America
- Department of Neurology, Washington University, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri, United States of America
| | - Bruno A. Benitez
- Department of Neurology and Neuroscience, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Oscar Harari
- Department of Psychiatry, Washington University, Saint Louis, St. Louis, Missouri, United States of America
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University, St. Louis, Missouri, United States of America
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14
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Timonidis N, Rubio-Teves M, Alonso-Martínez C, Bakker R, García-Amado M, Tiesinga P, Clascá F. Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference Space. Neuroinformatics 2024; 22:23-43. [PMID: 37864741 PMCID: PMC10917831 DOI: 10.1007/s12021-023-09644-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2023] [Indexed: 10/23/2023]
Abstract
Current mesoscale connectivity atlases provide limited information about the organization of thalamocortical projections in the mouse brain. Labeling the projections of spatially restricted neuron populations in thalamus can provide a functionally relevant level of connectomic analysis, but these need to be integrated within the same common reference space. Here, we present a pipeline for the segmentation, registration, integration and analysis of multiple tract-tracing experiments. The key difference with other workflows is that the data is transformed to fit the reference template. As a test-case, we investigated the axonal projections and intranuclear arrangement of seven neuronal populations of the ventral posteromedial nucleus of the thalamus (VPM), which we labeled with an anterograde tracer. Their soma positions corresponded, from dorsal to ventral, to cortical representations of the whiskers, nose and mouth. They strongly targeted layer 4, with the majority exclusively targeting one cortical area and the ones in ventrolateral VPM branching to multiple somatosensory areas. We found that our experiments were more topographically precise than similar experiments from the Allen Institute and projections to the primary somatosensory area were in agreement with single-neuron morphological reconstructions from publicly available databases. This pilot study sets the basis for a shared virtual connectivity atlas that could be enriched with additional data for studying the topographical organization of different thalamic nuclei. The pipeline is accessible with only minimal programming skills via a Jupyter Notebook, and offers multiple visualization tools such as cortical flatmaps, subcortical plots and 3D renderings and can be used with custom anatomical delineations.
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Affiliation(s)
- Nestor Timonidis
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Mario Rubio-Teves
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, C. Arzobispo Morcillo 4, 28029, Madrid, Spain
| | - Carmen Alonso-Martínez
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, C. Arzobispo Morcillo 4, 28029, Madrid, Spain
| | - Rembrandt Bakker
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Inst. of Neuroscience and Medicine (INM-6) and Inst. for Advanced Simulation (IAS-6) and JARA BRAIN Inst. I, Jülich Research Centre, Wilhelm-Johnen-Strasse, 52425, Jülich, Germany
| | - María García-Amado
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, C. Arzobispo Morcillo 4, 28029, Madrid, Spain
| | - Paul Tiesinga
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Francisco Clascá
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, C. Arzobispo Morcillo 4, 28029, Madrid, Spain
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15
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Ortega-de San Luis C, Pezzoli M, Urrieta E, Ryan TJ. Engram cell connectivity as a mechanism for information encoding and memory function. Curr Biol 2023; 33:5368-5380.e5. [PMID: 37992719 DOI: 10.1016/j.cub.2023.10.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/18/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023]
Abstract
Information derived from experiences is incorporated into the brain as changes to ensembles of cells, termed engram cells, which allow memory storage and recall. The mechanism by which those changes hold specific information is unclear. Here, we test the hypothesis that the specific synaptic wiring between engram cells is the substrate of information storage. First, we monitor how learning modifies the connectivity pattern between engram cells at a monosynaptic connection involving the hippocampal ventral CA1 (vCA1) region and the amygdala. Then, we assess the functional significance of these connectivity changes by artificially activating or inhibiting its presynaptic and postsynaptic components, respectively. Finally, we identify a synaptic plasticity mechanism mediated by postsynaptic density protein 95 (PSD-95), which impacts the connectivity pattern among engram cells and contributes to the long-term stability of the memory. These findings impact our theory of learning and memory by helping us explain the translation of specific information into engram cells and how these connections shape brain function.
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Affiliation(s)
- Clara Ortega-de San Luis
- School of Biochemistry and Immunology, Trinity College of Dublin, Dublin D02 PN40, Ireland; Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Maurizio Pezzoli
- School of Biochemistry and Immunology, Trinity College of Dublin, Dublin D02 PN40, Ireland; Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Esteban Urrieta
- School of Biochemistry and Immunology, Trinity College of Dublin, Dublin D02 PN40, Ireland; Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Tomás J Ryan
- School of Biochemistry and Immunology, Trinity College of Dublin, Dublin D02 PN40, Ireland; Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin D02 PN40, Ireland; Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Melbourne, VIC 3052, Australia; Child & Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada.
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16
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Micheva KD, Gong B, Collman F, Weinberg RJ, Smith SJ, Trimmer JS, Murray KD. Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses. eNeuro 2023; 10:ENEURO.0290-23.2023. [PMID: 37945352 PMCID: PMC10748464 DOI: 10.1523/eneuro.0290-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Antibody (Ab)-based imaging techniques rely on reagents whose performance may be application specific. Because commercial antibodies are validated for only a few purposes, users interested in other applications may have to perform extensive in-house antibody testing. Here, we present a novel application-specific proxy screening step to efficiently identify candidate antibodies for array tomography (AT), a serial section volume microscopy technique for high-dimensional quantitative analysis of the cellular proteome. To identify antibodies suitable for AT-based analysis of synapses in mammalian brain, we introduce a heterologous cell-based assay that simulates characteristic features of AT, such as chemical fixation and resin embedding that are likely to influence antibody binding. The assay was included into an initial screening strategy to generate monoclonal antibodies that can be used for AT. This approach simplifies the screening of candidate antibodies and has high predictive value for identifying antibodies suitable for AT analyses. In addition, we have created a comprehensive database of AT-validated antibodies with a neuroscience focus and show that these antibodies have a high likelihood of success for postembedding applications in general, including immunogold electron microscopy. The generation of a large and growing toolbox of AT-compatible antibodies will further enhance the value of this imaging technique.
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Affiliation(s)
- Kristina D Micheva
- Department of Cellular and Molecular Physiology, Stanford School of Medicine, Stanford, 94305, CA
| | - Belvin Gong
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, 95618, CA
| | | | - Richard J Weinberg
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, 27514, NC
| | | | - James S Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, 95618, CA
| | - Karl D Murray
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, 95618, CA
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, 95618, CA
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17
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Su C, Miao J, Guo J. The relationship between TGF-β1 and cognitive function in the brain. Brain Res Bull 2023; 205:110820. [PMID: 37979810 DOI: 10.1016/j.brainresbull.2023.110820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/05/2023] [Accepted: 11/15/2023] [Indexed: 11/20/2023]
Abstract
Transforming growth factor-β1 (TGF-β1), a multifunctional cytokine, plays a pivotal role in synaptic formation, plasticity, and neurovascular unit regulation. This review highlights TGF-β1's potential impact on cognitive function, particularly in the context of neurodegenerative disorders. However, despite the growing body of evidence, a comprehensive understanding of TGF-β1's precise role remains elusive. Further research is essential to unravel the complex mechanisms through which TGF-β1 influences cognitive function and to explore therapeutic avenues for targeting TGF-β1 in neurodegenerative conditions. This investigation sheds light on TGF-β1's contribution to cognitive function and offers prospects for innovative treatments and interventions. This review delves into the intricate relationship between TGF-β1 and cognitive function.
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Affiliation(s)
- Chen Su
- Department of Neurology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province 030000, China
| | - Jie Miao
- Department of Neurology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province 030000, China
| | - Junhong Guo
- Department of Neurology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province 030000, China.
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18
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Woelfle S, Pedro MT, Wagner J, Schön M, Boeckers TM. Expression profiles of the autism-related SHANK proteins in the human brain. BMC Biol 2023; 21:254. [PMID: 37953224 PMCID: PMC10641957 DOI: 10.1186/s12915-023-01712-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/25/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND SHANKs are major scaffolding proteins at postsynaptic densities (PSDs) in the central nervous system. Mutations in all three family members have been associated with neurodevelopmental disorders such as autism spectrum disorders (ASDs). Despite the pathophysiological importance of SHANK2 and SHANK3 mutations in humans, research on the expression of these proteins is mostly based on rodent model organisms. RESULTS In the present study, cellular and neuropil SHANK2 expression was analyzed by immunofluorescence (IF) staining of post mortem human brain tissue from four male individuals (19 brain regions). Mouse brains were analyzed in comparison to evaluate the degree of phylogenetic conservation. Furthermore, SHANK2 and SHANK3 isoform patterns were compared in human and mouse brain lysates. While isoform expression and subcellular distribution were largely conserved, differences in neuropil levels of SHANK2 were found by IF staining: Maximum expression was concordantly measured in the cerebellum; however, higher SHANK2 expression was detected in the human brainstem and thalamus when compared to mice. One of the lowest SHANK2 levels was found in the human amygdala, a moderately expressing region in mouse. Quantification of SHANK3 IF in mouse brains unveiled a distribution comparable to humans. CONCLUSIONS In summary, these data show that the overall expression pattern of SHANK is largely conserved in defined brain regions; however, differences do exist, which need to be considered in the translation of rodent studies. The summarized expression patterns of SHANK2 and SHANK3 should serve as a reference for future studies.
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Affiliation(s)
- Sarah Woelfle
- Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Maria T Pedro
- Department of Neurosurgery, Ulm University, Campus Günzburg, Lindenallee 2, 89312, Günzburg, Germany
| | - Jan Wagner
- Department of Neurology, Ulm University and Universitäts- and Rehabilitationskliniken Ulm, 89081, Ulm, Germany
| | - Michael Schön
- Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
| | - Tobias M Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
- Deutsches Zentrum Für Neurodegenerative Erkrankungen, DZNE, Ulm Site, 89081, Ulm, Germany.
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19
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Micheva KD, Gong B, Collman F, Weinberg RJ, Smith SJ, Trimmer JS, Murray KD. Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546920. [PMID: 37425759 PMCID: PMC10327040 DOI: 10.1101/2023.06.28.546920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Antibody-based imaging techniques rely on reagents whose performance may be application-specific. Because commercial antibodies are validated for only a few purposes, users interested in other applications may have to perform extensive in-house antibody testing. Here we present a novel application-specific proxy screening step to efficiently identify candidate antibodies for array tomography (AT), a serial section volume microscopy technique for high-dimensional quantitative analysis of the cellular proteome. To identify antibodies suitable for AT-based analysis of synapses in mammalian brain, we introduce a heterologous cell-based assay that simulates characteristic features of AT, such as chemical fixation and resin embedding that are likely to influence antibody binding. The assay was included into an initial screening strategy to generate monoclonal antibodies that can be used for AT. This approach simplifies the screening of candidate antibodies and has high predictive value for identifying antibodies suitable for AT analyses. In addition, we have created a comprehensive database of AT-validated antibodies with a neuroscience focus and show that these antibodies have a high likelihood of success for postembedding applications in general, including immunogold electron microscopy. The generation of a large and growing toolbox of AT-compatible antibodies will further enhance the value of this imaging technique.
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Affiliation(s)
- Kristina D. Micheva
- Department of Cellular and Molecular Physiology, Stanford School of Medicine, Stanford, CA
| | - Belvin Gong
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
| | | | - Richard J. Weinberg
- Department of Cell Biology & Physiology, University of North Carolina, Chapel Hill, NC
| | | | - James S. Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
| | - Karl D. Murray
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA
- Department of Psychiatry & Behavioral Sciences, University of California, Davis, CA
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20
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Luis CODS, Pezzoli M, Urrieta E, Ryan TJ. Engram cell connectivity as a mechanism for information encoding and memory function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558774. [PMID: 37790352 PMCID: PMC10542553 DOI: 10.1101/2023.09.21.558774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Information derived from experiences is incorporated into the brain as changes to ensembles of cells, termed engram cells, that allow memory storage and recall. The mechanism by which those changes hold specific information is unclear. Here we test the hypothesis that the specific synaptic wiring between engram cells is the substrate of information storage. First, we monitor how learning modifies the connectivity pattern between engram cells at a monosynaptic connection involving the hippocampal vCA1 region and the amygdala. Then, we assess the functional significance of these connectivity changes by artificially activating or inhibiting its presynaptic and postsynaptic components respectively. Finally, we identify a synaptic plasticity mechanism mediated by PSD-95, which impacts the connectivity pattern among engram cells and contributes to the long-term stability of the memory. These findings impact our theory of learning and memory by helping us explain the translation of specific information into engram cells and how these connections shape brain function.
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Affiliation(s)
- Clara Ortega-de San Luis
- School of Biochemistry and Immunology, Trinity College of Dublin, Dublin, Ireland
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Maurizio Pezzoli
- School of Biochemistry and Immunology, Trinity College of Dublin, Dublin, Ireland
- Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Esteban Urrieta
- School of Biochemistry and Immunology, Trinity College of Dublin, Dublin, Ireland
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Tomás J Ryan
- School of Biochemistry and Immunology, Trinity College of Dublin, Dublin, Ireland
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
- Florey Institute of Neuroscience and Mental Health, Melbourne Brain Centre, University of Melbourne, Melbourne, Victoria, Australia
- Child & Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada
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21
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Metzbower SR, Dharmasri PA, Levy AD, Anderson MC, Blanpied TA. Distinct SAP102 and PSD-95 nano-organization defines multiple types of synaptic scaffold protein domains at single synapses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557372. [PMID: 37745494 PMCID: PMC10515860 DOI: 10.1101/2023.09.12.557372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The MAGUK family of scaffold proteins plays a central role in maintaining and modulating synaptic signaling, providing a framework to retain and position receptors, signaling molecules, and other synaptic components. Of these scaffold proteins, SAP102 and PSD-95 are essential for synaptic function at distinct developmental timepoints and perform overlapping as well as unique roles. While their similar structures allow for common binding partners, SAP102 is expressed earlier in synapse development and is required for synaptogenesis, whereas PSD-95 expression peaks later in development and is associated with synapse maturation. PSD-95 and other key synaptic proteins organize into subsynaptic nanodomains that have a significant impact on synaptic transmission, but the nanoscale organization of SAP102 is unknown. How SAP102 is organized within the synapse, and how it relates spatially to PSD-95 on a nanometer scale, could impact how SAP102 clusters synaptic proteins and underlie its ability to perform its unique functions. Here we used DNA-PAINT super-resolution microscopy to measure SAP102 nano-organization and its spatial relationship to PSD-95 at individual synapses. We found that like PSD-95, SAP102 accumulates in high-density subsynaptic nanoclusters. However, SAP102 nanoclusters were smaller and denser than PSD-95 nanoclusters across development. Additionally, only a subset of SAP102 nanoclusters co-organized with PSD-95, revealing that within individual synapses there are nanodomains that contain either one or both proteins. This organization into both shared and distinct subsynaptic nanodomains may underlie the ability of SAP102 and PSD-95 to perform both common and unique synaptic functions.
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Affiliation(s)
- Sarah R. Metzbower
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Poorna A. Dharmasri
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Aaron D. Levy
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Michael C. Anderson
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Thomas A. Blanpied
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201
- University of Maryland Medicine Institute for Neuroscience Discovery, University of Maryland School of Medicine, Baltimore, MD 21201
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22
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Ulloa Severino FP, Lawal OO, Sakers K, Wang S, Kim N, Friedman AD, Johnson SA, Sriworarat C, Hughes RH, Soderling SH, Kim IH, Yin HH, Eroglu C. Training-induced circuit-specific excitatory synaptogenesis in mice is required for effort control. Nat Commun 2023; 14:5522. [PMID: 37684234 PMCID: PMC10491649 DOI: 10.1038/s41467-023-41078-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Synaptogenesis is essential for circuit development; however, it is unknown whether it is critical for the establishment and performance of goal-directed voluntary behaviors. Here, we show that operant conditioning via lever-press for food reward training in mice induces excitatory synapse formation onto a subset of anterior cingulate cortex neurons projecting to the dorsomedial striatum (ACC→DMS). Training-induced synaptogenesis is controlled by the Gabapentin/Thrombospondin receptor α2δ-1, which is an essential neuronal protein for proper intracortical excitatory synaptogenesis. Using germline and conditional knockout mice, we found that deletion of α2δ-1 in the adult ACC→DMS circuit diminishes training-induced excitatory synaptogenesis. Surprisingly, this manipulation does not impact learning but results in a significant increase in effort exertion without affecting sensitivity to reward value or changing contingencies. Bidirectional optogenetic manipulation of ACC→DMS neurons rescues or phenocopies the behaviors of the α2δ-1 cKO mice, highlighting the importance of synaptogenesis within this cortico-striatal circuit in regulating effort exertion.
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Affiliation(s)
- Francesco Paolo Ulloa Severino
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Psychology and Neuroscience, Duke University, Durham, NC, 27710, USA.
- Cajal Institute (CSIC), Madrid, 28001, Spain.
| | | | - Kristina Sakers
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Shiyi Wang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Namsoo Kim
- Department of Psychology and Neuroscience, Duke University, Durham, NC, 27710, USA
| | | | - Sarah Anne Johnson
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | | | - Ryan H Hughes
- Department of Psychology and Neuroscience, Duke University, Durham, NC, 27710, USA
| | - Scott H Soderling
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Institute for Brain Sciences (DIBS), Durham, NC, 27710, USA
| | - Il Hwan Kim
- Department of Anatomy & Neurobiology, University of Tennessee Health and Science Center, Memphis, TN, 38103, USA
| | - Henry H Yin
- Department of Psychology and Neuroscience, Duke University, Durham, NC, 27710, USA.
- Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Duke Institute for Brain Sciences (DIBS), Durham, NC, 27710, USA.
| | - Cagla Eroglu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Duke Institute for Brain Sciences (DIBS), Durham, NC, 27710, USA.
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27710, USA.
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23
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Niu M, Cao W, Wang Y, Zhu Q, Luo J, Wang B, Zheng H, Weitz DA, Zong C. Droplet-based transcriptome profiling of individual synapses. Nat Biotechnol 2023; 41:1332-1344. [PMID: 36646931 DOI: 10.1038/s41587-022-01635-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/06/2022] [Indexed: 01/17/2023]
Abstract
Synapses are crucial structures that mediate signal transmission between neurons in complex neural circuits and display considerable morphological and electrophysiological heterogeneity. So far we still lack a high-throughput method to profile the molecular heterogeneity among individual synapses. In the present study, we develop a droplet-based single-cell (sc) total-RNA-sequencing platform, called Multiple-Annealing-and-Tailing-based Quantitative scRNA-seq in Droplets, for transcriptome profiling of individual neurites, primarily composed of synaptosomes. In the synaptosome transcriptome, or 'synaptome', profiling of both mouse and human brain samples, we detect subclusters among synaptosomes that are associated with neuronal subtypes and characterize the landscape of transcript splicing that occurs within synapses. We extend synaptome profiling to synaptopathy in an Alzheimer's disease (AD) mouse model and discover AD-associated synaptic gene expression changes that cannot be detected by single-nucleus transcriptome profiling. Overall, our results show that this platform provides a high-throughput, single-synaptosome transcriptome profiling tool that will facilitate future discoveries in neuroscience.
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Affiliation(s)
- Muchun Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Wenjian Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, TX, USA
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, China
| | - Yongcheng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Wyss Institute of Bioinspired Engineering, Harvard University, Cambridge, MA, USA
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Qiangyuan Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, China
| | - Jiayi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Baiping Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Hui Zheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - David A Weitz
- Wyss Institute of Bioinspired Engineering, Harvard University, Cambridge, MA, USA.
- Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- McNair Medical Institute, Baylor College of Medicine, Houston, TX, USA.
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24
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Li C, Kühn NK, Alkislar I, Sans-Dublanc A, Zemmouri F, Paesmans S, Calzoni A, Ooms F, Reinhard K, Farrow K. Pathway-specific inputs to the superior colliculus support flexible responses to visual threat. SCIENCE ADVANCES 2023; 9:eade3874. [PMID: 37647395 PMCID: PMC10468139 DOI: 10.1126/sciadv.ade3874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Behavioral flexibility requires directing feedforward sensory information to appropriate targets. In the superior colliculus, divergent outputs orchestrate different responses to visual threats, but the circuit organization enabling the flexible routing of sensory information remains unknown. To determine this structure, we focused on inhibitory projection (Gad2) neurons. Trans-synaptic tracing and neuronal recordings revealed that Gad2 neurons projecting to the lateral geniculate nucleus (LGN) and the parabigeminal nucleus (PBG) form two separate populations, each receiving a different set of non-retinal inputs. Inhibiting the LGN- or PBG-projecting Gad2 neurons resulted in opposing effects on behavior; increasing freezing or escape probability to visual looming, respectively. Optogenetic activation of selected inputs to the LGN- and PBG-projecting Gad2 cells predictably regulated responses to visual threat. These data suggest that projection-specific sampling of brain-wide inputs provides a circuit design principle that enables visual inputs to be selectively routed to produce context-specific behavior.
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Affiliation(s)
- Chen Li
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Norma K. Kühn
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Ilayda Alkislar
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Northeastern University, Boston, MA, USA
| | - Arnau Sans-Dublanc
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Firdaouss Zemmouri
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Faculty of Pharmaceutical, Biomedical, and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Soraya Paesmans
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Alex Calzoni
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Frédérique Ooms
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Imec, Leuven, Belgium
| | - Katja Reinhard
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Karl Farrow
- Neuro-Electronics Research Flanders, VIB, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
- Imec, Leuven, Belgium
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25
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Hobson BD, Herzog E. Methodological concerns and lack of evidence for single-synapse RNA-seq. Nat Biotechnol 2023; 41:1221-1224. [PMID: 37500915 DOI: 10.1038/s41587-023-01877-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Affiliation(s)
- Benjamin D Hobson
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA.
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Psychiatry, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA.
| | - Etienne Herzog
- University of Bordeaux, CNRS, IINS, UMR 5297, Bordeaux, France.
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26
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Broadhead MJ, Ayvazian-Hancock A, Doucet K, Kantelberg O, Motherwell L, Zhu F, Grant SGN, Horrocks MH, Miles GB. Synaptic expression of TAR-DNA-binding protein 43 in the mouse spinal cord determined using super-resolution microscopy. Front Mol Neurosci 2023; 16:1027898. [PMID: 37671010 PMCID: PMC10475998 DOI: 10.3389/fnmol.2023.1027898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/22/2023] [Indexed: 09/07/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is characterised by a loss of motor neurons in the brain and spinal cord that is preceded by early-stage changes in synapses that may be associated with TAR-DNA-Binding Protein 43 (TDP-43) pathology. Cellular inclusions of hyperphosphorylated TDP-43 (pTDP-43) are a key hallmark of neurodegenerative diseases such ALS. However, there has been little characterisation of the synaptic expression of TDP-43 inside subpopulations of spinal cord synapses. This study utilises a range of high-resolution and super-resolution microscopy techniques with immunolabelling, as well as an aptamer-based TDP-43 labelling strategy visualised with single-molecule localisation microscopy, to characterise and quantify the presence of pTDP-43 in populations of excitatory synapses near where motor neurons reside in the lateral ventral horn of the mouse lumbar spinal cord. We observe that TDP-43 is expressed in approximately half of spinal cord synapses as nanoscale clusters. Synaptic TDP-43 clusters are found most abundantly at synapses associated with VGLUT1-positive presynaptic terminals, compared to VGLUT2-associated synapses. Our nanoscopy techniques showed no difference in the subsynaptic expression of pTDP-43 in the ALS mouse model, SOD1G93a, compared to healthy controls, despite prominent structural deficits in VGLUT1-associated synapses in SOD1G93a mice. This research characterises the basic synaptic expression of TDP-43 with nanoscale precision and provides a framework with which to investigate the potential relationship between TDP-43 pathology and synaptic pathology in neurodegenerative diseases.
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Affiliation(s)
- Matthew J. Broadhead
- School of Psychology and Neuroscience, University of St. Andrews, St. Andrews, United Kingdom
- Centre of Biophotonics, University of St. Andrews, St. Andrews, United Kingdom
- Edinburgh Super-Resolution Imaging Consortium, Heriot-Watt University, Edinburgh, United Kingdom
| | - Ani Ayvazian-Hancock
- School of Psychology and Neuroscience, University of St. Andrews, St. Andrews, United Kingdom
- Centre of Biophotonics, University of St. Andrews, St. Andrews, United Kingdom
| | - Katherine Doucet
- School of Psychology and Neuroscience, University of St. Andrews, St. Andrews, United Kingdom
- Centre of Biophotonics, University of St. Andrews, St. Andrews, United Kingdom
| | - Owen Kantelberg
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Lesley Motherwell
- School of Psychology and Neuroscience, University of St. Andrews, St. Andrews, United Kingdom
- Centre of Biophotonics, University of St. Andrews, St. Andrews, United Kingdom
| | - Fei Zhu
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Seth G. N. Grant
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mathew H. Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
- IRR Chemistry Hub, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Gareth B. Miles
- School of Psychology and Neuroscience, University of St. Andrews, St. Andrews, United Kingdom
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27
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Dowling P, Zweyer M, Sabir H, Henry M, Meleady P, Swandulla D, Ohlendieck K. Mass spectrometry-based proteomic characterization of the middle-aged mouse brain for animal model research of neuromuscular diseases. Eur J Transl Myol 2023; 33:11553. [PMID: 37545360 PMCID: PMC10583138 DOI: 10.4081/ejtm.2023.11553] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023] Open
Abstract
Neuromuscular diseases with primary muscle wasting symptoms may also display multi-systemic changes in the body and exhibit secondary pathophysiological alterations in various non-muscle tissues. In some cases, this includes proteome-wide alterations and/or adaptations in the central nervous system. Thus, in order to provide an improved bioanalytical basis for the comprehensive evaluation of animal models that are routinely used in muscle research, this report describes the mass spectrometry-based proteomic characterization of the mouse brain. Crude tissue extracts were examined by bottom-up proteomics and detected 4558 distinct protein species. The detailed analysis of the brain proteome revealed the presence of abundant cellular proteoforms in the neuronal cytoskeleton, as well as various brain region enriched proteins, including markers of the cerebral cortex, cerebellum, hippocampus and the olfactory bulb. Neuroproteomic markers of specific cell types in the brain were identified in association with various types of neurons and glia cells. Markers of subcellular structures were established for the plasmalemma, nucleus, endoplasmic reticulum, mitochondria and other crucial organelles, as well as synaptic components that are involved in presynaptic vesicle docking, neurotransmitter release and synapse remodelling.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; German Centre for Neurodegenerative Diseases, University of Bonn, Bonn.
| | - Hemmen Sabir
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; German Centre for Neurodegenerative Diseases, University of Bonn, Bonn.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
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28
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Zhu WH, Yang XX, Gou XZ, Fu SM, Chen JH, Gao F, Shen Y, Bi DL, Tang AH. Nanoscale reorganisation of synaptic proteins in Alzheimer's disease. Neuropathol Appl Neurobiol 2023; 49:e12924. [PMID: 37461203 DOI: 10.1111/nan.12924] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 05/30/2023] [Accepted: 06/24/2023] [Indexed: 08/31/2023]
Abstract
AIMS Synaptic strength depends strongly on the subsynaptic organisation of presynaptic transmitter release and postsynaptic receptor densities, and their alterations are expected to underlie pathologies. Although synaptic dysfunctions are common pathogenic traits of Alzheimer's disease (AD), it remains unknown whether synaptic protein nano-organisation is altered in AD. Here, we systematically characterised the alterations in the subsynaptic organisation in cellular and mouse models of AD. METHODS We used immunostaining and super-resolution stochastic optical reconstruction microscopy imaging to quantitatively examine the synaptic protein nano-organisation in both Aβ1-42-treated neuronal cultures and cortical sections from a mouse model of AD, APP23 mice. RESULTS We found that Aβ1-42-treatment of cultured hippocampal neurons decreased the synaptic retention of postsynaptic scaffolds and receptors and disrupted their nanoscale alignment to presynaptic transmitter release sites. In cortical sections, we found that while GluA1 receptors in wild-type mice were organised in subsynaptic nanoclusters with high local densities, receptors in APP23 mice distributed more homogeneously within synapses. This reorganisation, together with the reduced overall receptor density, led to reduced glutamatergic synaptic transmission. Meanwhile, the transsynaptic alignment between presynaptic release-guiding RIM1/2 and postsynaptic scaffolding protein PSD-95 was reduced in APP23 mice. Importantly, these reorganisations were progressive with age and were more pronounced in synapses in close vicinity of Aβ plaques with dense cores. CONCLUSIONS Our study revealed a spatiotemporal-specific reorganisation of synaptic nanostructures in AD and identifies dense-core amyloid plaques as the major local inductor in APP23 mice.
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Affiliation(s)
- Wang-Hui Zhu
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Xiao-Xu Yang
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Sciences and Technology of China, Hefei, China
- Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei, China
| | - Xu-Zhuo Gou
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Shu-Mei Fu
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Sciences and Technology of China, Hefei, China
- Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei, China
| | - Jia-Hui Chen
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei, China
| | - Feng Gao
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Sciences and Technology of China, Hefei, China
| | - Yong Shen
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Sciences and Technology of China, Hefei, China
- Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, China
| | - Dan-Lei Bi
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Sciences and Technology of China, Hefei, China
- Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, China
| | - Ai-Hui Tang
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute on Aging and Brain Disorders, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Sciences and Technology of China, Hefei, China
- Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei, China
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29
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Pitcher GM, Garzia L, Morrissy AS, Taylor MD, Salter MW. Synapse-specific diversity of distinct postsynaptic GluN2 subtypes defines transmission strength in spinal lamina I. Front Synaptic Neurosci 2023; 15:1197174. [PMID: 37503309 PMCID: PMC10368998 DOI: 10.3389/fnsyn.2023.1197174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/16/2023] [Indexed: 07/29/2023] Open
Abstract
The unitary postsynaptic response to presynaptic quantal glutamate release is the fundamental basis of excitatory information transfer between neurons. The view, however, of individual glutamatergic synaptic connections in a population as homogenous, fixed-strength units of neural communication is becoming increasingly scrutinized. Here, we used minimal stimulation of individual glutamatergic afferent axons to evoke single synapse resolution postsynaptic responses from central sensory lamina I neurons in an ex vivo adult rat spinal slice preparation. We detected unitary events exhibiting a NMDA receptor component with distinct kinetic properties across synapses conferred by specific GluN2 subunit composition, indicative of GluN2 subtype-based postsynaptic heterogeneity. GluN2A, 2A and 2B, or 2B and 2D synaptic predominance functioned on distinct lamina I neuron types to narrowly, intermediately, or widely tune, respectively, the duration of evoked unitary depolarization events from resting membrane potential, which enabled individual synapses to grade differentially depolarizing steps during temporally patterned afferent input. Our results lead to a model wherein a core locus of proteomic complexity prevails at this central glutamatergic sensory synapse that involves distinct GluN2 subtype configurations. These findings have major implications for subthreshold integrative capacity and transmission strength in spinal lamina I and other CNS regions.
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Affiliation(s)
- Graham M. Pitcher
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Livia Garzia
- Department of Surgery, Faculty of Medicine, McGill University, and Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - A. Sorana Morrissy
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael D. Taylor
- Brain Tumor Program, Texas Medical Centre, Houston, TX, United States
| | - Michael W. Salter
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
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30
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Kopsick JD, Tecuatl C, Moradi K, Attili SM, Kashyap HJ, Xing J, Chen K, Krichmar JL, Ascoli GA. Robust Resting-State Dynamics in a Large-Scale Spiking Neural Network Model of Area CA3 in the Mouse Hippocampus. Cognit Comput 2023; 15:1190-1210. [PMID: 37663748 PMCID: PMC10473858 DOI: 10.1007/s12559-021-09954-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/10/2021] [Indexed: 12/19/2022]
Abstract
Hippocampal area CA3 performs the critical auto-associative function underlying pattern completion in episodic memory. Without external inputs, the electrical activity of this neural circuit reflects the spontaneous spiking interplay among glutamatergic pyramidal neurons and GABAergic interneurons. However, the network mechanisms underlying these resting-state firing patterns are poorly understood. Leveraging the Hippocampome.org knowledge base, we developed a data-driven, large-scale spiking neural network (SNN) model of mouse CA3 with 8 neuron types, 90,000 neurons, 51 neuron-type specific connections, and 250,000,000 synapses. We instantiated the SNN in the CARLsim4 multi-GPU simulation environment using the Izhikevich and Tsodyks-Markram formalisms for neuronal and synaptic dynamics, respectively. We analyzed the resultant population activity upon transient activation. The SNN settled into stable oscillations with a biologically plausible grand-average firing frequency, which was robust relative to a wide range of transient activation. The diverse firing patterns of individual neuron types were consistent with existing knowledge of cell type-specific activity in vivo. Altered network structures that lacked neuron- or connection-type specificity were neither stable nor robust, highlighting the importance of neuron type circuitry. Additionally, external inputs reflecting dentate mossy fibers shifted the observed rhythms to the gamma band. We freely released the CARLsim4-Hippocampome framework on GitHub to test hippocampal hypotheses. Our SNN may be useful to investigate the circuit mechanisms underlying the computational functions of CA3. Moreover, our approach can be scaled to the whole hippocampal formation, which may contribute to elucidating how the unique neuronal architecture of this system subserves its crucial cognitive roles.
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Affiliation(s)
- Jeffrey D. Kopsick
- Interdepartmental Program in Neuroscience, George Mason University, Fairfax, VA, USA
| | - Carolina Tecuatl
- Bioengineering Department, Volgenau School of Engineering, George Mason University, Fairfax, VA, USA
| | - Keivan Moradi
- Interdepartmental Program in Neuroscience, George Mason University, Fairfax, VA, USA
| | - Sarojini M. Attili
- Interdepartmental Program in Neuroscience, George Mason University, Fairfax, VA, USA
| | - Hirak J. Kashyap
- Department of Computer Science, University of California, Irvine, Irvine, CA, USA
| | - Jinwei Xing
- Department of Cognitive Sciences, University of California, Irvine, Irvine, CA, USA
| | - Kexin Chen
- Department of Cognitive Sciences, University of California, Irvine, Irvine, CA, USA
| | - Jeffrey L. Krichmar
- Department of Cognitive Sciences, University of California, Irvine, Irvine, CA, USA
- Department of Computer Science, University of California, Irvine, Irvine, CA, USA
| | - Giorgio A. Ascoli
- Interdepartmental Program in Neuroscience, George Mason University, Fairfax, VA, USA
- Bioengineering Department, Volgenau School of Engineering, George Mason University, Fairfax, VA, USA
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31
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Yim YY, Nestler EJ. Cell-Type-Specific Neuroproteomics of Synapses. Biomolecules 2023; 13:998. [PMID: 37371578 PMCID: PMC10296650 DOI: 10.3390/biom13060998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
In the last two decades, our knowledge of synaptic proteomes and their relationship to normal brain function and neuropsychiatric disorders has been expanding rapidly through the use of more powerful neuroproteomic approaches. However, mass spectrometry (MS)-based neuroproteomic studies of synapses still require cell-type, spatial, and temporal proteome information. With the advancement of sample preparation and MS techniques, we have just begun to identify and understand proteomes within a given cell type, subcellular compartment, and cell-type-specific synapse. Here, we review the progress and limitations of MS-based neuroproteomics of synapses in the mammalian CNS and highlight the recent applications of these approaches in studying neuropsychiatric disorders such as major depressive disorder and substance use disorders. Combining neuroproteomic findings with other omics studies can generate an in-depth, comprehensive map of synaptic proteomes and possibly identify new therapeutic targets and biomarkers for several central nervous system disorders.
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Affiliation(s)
- Yun Young Yim
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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32
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Kaiser M. Connectomes: from a sparsity of networks to large-scale databases. Front Neuroinform 2023; 17:1170337. [PMID: 37377946 PMCID: PMC10291062 DOI: 10.3389/fninf.2023.1170337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
The analysis of whole brain networks started in the 1980s when only a handful of connectomes were available. In these early days, information about the human connectome was absent and one could only dream about having information about connectivity in a single human subject. Thanks to non-invasive methods such as diffusion imaging, we now know about connectivity in many species and, for some species, in many individuals. To illustrate the rapid change in availability of connectome data, the UK Biobank is on track to record structural and functional connectivity in 100,000 human subjects. Moreover, connectome data from a range of species is now available: from Caenorhabditis elegans and the fruit fly to pigeons, rodents, cats, non-human primates, and humans. This review will give a brief overview of what structural connectivity data is now available, how connectomes are organized, and how their organization shows common features across species. Finally, I will outline some of the current challenges and potential future work in making use of connectome information.
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Affiliation(s)
- Marcus Kaiser
- NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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33
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Mercaldo V, Vidimova B, Gastaldo D, Fernández E, Lo AC, Cencelli G, Pedini G, De Rubeis S, Longo F, Klann E, Smit AB, Grant SGN, Achsel T, Bagni C. Altered striatal actin dynamics drives behavioral inflexibility in a mouse model of fragile X syndrome. Neuron 2023; 111:1760-1775.e8. [PMID: 36996810 DOI: 10.1016/j.neuron.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 12/21/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023]
Abstract
The proteome of glutamatergic synapses is diverse across the mammalian brain and involved in neurodevelopmental disorders (NDDs). Among those is fragile X syndrome (FXS), an NDD caused by the absence of the functional RNA-binding protein FMRP. Here, we demonstrate how the brain region-specific composition of postsynaptic density (PSD) contributes to FXS. In the striatum, the FXS mouse model shows an altered association of the PSD with the actin cytoskeleton, reflecting immature dendritic spine morphology and reduced synaptic actin dynamics. Enhancing actin turnover with constitutively active RAC1 ameliorates these deficits. At the behavioral level, the FXS model displays striatal-driven inflexibility, a typical feature of FXS individuals, which is rescued by exogenous RAC1. Striatal ablation of Fmr1 is sufficient to recapitulate behavioral impairments observed in the FXS model. These results indicate that dysregulation of synaptic actin dynamics in the striatum, a region largely unexplored in FXS, contributes to the manifestation of FXS behavioral phenotypes.
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Affiliation(s)
- Valentina Mercaldo
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Barbora Vidimova
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Denise Gastaldo
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Esperanza Fernández
- VIB & UGent Center for Medical Biotechnology, Universiteit Gent, 9052 Ghent, Belgium
| | - Adrian C Lo
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Giulia Cencelli
- Department of Biomedicine and Prevention, Università degli Studi di Roma "Tor Vergata", 00133 Rome, Italy; Institute of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Giorgia Pedini
- Department of Biomedicine and Prevention, Università degli Studi di Roma "Tor Vergata", 00133 Rome, Italy
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesco Longo
- Center for Neural Science, New York University, New York, NY 10029, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY 10029, USA
| | - August B Smit
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Seth G N Grant
- Center for the Clinical Brain Sciences and Simons Initiatives for the Developing Brain, The University of Edinburgh, Edinburgh EH16 4SB, Scotland
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland.
| | - Claudia Bagni
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland; Department of Biomedicine and Prevention, Università degli Studi di Roma "Tor Vergata", 00133 Rome, Italy.
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34
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Leistner C, Wilkinson M, Burgess A, Lovatt M, Goodbody S, Xu Y, Deuchars S, Radford SE, Ranson NA, Frank RAW. The in-tissue molecular architecture of β-amyloid pathology in the mammalian brain. Nat Commun 2023; 14:2833. [PMID: 37198197 PMCID: PMC10192217 DOI: 10.1038/s41467-023-38495-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
Amyloid plaques composed of Aβ fibrils are a hallmark of Alzheimer's disease (AD). However, the molecular architecture of amyloid plaques in the context of fresh mammalian brain tissue is unknown. Here, using cryogenic correlated light and electron tomography we report the in situ molecular architecture of Aβ fibrils in the AppNL-G-F familial AD mouse model containing the Arctic mutation and an atomic model of ex vivo purified Arctic Aβ fibrils. We show that in-tissue Aβ fibrils are arranged in a lattice or parallel bundles, and are interdigitated by subcellular compartments, extracellular vesicles, extracellular droplets and extracellular multilamellar bodies. The Arctic Aβ fibril differs significantly from an earlier AppNL-F fibril structure, indicating a striking effect of the Arctic mutation. These structural data also revealed an ensemble of additional fibrillar species, including thin protofilament-like rods and branched fibrils. Together, these results provide a structural model for the dense network architecture that characterises β-amyloid plaque pathology.
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Affiliation(s)
- Conny Leistner
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Ailidh Burgess
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Megan Lovatt
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Stanley Goodbody
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Susan Deuchars
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - René A W Frank
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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35
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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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36
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Porta-de-la-Riva M, Gonzalez AC, Sanfeliu-Cerdán N, Karimi S, Malaiwong N, Pidde A, Morales-Curiel LF, Fernandez P, González-Bolívar S, Hurth C, Krieg M. Neural engineering with photons as synaptic transmitters. Nat Methods 2023; 20:761-769. [PMID: 37024651 DOI: 10.1038/s41592-023-01836-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/03/2023] [Indexed: 04/08/2023]
Abstract
Neuronal computation is achieved through connections of individual neurons into a larger network. To expand the repertoire of endogenous cellular communication, we developed a synthetic, photon-assisted synaptic transmission (PhAST) system. PhAST is based on luciferases and channelrhodopsins that enable the transmission of a neuronal state across space, using photons as neurotransmitters. PhAST overcomes synaptic barriers and rescues the behavioral deficit of a glutamate mutant with conditional, calcium-triggered photon emission between two neurons of the Caenorhabditis elegans nociceptive avoidance circuit. To demonstrate versatility and flexibility, we generated de novo synaptic transmission between two unconnected cells in a sexually dimorphic neuronal circuit, suppressed endogenous nocifensive response through activation of an anion channelrhodopsin and switched attractive to aversive behavior in an olfactory circuit. Finally, we applied PhAST to dissect the calcium dynamics of the temporal pattern generator in a motor circuit for ovipositioning. In summary, we established photon-based synaptic transmission that facilitates the modification of animal behavior.
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Affiliation(s)
| | | | | | - Shadi Karimi
- Institut de Ciències Fotòniques, Castelldefels, Spain
| | | | | | | | | | | | - Cedric Hurth
- Institut de Ciències Fotòniques, Castelldefels, Spain
| | - Michael Krieg
- Institut de Ciències Fotòniques, Castelldefels, Spain.
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37
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Johnson GA, Tian Y, Ashbrook DG, Cofer GP, Cook JJ, Gee JC, Hall A, Hornburg K, Qi Y, Yeh FC, Wang N, White LE, Williams RW. Merged magnetic resonance and light sheet microscopy of the whole mouse brain. Proc Natl Acad Sci U S A 2023; 120:e2218617120. [PMID: 37068254 PMCID: PMC10151475 DOI: 10.1073/pnas.2218617120] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/10/2023] [Indexed: 04/19/2023] Open
Abstract
We have developed workflows to align 3D magnetic resonance histology (MRH) of the mouse brain with light sheet microscopy (LSM) and 3D delineations of the same specimen. We start with MRH of the brain in the skull with gradient echo and diffusion tensor imaging (DTI) at 15 μm isotropic resolution which is ~ 1,000 times higher than that of most preclinical MRI. Connectomes are generated with superresolution tract density images of ~5 μm. Brains are cleared, stained for selected proteins, and imaged by LSM at 1.8 μm/pixel. LSM data are registered into the reference MRH space with labels derived from the ABA common coordinate framework. The result is a high-dimensional integrated volume with registration (HiDiver) with alignment precision better than 50 µm. Throughput is sufficiently high that HiDiver is being used in quantitative studies of the impact of gene variants and aging on mouse brain cytoarchitecture and connectomics.
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Affiliation(s)
| | - Yuqi Tian
- Center for In Vivo Microscopy, Duke University, Durham, NC27710
| | - David G. Ashbrook
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN38162
| | - Gary P. Cofer
- Center for In Vivo Microscopy, Duke University, Durham, NC27710
| | - James J. Cook
- Center for In Vivo Microscopy, Duke University, Durham, NC27710
| | - James C. Gee
- Department of Radiology, University of Pennsylvania, Philadelphia, PA19104
| | - Adam Hall
- LifeCanvas Technology, Cambridge, MA02141
| | | | - Yi Qi
- Center for In Vivo Microscopy, Duke University, Durham, NC27710
| | - Fang-Cheng Yeh
- Department of Neurologic Surgery, University of Pittsburgh, Pittsburgh, PA15260
| | - Nian Wang
- Department of Radiology, Indiana University, Bloomington, IN47401
| | | | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN38162
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38
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Falkovich R, Danielson EW, Perez de Arce K, Wamhoff EC, Strother J, Lapteva AP, Sheng M, Cottrell JR, Bathe M. A synaptic molecular dependency network in knockdown of autism- and schizophrenia-associated genes revealed by multiplexed imaging. Cell Rep 2023; 42:112430. [PMID: 37099425 DOI: 10.1016/j.celrep.2023.112430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/29/2023] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
The complex functions of neuronal synapses depend on their tightly interconnected protein network, and their dysregulation is implicated in the pathogenesis of autism spectrum disorders and schizophrenia. However, it remains unclear how synaptic molecular networks are altered biochemically in these disorders. Here, we apply multiplexed imaging to probe the effects of RNAi knockdown of 16 autism- and schizophrenia-associated genes on the simultaneous joint distribution of 10 synaptic proteins, observing several protein composition phenotypes associated with these risk genes. We apply Bayesian network analysis to infer hierarchical dependencies among eight excitatory synaptic proteins, yielding predictive relationships that can only be accessed with single-synapse, multiprotein measurements performed simultaneously in situ. Finally, we find that central features of the network are affected similarly across several distinct gene knockdowns. These results offer insight into the convergent molecular etiology of these widespread disorders and provide a general framework to probe subcellular molecular networks.
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Affiliation(s)
- Reuven Falkovich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric W Danielson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karen Perez de Arce
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eike-C Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Juliana Strother
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna P Lapteva
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Morgan Sheng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey R Cottrell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School Initiative for RNA Medicine, Harvard University, Cambridge, MA, USA.
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39
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Kilisch M, Gere-Becker M, Wüstefeld L, Bonnas C, Crauel A, Mechmershausen M, Martens H, Götzke H, Opazo F, Frey S. Simple and Highly Efficient Detection of PSD95 Using a Nanobody and Its Recombinant Heavy-Chain Antibody Derivatives. Int J Mol Sci 2023; 24:ijms24087294. [PMID: 37108454 PMCID: PMC10138605 DOI: 10.3390/ijms24087294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The post-synaptic density protein 95 (PSD95) is a crucial scaffolding protein participating in the organization and regulation of synapses. PSD95 interacts with numerous molecules, including neurotransmitter receptors and ion channels. The functional dysregulation of PSD95 as well as its abundance and localization has been implicated with several neurological disorders, making it an attractive target for developing strategies able to monitor PSD95 accurately for diagnostics and therapeutics. This study characterizes a novel camelid single-domain antibody (nanobody) that binds strongly and with high specificity to rat, mouse, and human PSD95. This nanobody allows for more precise detection and quantification of PSD95 in various biological samples. We expect that the flexibility and unique performance of this thoroughly characterized affinity tool will help to further understand the role of PSD95 in normal and diseased neuronal synapses.
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Affiliation(s)
- Markus Kilisch
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Maja Gere-Becker
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Liane Wüstefeld
- Synaptic Systems GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Christel Bonnas
- Synaptic Systems GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Alexander Crauel
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Maja Mechmershausen
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Henrik Martens
- Synaptic Systems GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Hansjörg Götzke
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Felipe Opazo
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany
| | - Steffen Frey
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
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40
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Marcassa G, Dascenco D, de Wit J. Proteomics-based synapse characterization: From proteins to circuits. Curr Opin Neurobiol 2023; 79:102690. [PMID: 36805717 DOI: 10.1016/j.conb.2023.102690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/15/2022] [Accepted: 01/10/2023] [Indexed: 02/19/2023]
Abstract
The highly heterogeneous nature of neuronal cell types and their connections presents a major challenge to the characterization of neural circuits at the protein level. New approaches now enable an increasingly sophisticated dissection of cell type- and cellular compartment-specific proteomes, as well as the profiling of the protein composition of specific synaptic connections. Here, we provide an overview of these approaches and discuss how they hold considerable promise toward unravelling the molecular mechanisms of neural circuit formation and function. Finally, we provide an outlook of technological developments that may bring the characterization of synaptic proteomes at the single-synapse level within reach.
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Affiliation(s)
- Gabriele Marcassa
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Dan Dascenco
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium. https://twitter.com/ddascenco
| | - Joris de Wit
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium.
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41
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Griffiths J, Grant SGN. Synapse pathology in Alzheimer's disease. Semin Cell Dev Biol 2023; 139:13-23. [PMID: 35690535 DOI: 10.1016/j.semcdb.2022.05.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/12/2022] [Accepted: 05/27/2022] [Indexed: 12/31/2022]
Abstract
Synapse loss and damage are central features of Alzheimer's disease (AD) and contribute to the onset and progression of its behavioural and physiological features. Here we review the literature describing synapse pathology in AD, from what we have learned from microscopy in terms of its impacts on synapse architecture, to the mechanistic role of Aβ, tau and glial cells, mitochondrial dysfunction, and the link with AD risk genes. We consider the emerging view that synapse pathology may operate at a further level, that of synapse diversity, and discuss the prospects for leveraging new synaptome mapping methods to comprehensively understand the molecular properties of vulnerable and resilient synapses. Uncovering AD impacts on brain synapse diversity should inform therapeutic approaches targeted at preserving or replenishing lost and damaged synapses and aid the interpretation of clinical imaging approaches that aim to measure synapse damage.
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Affiliation(s)
- Jessica Griffiths
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Dementia Research Institute at Imperial College, Department of Brain Sciences, Imperial College London, London W12 0NN, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
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Su S, Chen G, Gao M, Zhong G, Zhang Z, Wei D, Luo X, Wang Q. Kai-Xin-San protects against mitochondrial dysfunction in Alzheimer's disease through SIRT3/NLRP3 pathway. Chin Med 2023; 18:26. [PMID: 36918872 PMCID: PMC10012453 DOI: 10.1186/s13020-023-00722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/07/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Kai-Xin-San (KXS) has been reported to have a good curative impact on dementia. The purpose of the study was to determine whether KXS might ameliorate cognitive deficits in APP/PS1 mice and to evaluate its neuroprotective mechanism. METHODS APP/PS1 mice were employed as an AD animal model; Aβ1-42 and KXS-containing serum were used in HT22 cells. Four different behavioral tests were used to determine the cognitive ability of mice. Nissl staining was utilized to detect hippocampal neuron changes. ROS, SOD, and MDA were used to detect oxidative stress levels. Transmission electron microscopy and Western blot were used to evaluate mitochondrial morphology, mitochondrial division, and fusion state. Western blotting and immunofluorescence identified PSD95, BDNF, NGF, SYN, SIRT3, and NLRP3 inflammasome levels. RESULTS The results indicated that KXS protected APP/PS1 mice against cognitive impairments. KXS suppressed neuronal apoptosis and oxidative stress among APP/PS1 mice. KXS and KXS-containing serum improved mitochondrial dysfunction and synaptic and neurotrophic factors regarding APP/PS1 mice. In addition, KXS and KXS-containing serum enhanced mitochondrial SIRT3 expression and reduced NLRP3 inflammasome expression in APP/PS1 mice. CONCLUSION KXS improves cognitive dysfunction among APP/PS1 mice via regulating SIRT3-mediated neuronal cell apoptosis. These results suggested that KXS was proposed as a neuroprotective agent for AD progression.
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Affiliation(s)
- ShiJie Su
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Gongcan Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Minghuang Gao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guangcheng Zhong
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zerong Zhang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongyun Wei
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xue Luo
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.
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Lu Y, Bu FQ, Wang F, Liu L, Zhang S, Wang G, Hu XY. Recent advances on the molecular mechanisms of exercise-induced improvements of cognitive dysfunction. Transl Neurodegener 2023; 12:9. [PMID: 36850004 PMCID: PMC9972637 DOI: 10.1186/s40035-023-00341-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/09/2023] [Indexed: 03/01/2023] Open
Abstract
Physical exercise is of great significance for maintaining human health. Exercise can provide varying degrees of benefits to cognitive function at all stages of life cycle. Currently, with the aging of the world's population and increase of life expectancy, cognitive dysfunction has gradually become a disease of high incidence, which is accompanied by neurodegenerative diseases in elderly individuals. Patients often exhibit memory loss, aphasia and weakening of orientation once diagnosed, and are unable to have a normal life. Cognitive dysfunction largely affects the physical and mental health, reduces the quality of life, and causes a great economic burden to the society. At present, most of the interventions are aimed to maintain the current cognitive level and delay deterioration of cognition. In contrast, exercise as a nonpharmacological therapy has great advantages in its nontoxicity, low cost and universal application. The molecular mechanisms underlying the effect of exercise on cognition are complex, and studies have been extensively centered on neural plasticity, the direct target of exercise in the brain. In addition, mitochondrial stability and energy metabolism are essential for brain status. Meanwhile, the organ-brain axis responds to exercise and induces release of cytokines related to cognition. In this review, we summarize the latest evidence on the molecular mechanisms underlying the effects of exercise on cognition, and point out directions for future research.
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Affiliation(s)
- Yi Lu
- grid.13291.380000 0001 0807 1581West China School of Nursing, Sichuan University/Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Fa-Qian Bu
- grid.13291.380000 0001 0807 1581West China School of Nursing, Sichuan University/Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Fang Wang
- grid.13291.380000 0001 0807 1581West China School of Nursing, Sichuan University/Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Li Liu
- grid.13291.380000 0001 0807 1581West China School of Nursing, Sichuan University/Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Shuai Zhang
- grid.13291.380000 0001 0807 1581West China School of Nursing, Sichuan University/Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 China
| | - Guan Wang
- West China School of Nursing, Sichuan University/Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Xiu-Ying Hu
- West China School of Nursing, Sichuan University/Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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KASAI H. Unraveling the mysteries of dendritic spine dynamics: Five key principles shaping memory and cognition. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:254-305. [PMID: 37821392 PMCID: PMC10749395 DOI: 10.2183/pjab.99.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/11/2023] [Indexed: 10/13/2023]
Abstract
Recent research extends our understanding of brain processes beyond just action potentials and chemical transmissions within neural circuits, emphasizing the mechanical forces generated by excitatory synapses on dendritic spines to modulate presynaptic function. From in vivo and in vitro studies, we outline five central principles of synaptic mechanics in brain function: P1: Stability - Underpinning the integral relationship between the structure and function of the spine synapses. P2: Extrinsic dynamics - Highlighting synapse-selective structural plasticity which plays a crucial role in Hebbian associative learning, distinct from pathway-selective long-term potentiation (LTP) and depression (LTD). P3: Neuromodulation - Analyzing the role of G-protein-coupled receptors, particularly dopamine receptors, in time-sensitive modulation of associative learning frameworks such as Pavlovian classical conditioning and Thorndike's reinforcement learning (RL). P4: Instability - Addressing the intrinsic dynamics crucial to memory management during continual learning, spotlighting their role in "spine dysgenesis" associated with mental disorders. P5: Mechanics - Exploring how synaptic mechanics influence both sides of synapses to establish structural traces of short- and long-term memory, thereby aiding the integration of mental functions. We also delve into the historical background and foresee impending challenges.
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Affiliation(s)
- Haruo KASAI
- International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Moroz LL, Romanova DY. Alternative neural systems: What is a neuron? (Ctenophores, sponges and placozoans). Front Cell Dev Biol 2022; 10:1071961. [PMID: 36619868 PMCID: PMC9816575 DOI: 10.3389/fcell.2022.1071961] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
How to make a neuron, a synapse, and a neural circuit? Is there only one 'design' for a neural architecture with a universally shared genomic blueprint across species? The brief answer is "No." Four early divergent lineages from the nerveless common ancestor of all animals independently evolved distinct neuroid-type integrative systems. One of these is a subset of neural nets in comb jellies with unique synapses; the second lineage is the well-known Cnidaria + Bilateria; the two others are non-synaptic neuroid systems in sponges and placozoans. By integrating scRNA-seq and microscopy data, we revise the definition of neurons as synaptically-coupled polarized and highly heterogenous secretory cells at the top of behavioral hierarchies with learning capabilities. This physiological (not phylogenetic) definition separates 'true' neurons from non-synaptically and gap junction-coupled integrative systems executing more stereotyped behaviors. Growing evidence supports the hypothesis of multiple origins of neurons and synapses. Thus, many non-bilaterian and bilaterian neuronal classes, circuits or systems are considered functional rather than genetic categories, composed of non-homologous cell types. In summary, little-explored examples of convergent neuronal evolution in representatives of early branching metazoans provide conceptually novel microanatomical and physiological architectures of behavioral controls in animals with prospects of neuro-engineering and synthetic biology.
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Affiliation(s)
- Leonid L. Moroz
- Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, United States,Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, United States,*Correspondence: Leonid L. Moroz, ; Daria Y. Romanova,
| | - Daria Y. Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, 5A Butlerova, Moscow, Russia,*Correspondence: Leonid L. Moroz, ; Daria Y. Romanova,
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Bulovaite E, Qiu Z, Kratschke M, Zgraj A, Fricker DG, Tuck EJ, Gokhale R, Koniaris B, Jami SA, Merino-Serrais P, Husi E, Mendive-Tapia L, Vendrell M, O'Dell TJ, DeFelipe J, Komiyama NH, Holtmaat A, Fransén E, Grant SGN. A brain atlas of synapse protein lifetime across the mouse lifespan. Neuron 2022; 110:4057-4073.e8. [PMID: 36202095 PMCID: PMC9789179 DOI: 10.1016/j.neuron.2022.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/01/2022] [Accepted: 09/07/2022] [Indexed: 11/12/2022]
Abstract
The lifetime of proteins in synapses is important for their signaling, maintenance, and remodeling, and for memory duration. We quantified the lifetime of endogenous PSD95, an abundant postsynaptic protein in excitatory synapses, at single-synapse resolution across the mouse brain and lifespan, generating the Protein Lifetime Synaptome Atlas. Excitatory synapses have a wide range of PSD95 lifetimes extending from hours to several months, with distinct spatial distributions in dendrites, neurons, and brain regions. Synapses with short protein lifetimes are enriched in young animals and in brain regions controlling innate behaviors, whereas synapses with long protein lifetimes accumulate during development, are enriched in the cortex and CA1 where memories are stored, and are preferentially preserved in old age. Synapse protein lifetime increases throughout the brain in a mouse model of autism and schizophrenia. Protein lifetime adds a further layer to synapse diversity and enriches prevailing concepts in brain development, aging, and disease.
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Affiliation(s)
- Edita Bulovaite
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Zhen Qiu
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Maximilian Kratschke
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Adrianna Zgraj
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - David G Fricker
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Eleanor J Tuck
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Ragini Gokhale
- 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
| | - Shekib A Jami
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Paula Merino-Serrais
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, UPM, 28223 Madrid, Spain; Instituto Cajal, CSIC, 28002 Madrid, Spain
| | - Elodie Husi
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Lorena Mendive-Tapia
- Centre for Inflammation Research, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Marc Vendrell
- Centre for Inflammation Research, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Thomas J O'Dell
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Javier DeFelipe
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, UPM, 28223 Madrid, Spain; Instituto Cajal, CSIC, 28002 Madrid, Spain
| | - 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; The Patrick Wild Centre for Research into Autism, Fragile X Syndrome & Intellectual Disabilities, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK; Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Anthony Holtmaat
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - 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, 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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Alonso‐Nanclares L, Rodríguez JR, Merchan‐Perez A, González‐Soriano J, Plaza‐Alonso S, Cano‐Astorga N, Naumann RK, Brecht M, DeFelipe J. Cortical synapses of the world's smallest mammal: An FIB/SEM study in the Etruscan shrew. J Comp Neurol 2022; 531:390-414. [PMID: 36413612 PMCID: PMC10100312 DOI: 10.1002/cne.25432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/23/2022]
Abstract
The main aim of the present study was to determine if synapses from the exceptionally small brain of the Etruscan shrew show any peculiarities compared to the much larger human brain. We analyzed the cortical synaptic density and a variety of structural characteristics of 7,239 3D reconstructed synapses, using using Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM). We found that some of the general synaptic characteristics are remarkably similar to those found in the human cerebral cortex. However, the cortical volume of the human brain is about 50,000 times larger than the cortical volume of the Etruscan shrew, while the total number of cortical synapses in human is only 20,000 times the number of synapses in the shrew, and synaptic junctions are 35% smaller in the Etruscan shrew. Thus, the differences in the number and size of synapses cannot be attributed to a brain size scaling effect but rather to adaptations of synaptic circuits to particular functions.
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Affiliation(s)
- Lidia Alonso‐Nanclares
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica Universidad Politécnica de Madrid, Pozuelo de Alarcón Madrid Spain
- Instituto Cajal, Interdisciplinary Platform Cajal Blue Brain Consejo Superior de Investigaciones Científicas (CSIC) Madrid Spain
| | - J. Rodrigo Rodríguez
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica Universidad Politécnica de Madrid, Pozuelo de Alarcón Madrid Spain
- Instituto Cajal, Interdisciplinary Platform Cajal Blue Brain Consejo Superior de Investigaciones Científicas (CSIC) Madrid Spain
| | - Angel Merchan‐Perez
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica Universidad Politécnica de Madrid, Pozuelo de Alarcón Madrid Spain
- Departamento de Arquitectura y Tecnología de Sistemas Informáticos Universidad Politécnica de Madrid, Pozuelo de Alarcón Madrid Spain
| | - Juncal González‐Soriano
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica Universidad Politécnica de Madrid, Pozuelo de Alarcón Madrid Spain
- Veterinary School Universidad Complutense de Madrid Madrid Spain
| | - Sergio Plaza‐Alonso
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica Universidad Politécnica de Madrid, Pozuelo de Alarcón Madrid Spain
- Instituto Cajal, Interdisciplinary Platform Cajal Blue Brain Consejo Superior de Investigaciones Científicas (CSIC) Madrid Spain
| | - Nicolás Cano‐Astorga
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica Universidad Politécnica de Madrid, Pozuelo de Alarcón Madrid Spain
- Instituto Cajal, Interdisciplinary Platform Cajal Blue Brain Consejo Superior de Investigaciones Científicas (CSIC) Madrid Spain
- PhD Program in Neuroscience Autonoma de Madrid University—Cajal Institute Madrid Spain
| | - Robert K. Naumann
- CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen‐Hong Kong Institute of Brain Science‐Shenzhen Fundamental Research Institutions Shenzhen 518055 People's Republic of China
| | - Michael Brecht
- Department of Animal Physiology/Systems Neurobiology and Neural Computation Bernstein Center for Computational Neuroscience Humboldt University of Berlin Berlin Germany
| | - Javier DeFelipe
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica Universidad Politécnica de Madrid, Pozuelo de Alarcón Madrid Spain
- Instituto Cajal, Interdisciplinary Platform Cajal Blue Brain Consejo Superior de Investigaciones Científicas (CSIC) Madrid Spain
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Niu R, Liu J. Circular RNA Involvement in Aging and Longevity. Curr Genomics 2022; 23:318-325. [PMID: 36778190 PMCID: PMC9878857 DOI: 10.2174/1389202923666220927110258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/22/2022] Open
Abstract
Background Circular RNAs (circRNAs) are transcribed by RNA polymerase II and are mostly generated by the back-splicing of exons in the protein-coding gene. Massive circRNAs are reported to be differentially expressed in different species, implicating their prospects as aging biomarkers or regulators in the aging progression. Methods The possible role of circRNAs in aging and longevity was reviewed by the query of circRNAs from literature reports related to tissue, organ or cellular senescence, and individual longevity. Results A number of circRNAs have been found to positively and negatively modulate aging and longevity through canonical aging pathways in the invertebrates Caenorhabditis elegans and Drosophila. Recent studies have also shown that circRNAs regulate age-related processes and pathologies such various mammalian tissues, as the brain, serum, heart, and muscle. Besides, three identified representative circRNAs (circSfl, circGRIA1, and circNF1-419) were elucidated to correlate with aging and longevity. Conclusion This review outlined the current studies of circRNAs in aging and longevity, highlighting the role of circRNAs as a biomarker of aging and as a regulator of longevity.
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Affiliation(s)
- Ruize Niu
- Laboratory Zoology Department, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Jia Liu
- Laboratory Zoology Department, Kunming Medical University, Kunming 650500, Yunnan, China,Address correspondence to this author at the Laboratory Zoology Department, Kunming Medical University, Kunming, Yunnan, 650500, China; Tel: 15288361011; E-mail:
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Tomas-Roca L, Qiu Z, Fransén E, Gokhale R, Bulovaite E, Price DJ, Komiyama NH, Grant SGN. Developmental disruption and restoration of brain synaptome architecture in the murine Pax6 neurodevelopmental disease model. Nat Commun 2022; 13:6836. [PMID: 36369219 PMCID: PMC9652404 DOI: 10.1038/s41467-022-34131-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
Neurodevelopmental disorders of genetic origin delay the acquisition of normal abilities and cause disabling phenotypes. Nevertheless, spontaneous attenuation and even complete amelioration of symptoms in early childhood and adolescence can occur in many disorders, suggesting that brain circuits possess an intrinsic capacity to overcome the deficits arising from some germline mutations. We examined the molecular composition of almost a trillion excitatory synapses on a brain-wide scale between birth and adulthood in mice carrying a mutation in the homeobox transcription factor Pax6, a neurodevelopmental disorder model. Pax6 haploinsufficiency had no impact on total synapse number at any age. By contrast, the molecular composition of excitatory synapses, the postnatal expansion of synapse diversity and the acquisition of normal synaptome architecture were delayed in all brain regions, interfering with networks and electrophysiological simulations of cognitive functions. Specific excitatory synapse types and subtypes were affected in two key developmental age-windows. These phenotypes were reversed within 2-3 weeks of onset, restoring synapse diversity and synaptome architecture to the normal developmental trajectory. Synapse subtypes with rapid protein turnover mediated the synaptome remodeling. This brain-wide capacity for remodeling of synapse molecular composition to recover and maintain the developmental trajectory of synaptome architecture may help confer resilience to neurodevelopmental genetic disorders.
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Affiliation(s)
- Laura Tomas-Roca
- grid.4305.20000 0004 1936 7988Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB UK
| | - Zhen Qiu
- grid.4305.20000 0004 1936 7988Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB UK
| | - Erik Fransén
- grid.5037.10000000121581746Science for Life Laboratory, KTH Royal Institute of Technology, SE-171 65 Solna, Sweden
| | - Ragini Gokhale
- grid.4305.20000 0004 1936 7988Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB UK
| | - Edita Bulovaite
- grid.4305.20000 0004 1936 7988Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB UK
| | - David J. Price
- grid.4305.20000 0004 1936 7988Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD UK
| | - Noboru H. Komiyama
- grid.4305.20000 0004 1936 7988Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB UK ,grid.4305.20000 0004 1936 7988Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD UK
| | - Seth G. N. Grant
- grid.4305.20000 0004 1936 7988Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB UK ,grid.4305.20000 0004 1936 7988Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD UK
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50
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Lovatt M, Leistner C, Frank RAW. Bridging length scales from molecules to the whole organism by cryoCLEM and cryoET. Faraday Discuss 2022; 240:114-126. [PMID: 35959706 PMCID: PMC9642002 DOI: 10.1039/d2fd00081d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Resolving atomic structures of isolated proteins has uncovered mechanisms and fundamental processes in biology. However, many functions can only be tested in the context of intact cells and tissues that are many orders of magnitude larger than the macromolecules on which they depend. Therefore, methods that interrogate macromolecular structure in situ provide a means of directly relating structure to function across length scales. Here, we developed several workflows using cryogenic correlated light and electron microscopy (cryoCLEM) and electron tomography (cryoET) that can bridge this gap to reveal the molecular infrastructure that underlies higher order functions within cells and tissues. We also describe experimental design considerations, including cryoCLEM labelling, sample preparation, and quality control, for determining the in situ molecular architectures within native, hydrated cells and tissues.
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Affiliation(s)
- Megan Lovatt
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLS2 9JTUK
| | - Conny Leistner
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLS2 9JTUK
| | - René A. W. Frank
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of LeedsLS2 9JTUK
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