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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; 34:3836-3843.e5. [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] [MESH Headings] [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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2
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Gao Y, Shonai D, Trn M, Zhao J, Soderblom EJ, Garcia-Moreno SA, Gersbach CA, Wetsel WC, Dawson G, Velmeshev D, Jiang YH, Sloofman LG, Buxbaum JD, Soderling SH. Proximity analysis of native proteomes reveals phenotypic modifiers in a mouse model of autism and related neurodevelopmental conditions. Nat Commun 2024; 15:6801. [PMID: 39122707 PMCID: PMC11316102 DOI: 10.1038/s41467-024-51037-x] [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: 02/20/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
One of the main drivers of autism spectrum disorder is risk alleles within hundreds of genes, which may interact within shared but unknown protein complexes. Here we develop a scalable genome-editing-mediated approach to target 14 high-confidence autism risk genes within the mouse brain for proximity-based endogenous proteomics, achieving the identification of high-specificity spatial proteomes. The resulting native proximity proteomes are enriched for human genes dysregulated in the brain of autistic individuals, and reveal proximity interactions between proteins from high-confidence risk genes with those of lower-confidence that may provide new avenues to prioritize genetic risk. Importantly, the datasets are enriched for shared cellular functions and genetic interactions that may underlie the condition. We test this notion by spatial proteomics and CRISPR-based regulation of expression in two autism models, demonstrating functional interactions that modulate mechanisms of their dysregulation. Together, these results reveal native proteome networks in vivo relevant to autism, providing new inroads for understanding and manipulating the cellular drivers underpinning its etiology.
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Affiliation(s)
- Yudong Gao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Daichi Shonai
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Matthew Trn
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Jieqing Zhao
- Department of Biology, Duke University, Durham, NC, USA
| | - Erik J Soderblom
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, NC, USA
| | | | - Charles A Gersbach
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - William C Wetsel
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Geraldine Dawson
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Dmitry Velmeshev
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Laura G Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott H Soderling
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
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3
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Couch ACM, Brown AM, Raimundo C, Solomon S, Taylor M, Sichlinger L, Matuleviciute R, Srivastava DP, Vernon AC. Transcriptional and cellular response of hiPSC-derived microglia-neural progenitor co-cultures exposed to IL-6. Brain Behav Immun 2024:S0889-1591(24)00529-4. [PMID: 39098436 DOI: 10.1016/j.bbi.2024.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/12/2024] [Accepted: 08/01/2024] [Indexed: 08/06/2024] Open
Abstract
Elevated interleukin (IL-)6 levels during prenatal development have been linked to increased risk for neurodevelopmental disorders (NDD) in the offspring, but the mechanism remains unclear. Human-induced pluripotent stem cell (hiPSC) models offer a valuable tool to study the effects of IL-6 on features relevant for human neurodevelopment in vitro. We previously reported that hiPSC-derived microglia-like cells (MGLs) respond to IL-6, but neural progenitor cells (NPCs) in monoculture do not. Therefore, we investigated whether co-culturing hiPSC-derived MGLs with NPCs would trigger a cellular response to IL-6 stimulation via secreted factors from the MGLs. Using N=4 donor lines without psychiatric diagnosis, we first confirmed that NPCs can respond to IL-6 through trans-signalling when recombinant IL-6Ra is present, and that this response is dose-dependent. MGLs secreted soluble IL-6R, but at lower levels than found in vivo and below that needed to activate trans-signalling in NPCs. Whilst transcriptomic and secretome analysis confirmed that MGLs undergo substantial transcriptomic changes after IL-6 exposure and subsequently secrete a cytokine milieu, NPCs in co-culture with MGLs exhibited a minimal transcriptional response. Furthermore, there were no significant cell fate-acquisition changes when differentiated into post-mitotic cultures, nor alterations in synaptic densities in mature neurons. These findings highlight the need to investigate if trans-IL-6 signalling to NPCs is a relevant disease mechanism linking prenatal IL-6 exposure to increased risk for psychiatric disorders. Moreover, our findings underscore the importance of establishing more complex in vitro human models with diverse cell types, which may show cell-specific responses to microglia-released cytokines to fully understand how IL-6 exposure may influence human neurodevelopment.
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Affiliation(s)
- Amalie C M Couch
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.
| | - Amelia M Brown
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Catarina Raimundo
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Shiden Solomon
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Morgan Taylor
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Laura Sichlinger
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Rugile Matuleviciute
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Anthony C Vernon
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.
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4
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Fernandes EFA, Palner M, Raval NR, Jeppesen TE, Danková D, Bærentzen SL, Werner C, Eilts J, Maric HM, Doose S, Aripaka SS, Kaalund SS, Aznar S, Kjaer A, Schlosser A, Haugaard-Kedström LM, Knudsen GM, Herth MM, Stro Mgaard K. Development of Peptide-Based Probes for Molecular Imaging of the Postsynaptic Density in the Brain. J Med Chem 2024; 67:11975-11988. [PMID: 38981131 DOI: 10.1021/acs.jmedchem.4c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
The postsynaptic density (PSD) comprises numerous scaffolding proteins, receptors, and signaling molecules that coordinate synaptic transmission in the brain. Postsynaptic density protein 95 (PSD-95) is a master scaffold protein within the PSD and one of its most abundant proteins and therefore constitutes a very attractive biomarker of PSD function and its pathological changes. Here, we exploit a high-affinity inhibitor of PSD-95, AVLX-144, as a template for developing probes for molecular imaging of the PSD. AVLX-144-based probes were labeled with the radioisotopes fluorine-18 and tritium, as well as a fluorescent tag. Tracer binding showed saturable, displaceable, and uneven distribution in rat brain slices, proving effective in quantitative autoradiography and cell imaging studies. Notably, we observed diminished tracer binding in human post-mortem Parkinson's disease (PD) brain slices, suggesting postsynaptic impairment in PD. We thus offer a suite of translational probes for visualizing and understanding PSD-related pathologies.
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Affiliation(s)
- Eduardo F A Fernandes
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Mikael Palner
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Nakul Ravi Raval
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, Connecticut 06520, United States
| | - Troels E Jeppesen
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Daniela Danková
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Simone L Bærentzen
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Christian Werner
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Janna Eilts
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Hans M Maric
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Julius-Maximilians-University, Josef-Schneider-Str. 2, Würzburg 97080, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Sanjay Sagar Aripaka
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Sanne Simone Kaalund
- Center for Neuroscience and Stereology, Bispebjerg University Hospital, Nielsine Nielsens Vej 6B, Copenhagen DK-2400, Denmark
| | - Susana Aznar
- Center for Neuroscience and Stereology, Bispebjerg University Hospital, Nielsine Nielsens Vej 6B, Copenhagen DK-2400, Denmark
- Center for Translational Research, Bispebjerg University Hospital, Nielsine Nielsens Vej 4B, Copenhagen DK-2400, Denmark
| | - Andreas Kjaer
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Andreas Schlosser
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Linda M Haugaard-Kedström
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Gitte M Knudsen
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Matthias M Herth
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Kristian Stro Mgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
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Foley K, McKee C, Mayer A, Ganguly A, Barnett D, Ward N, Zhang Y, Nairn A, Xia H. PP1β opposes classic PP1 function, inhibiting spine maturation and promoting LTP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.26.525737. [PMID: 36747779 PMCID: PMC9901188 DOI: 10.1101/2023.01.26.525737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Protein phosphatase 1 (PP1) regulates synaptic plasticity and has been described as a molecular constraint on learning and memory. There are three neuronal isoforms, PP1α, PP1β, and PP1γ, but little is known about their individual functions. PP1α and PP1γ are assumed to mediate the effects of PP1 on learning and memory based on their enrichment at dendritic spines and their preferential binding to neurabin and spinophilin, major PP1 synaptic scaffolding proteins. However, it was recently discovered that human de novo PP1β mutations cause intellectual disability, suggesting an important but ill-defined role for PP1β. In this study, we investigated the functions of each PP1 isoform in hippocampal synaptic physiology using conditional CA1-specific knockout mice. In stark contrast to classic PP1 function, we found that PP1β promotes synaptic plasticity as well as spatial memory. These changes in synaptic plasticity and memory are accompanied by changes in GluA1 phosphorylation, GluN2A levels, and dendritic spine density and morphology, including silent synapse number. These functions of PP1β reveal a previously unidentified signaling pathway regulating spine maturation and plasticity, broadening our understanding of the complex role of PP1 in synaptic physiology.
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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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7
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Ling T, Yin A, Cao Y, Li J, Li H, Zhou Y, Guo X, Li J, Zhang R, Wu H, Li P. Purinergic Astrocyte Signaling Driven by TNF-α After Cannabidiol Administration Restores Normal Synaptic Remodeling Following Traumatic Brain Injury. Neuroscience 2024; 545:31-46. [PMID: 38460903 DOI: 10.1016/j.neuroscience.2024.03.002] [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: 09/26/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Traumatic brain injury (TBI) is a prevalent form of cranial trauma that results in neural conduction disruptions and damage to synaptic structures and functions. Cannabidiol (CBD), a primary derivative from plant-based cannabinoids, exhibits a range of beneficial effects, including analgesic, sedative, anti-inflammatory, anticonvulsant, anti-anxiety, anti-apoptotic, and neuroprotective properties. Nevertheless, the effects of synaptic reconstruction and the mechanisms underlying these effects remain poorly understood. TBI is characterized by increased levels of tumor necrosis factor-alpha (TNF-α), a cytokine integral for the modulation of glutamate release by astrocytes. In the present study, the potential of CBD in regulating aberrant glutamate signal transmission in astrocytes following brain injury, as well as the underlying mechanisms involved, were investigated using immunofluorescence double staining, enzyme-linked immunosorbent assay (ELISA), western blot analysis, hematoxylin and eosin (H&E) staining, Nissl staining, transmission electron microscopy, and RT-qPCR. In this study, we examined the impact of CBD on neuronal synapses, focusing on the TNF-α-driven purinergic signaling pathway. Specifically, our research revealed that CBD pretreatment effectively reduced the secretion of TNF-α induced by astrocyte activation following TBI. This reduction inhibited the interaction between TNF-α and P2Y1 receptors, leading to a decrease in the release of neurotransmitters, including Ca2+ and glutamate, thereby initiating synaptic remodeling. Our study showed that CBD exhibits significant therapeutic potential for TBI-related synaptic dysfunction, offering valuable insights for future research and more effective TBI treatments. Further exploration of the potential applications of CBD in neuroprotection is required to develop innovative clinical strategies.
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Affiliation(s)
- Tenghan Ling
- Department of Anatomy and Histology/Embryology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming 650500, China.
| | - Aiping Yin
- Department of Anatomy and Histology/Embryology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming 650500, China.
| | - Yan Cao
- Department of Anatomy and Histology/Embryology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming 650500, China.
| | - Jiali Li
- Department of Anatomy and Histology/Embryology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming 650500, China.
| | - Hengxi Li
- Department of Anatomy and Histology/Embryology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming 650500, China.
| | - Ying Zhou
- Department of Kunming Medical University Electron Microscope Laboratory, Kunming Medical University, Kunming 650500, China.
| | - Xiaobing Guo
- Department of Anatomy and Histology/Embryology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming 650500, China.
| | - Jinghui Li
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China.
| | - Ruilin Zhang
- Department of Forensic Medicine of Kunming Medical University, Kunming 650500, China.
| | - Haiying Wu
- Department of Emergency and Intensive Care Unit, The First Affiliated Hospital, Kunming Medical University, Kunming 650032, China.
| | - Ping Li
- Department of Anatomy and Histology/Embryology, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming 650500, China.
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8
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Wang T, Yu M, Gu X, Liang X, Wang P, Peng W, Liu D, Chen D, Huang C, Tan Y, Liu K, Xiang B. Mechanism of electroconvulsive therapy in schizophrenia: a bioinformatics analysis study of RNA-seq data. Psychiatr Genet 2024; 34:54-60. [PMID: 38441120 DOI: 10.1097/ypg.0000000000000362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
OBJECTIVE The molecular mechanism of electroconvulsive therapy (ECT) for schizophrenia remains unclear. The aim of this study was to uncover the underlying biological mechanisms of ECT in the treatment of schizophrenia using a transcriptional dataset. METHODS The peripheral blood mRNA sequencing data of eight patients (before and after ECT) and eight healthy controls were analyzed by integrated co-expression network analysis and the differentially expressed genes were analyzed by cluster analysis. Gene set overlap analysis was performed using the hypergeometric distribution of phypfunction in R. Associations of these gene sets with psychiatric disorders were explored. Tissue-specific enrichment analysis, gene ontology enrichment analysis, and protein-protein interaction enrichment analysis were used for gene set organization localization and pathway analysis. RESULTS We found the genes of the green-yellow module were significantly associated with the effect of ECT treatment and the common gene variants of schizophrenia ( P = 0.0061; family-wise error correction). The genes of the green-yellow module are mainly enriched in brain tissue and mainly involved in the pathways of neurotrophin, mitogen-activated protein kinase and long-term potentiation. CONCLUSION Genes associated with the efficacy of ECT were predominantly enriched in neurotrophin, mitogen-activated protein kinase and long-term potentiation signaling pathways.
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Affiliation(s)
| | - Minglan Yu
- Medical Laboratory Center, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province
| | - Xiaochu Gu
- Clinical Laboratory, Suzhou Guangji Hospital, The Affiliated Guangji Hospital of Soochow University, Suzhou, Jiangsu Province
| | | | | | | | - Dongmei Liu
- Department of Psychiatry, Yibin Fourth People's Hospital, Yibin
| | - Dechao Chen
- Department of Psychiatry, Yibin Fourth People's Hospital, Yibin
| | | | - Youguo Tan
- Department of Psychiatry, Zigong Mental Health Center, Zigong, Sichuan Province, China
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9
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Kaizuka T, Suzuki T, Kishi N, Tamada K, Kilimann MW, Ueyama T, Watanabe M, Shimogori T, Okano H, Dohmae N, Takumi T. Remodeling of the postsynaptic proteome in male mice and marmosets during synapse development. Nat Commun 2024; 15:2496. [PMID: 38548776 PMCID: PMC10979008 DOI: 10.1038/s41467-024-46529-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
Postsynaptic proteins play crucial roles in synaptic function and plasticity. During brain development, alterations in synaptic number, shape, and stability occur, known as synapse maturation. However, the postsynaptic protein composition changes during development are not fully understood. Here, we show the trajectory of the postsynaptic proteome in developing male mice and common marmosets. Proteomic analysis of mice at 2, 3, 6, and 12 weeks of age shows that proteins involved in synaptogenesis are differentially expressed during this period. Analysis of published transcriptome datasets shows that the changes in postsynaptic protein composition in the mouse brain after 2 weeks of age correlate with gene expression changes. Proteomic analysis of marmosets at 0, 2, 3, 6, and 24 months of age show that the changes in the marmoset brain can be categorized into two parts: the first 2 months and after that. The changes observed in the first 2 months are similar to those in the mouse brain between 2 and 12 weeks of age. The changes observed in marmoset after 2 months old include differential expression of synaptogenesis-related molecules, which hardly overlap with that in mice. Our results provide a comprehensive proteomic resource that underlies developmental synapse maturation in rodents and primates.
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Affiliation(s)
- Takeshi Kaizuka
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Noriyuki Kishi
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
| | - Kota Tamada
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan
| | - Manfred W Kilimann
- Max Planck Institute for Experimental Medicine, Göttingen, 37075, Germany
| | - Takehiko Ueyama
- Laboratory of Molecular Pharmacology, Biosignal Research Center, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Kita, Sapporo, 060-8638, Japan
| | | | - Hideyuki Okano
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, 160-8585, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan.
- Department Physiology and Cell Biology, Kobe University School of Medicine, Chuo, Kobe, 650-0117, Japan.
- RIKEN Center for Biosystems Dynamics Research, Chuo, Kobe, 650-0047, Japan.
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10
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Kaizuka T, Hirouchi T, Saneyoshi T, Shirafuji T, Collins MO, Grant SGN, Hayashi Y, Takumi T. FAM81A is a postsynaptic protein that regulates the condensation of postsynaptic proteins via liquid-liquid phase separation. PLoS Biol 2024; 22:e3002006. [PMID: 38452102 PMCID: PMC10919877 DOI: 10.1371/journal.pbio.3002006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/17/2024] [Indexed: 03/09/2024] Open
Abstract
Proteome analyses of the postsynaptic density (PSD), a proteinaceous specialization beneath the postsynaptic membrane of excitatory synapses, have identified several thousands of proteins. While proteins with predictable functions have been well studied, functionally uncharacterized proteins are mostly overlooked. In this study, we conducted a comprehensive meta-analysis of 35 PSD proteome datasets, encompassing a total of 5,869 proteins. Employing a ranking methodology, we identified 97 proteins that remain inadequately characterized. From this selection, we focused our detailed analysis on the highest-ranked protein, FAM81A. FAM81A interacts with PSD proteins, including PSD-95, SynGAP, and NMDA receptors, and promotes liquid-liquid phase separation of those proteins in cultured cells or in vitro. Down-regulation of FAM81A in cultured neurons causes a decrease in the size of PSD-95 puncta and the frequency of neuronal firing. Our findings suggest that FAM81A plays a crucial role in facilitating the interaction and assembly of proteins within the PSD, and its presence is important for maintaining normal synaptic function. Additionally, our methodology underscores the necessity for further characterization of numerous synaptic proteins that still lack comprehensive understanding.
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Affiliation(s)
- Takeshi Kaizuka
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
- Centre for Clinical Brain Sciences, Chancellor’s Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
| | - Taisei Hirouchi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeo Saneyoshi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toshihiko Shirafuji
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
| | - Mark O. Collins
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
- biOMICS Facility, Mass Spectrometry Centre, University of Sheffield, Sheffield, United Kingdom
| | - Seth G. N. Grant
- Centre for Clinical Brain Sciences, Chancellor’s Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Chuo, Kobe, Japan
- RIKEN Center for Biosystems Dynamics Research, Chuo, Kobe, Japan
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11
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Ye J, Huang Z, Li Q, Li Z, Lan Y, Wang Z, Ni C, Wu X, Jiang T, Li Y, Yang Q, Lim J, Ren CY, Jiang M, Li S, Jin P, Chen JH, Zhao C. Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders. BMC Med 2023; 21:491. [PMID: 38082312 PMCID: PMC10714646 DOI: 10.1186/s12916-023-03177-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Major psychiatric disorders such as schizophrenia (SCZ) and bipolar disorder (BPD) are complex genetic mental illnesses. Their non-Mendelian features, such as those observed in monozygotic twins discordant for SCZ or BPD, are likely complicated by environmental modifiers of genetic effects. 5-Hydroxymethylcytosine (5hmC) is an important epigenetic mark in gene regulation, and whether it is linked to genetic variants that contribute to non-Mendelian features remains largely unexplored. METHODS We combined the 5hmC-selective chemical labeling method (5hmC-seq) and whole-genome sequencing (WGS) analysis of peripheral blood DNA obtained from monozygotic (MZ) twins discordant for SCZ or BPD to identify allelic imbalances in hydroxymethylome maps, and examined association of allele-specific hydroxymethylation (AShM) transition with disease susceptibility based on Bayes factors (BF) derived from the Bayesian generalized additive linear mixed model. We then performed multi-omics integrative analysis to determine the molecular pathogenic basis of those AShM sites. We finally employed luciferase reporter, CRISPR/Cas9 technology, electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP), PCR, FM4-64 imaging analysis, and RNA sequencing to validate the function of interested AShM sites in the human neuroblastoma SK-N-SH cells and human embryonic kidney 293T (HEK293T) cells. RESULTS We identified thousands of genetic variants associated with AShM imbalances that exhibited phenotypic variation-associated AShM changes at regulatory loci. These AShM marks showed plausible associations with SCZ or BPD based on their effects on interactions among transcription factors (TFs), DNA methylation levels, or other epigenomic marks and thus contributed to dysregulated gene expression, which ultimately increased disease susceptibility. We then validated that competitive binding of POU3F2 on the alternative allele at the AShM site rs4558409 (G/T) in PLLP-enhanced PLLP expression, while the hydroxymethylated alternative allele, which alleviated the POU3F2 binding activity at the rs4558409 site, might be associated with the downregulated PLLP expression observed in BPD or SCZ. Moreover, disruption of rs4558409 promoted neural development and vesicle trafficking. CONCLUSION Our study provides a powerful strategy for prioritizing regulatory risk variants and contributes to our understanding of the interplay between genetic and epigenetic factors in mediating SCZ or BPD susceptibility.
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Affiliation(s)
- Junping Ye
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhanwang Huang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qiyang Li
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Department of Rehabilitation, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Zhongwei Li
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yuting Lan
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Zhongju Wang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Chaoying Ni
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaohui Wu
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Tingyun Jiang
- The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Yujing Li
- Departments of Human Genetics, Emory University, Atlanta, GA, USA
| | - Qiong Yang
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Junghwa Lim
- Departments of Human Genetics, Emory University, Atlanta, GA, USA
| | - Cun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Meijun Jiang
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Science), Guangdong Mental Health Center, Southern Medical University, Guangzhou, China
| | - Shufen Li
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Peng Jin
- Departments of Human Genetics, Emory University, Atlanta, GA, USA
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China.
| | - Cunyou Zhao
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong Province Key Laboratory of Psychiatric Disorders, and Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Department of Rehabilitation, Zhujiang Hospital of Southern Medical University, Guangzhou, China.
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Science), Guangdong Mental Health Center, Southern Medical University, Guangzhou, China.
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, China.
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12
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Jiang M, Wang Z, Lu T, Li X, Yang K, Zhao L, Zhang D, Li J, Wang L. Integrative analysis of long noncoding RNAs dysregulation and synapse-associated ceRNA regulatory axes in autism. Transl Psychiatry 2023; 13:375. [PMID: 38057311 DOI: 10.1038/s41398-023-02662-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex disorder of neurodevelopment, the function of long noncoding RNA (lncRNA) in ASD remains essentially unknown. In the present study, gene networks were used to explore the ASD disease mechanisms integrating multiple data types (for example, RNA expression, whole-exome sequencing signals, weighted gene co-expression network analysis, and protein-protein interaction) and datasets (five human postmortem datasets). A total of 388 lncRNAs and five co-expression modules were found to be altered in ASD. The downregulated co-expression M4 module was significantly correlated with ASD, enriched with autism susceptibility genes and synaptic signaling. Integrating lncRNAs from the M4 module and microRNA (miRNA) dysregulation data from the literature identified competing endogenous RNA (ceRNA) network. We identified the downregulated mRNAs that interact with miRNAs by the miRTarBase, miRDB, and TargetScan databases. Our analysis reveals that MIR600HG was downregulated in multiple brain tissue datasets and was closely associated with 9 autism-susceptible miRNAs in the ceRNA network. MIR600HG and target mRNAs (EPHA4, MOAP1, MAP3K9, STXBP1, PRKCE, and SCAMP5) were downregulated in the peripheral blood by quantitative reverse transcription polymerase chain reaction analysis (false discovery rate <0.05). Subsequently, we assessed the role of lncRNA dysregulation in altered mRNA levels. Experimental verification showed that some synapse-associated mRNAs were downregulated after the MIR600HG knockdown. BrainSpan project showed that the expression patterns of MIR600HG (primate-specific lncRNA) and synapse-associated mRNA were similar in different human brain regions and at different stages of development. A combination of support vector machine and random forest machine learning algorithms retrieved the marker gene for ASD in the ceRNA network, and the area under the curve of the diagnostic nomogram was 0.851. In conclusion, dysregulation of MIR600HG, a novel specific lncRNA associated with ASD, is responsible for the ASD-associated miRNA-mRNA axes, thereby potentially regulating synaptogenesis.
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Affiliation(s)
- Miaomiao Jiang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Ziqi Wang
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Tianlan Lu
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Xianjing Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Kang Yang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Liyang Zhao
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Dai Zhang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
- Guangdong Key Laboratory of Mental Health and Cognitive Science, Institute for Brain Research and Rehabilitation (IBRR), South China Normal University, Guangzhou, China
| | - Jun Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China.
| | - Lifang Wang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China.
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13
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van Oostrum M, Blok TM, Giandomenico SL, Tom Dieck S, Tushev G, Fürst N, Langer JD, Schuman EM. The proteomic landscape of synaptic diversity across brain regions and cell types. Cell 2023; 186:5411-5427.e23. [PMID: 37918396 PMCID: PMC10686415 DOI: 10.1016/j.cell.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/18/2023] [Accepted: 09/28/2023] [Indexed: 11/04/2023]
Abstract
Neurons build synaptic contacts using different protein combinations that define the specificity, function, and plasticity potential of synapses; however, the diversity of synaptic proteomes remains largely unexplored. We prepared synaptosomes from 7 different transgenic mouse lines with fluorescently labeled presynaptic terminals. Combining microdissection of 5 different brain regions with fluorescent-activated synaptosome sorting (FASS), we isolated and analyzed the proteomes of 18 different synapse types. We discovered ∼1,800 unique synapse-type-enriched proteins and allocated thousands of proteins to different types of synapses (https://syndive.org/). We identify shared synaptic protein modules and highlight the proteomic hotspots for synapse specialization. We reveal unique and common features of the striatal dopaminergic proteome and discover the proteome signatures that relate to the functional properties of different interneuron classes. This study provides a molecular systems-biology analysis of synapses and a framework to integrate proteomic information for synapse subtypes of interest with cellular or circuit-level experiments.
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Affiliation(s)
- Marc van Oostrum
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Thomas M Blok
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | | | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Nicole Fürst
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
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14
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Wang L, Pang K, Zhou L, Cebrián-Silla A, González-Granero S, Wang S, Bi Q, White ML, Ho B, Li J, Li T, Perez Y, Huang EJ, Winkler EA, Paredes MF, Kovner R, Sestan N, Pollen AA, Liu P, Li J, Piao X, García-Verdugo JM, Alvarez-Buylla A, Liu Z, Kriegstein AR. A cross-species proteomic map reveals neoteny of human synapse development. Nature 2023; 622:112-119. [PMID: 37704727 PMCID: PMC10576238 DOI: 10.1038/s41586-023-06542-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
The molecular mechanisms and evolutionary changes accompanying synapse development are still poorly understood1,2. Here we generate a cross-species proteomic map of synapse development in the human, macaque and mouse neocortex. By tracking the changes of more than 1,000 postsynaptic density (PSD) proteins from midgestation to young adulthood, we find that PSD maturation in humans separates into three major phases that are dominated by distinct pathways. Cross-species comparisons reveal that human PSDs mature about two to three times slower than those of other species and contain higher levels of Rho guanine nucleotide exchange factors (RhoGEFs) in the perinatal period. Enhancement of RhoGEF signalling in human neurons delays morphological maturation of dendritic spines and functional maturation of synapses, potentially contributing to the neotenic traits of human brain development. In addition, PSD proteins can be divided into four modules that exert stage- and cell-type-specific functions, possibly explaining their differential associations with cognitive functions and diseases. Our proteomic map of synapse development provides a blueprint for studying the molecular basis and evolutionary changes of synapse maturation.
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Affiliation(s)
- Li Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
| | - Kaifang Pang
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Li Zhou
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Arantxa Cebrián-Silla
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Susana González-Granero
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia and CIBERNED, Valencia, Spain
| | - Shaohui Wang
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Qiuli Bi
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew L White
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Brandon Ho
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Jiani Li
- Gilead Sciences, Foster City, CA, USA
| | - Tao Li
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Yonatan Perez
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Huang
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Ethan A Winkler
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Mercedes F Paredes
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Rothem Kovner
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Alex A Pollen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Pengyuan Liu
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - Jingjing Li
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Xianhua Piao
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Division of Neonatology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Newborn Brain Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - José Manuel García-Verdugo
- Laboratory of Comparative Neurobiology, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia and CIBERNED, Valencia, Spain
| | - Arturo Alvarez-Buylla
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Arnold R Kriegstein
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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15
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Barbu MC, Viejo-Romero M, Thng G, Adams MJ, Marwick K, Grant SG, McIntosh AM, Lawrie SM, Whalley HC. Pathway-Based Polygenic Risk Scores for Schizophrenia and Associations With Reported Psychotic-like Experiences and Neuroimaging Phenotypes in the UK Biobank. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2023; 3:814-823. [PMID: 37881537 PMCID: PMC10593950 DOI: 10.1016/j.bpsgos.2023.03.004] [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: 10/17/2022] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/28/2023] Open
Abstract
Background Schizophrenia is a heritable psychiatric disorder with a polygenic architecture. Genome-wide association studies have reported that an increasing number of risk-associated variants and polygenic risk scores (PRSs) explain 17% of the variance in the disorder. Substantial heterogeneity exists in the effect of these variants, and aggregating them based on biologically relevant functions may provide mechanistic insight into the disorder. Methods Using the largest schizophrenia genome-wide association study conducted to date, we associated PRSs based on 5 gene sets previously found to contribute to schizophrenia pathophysiology-postsynaptic density of excitatory synapses, postsynaptic membrane, dendritic spine, axon, and histone H3-K4 methylation-along with respective whole-genome PRSs, with neuroimaging (n > 29,000) and reported psychotic-like experiences (n > 119,000) variables in healthy UK Biobank subjects. Results Several variables were significantly associated with the axon gene-set (psychotic-like communications, parahippocampal gyrus volume, fractional anisotropy thalamic radiations, and fractional anisotropy posterior thalamic radiations (β range -0.016 to 0.0916, false discovery rate-corrected p [pFDR] ≤ .05), postsynaptic density gene-set (psychotic-like experiences distress, global surface area, and cingulate lobe surface area [β range -0.014 to 0.0588, pFDR ≤ .05]), and histone gene set (entorhinal surface area: β = -0.016, pFDR = .035). From these, whole-genome PRSs were significantly associated with psychotic-like communications (β = 0.2218, pFDR = 1.34 × 10-7), distress (β = 0.1943, pFDR = 7.28 × 10-16), and fractional anisotropy thalamic radiations (β = -0.0143, pFDR = .036). Permutation analysis revealed that these associations were not due to chance. Conclusions Our results indicate that genetic variation in 3 gene sets relevant to schizophrenia may confer risk for the disorder through effects on previously implicated neuroimaging variables. Because associations were stronger overall for whole-genome PRSs, findings here highlight that selection of biologically relevant variants is not yet sufficient to address the heterogeneity of the disorder.
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Affiliation(s)
- Miruna C. Barbu
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland, United Kingdom
| | - Maria Viejo-Romero
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland, United Kingdom
| | - Gladi Thng
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland, United Kingdom
| | - Mark J. Adams
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland, United Kingdom
| | - Katie Marwick
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland, United Kingdom
| | - Seth G.N. Grant
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Andrew M. McIntosh
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland, United Kingdom
| | - Stephen M. Lawrie
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland, United Kingdom
| | - Heather C. Whalley
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, Scotland, United Kingdom
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16
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Zhang S, Zhang H, Forrest MP, Zhou Y, Sun X, Bagchi VA, Kozlova A, Santos MD, Piguel NH, Dionisio LE, Sanders AR, Pang ZP, He X, Penzes P, Duan J. Multiple genes in a single GWAS risk locus synergistically mediate aberrant synaptic development and function in human neurons. CELL GENOMICS 2023; 3:100399. [PMID: 37719141 PMCID: PMC10504676 DOI: 10.1016/j.xgen.2023.100399] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 08/07/2023] [Indexed: 09/19/2023]
Abstract
The mechanistic tie between genome-wide association study (GWAS)-implicated risk variants and disease-relevant cellular phenotypes remains largely unknown. Here, using human induced pluripotent stem cell (hiPSC)-derived neurons as a neurodevelopmental model, we identify multiple schizophrenia (SZ) risk variants that display allele-specific open chromatin (ASoC) and are likely to be functional. Editing the strongest ASoC SNP, rs2027349, near vacuolar protein sorting 45 homolog (VPS45) alters the expression of VPS45, lncRNA AC244033.2, and a distal gene, C1orf54. Notably, the transcriptomic changes in neurons are associated with SZ and other neuropsychiatric disorders. Neurons carrying the risk allele exhibit increased dendritic complexity and hyperactivity. Interestingly, individual/combinatorial gene knockdown shows that these genes alter cellular phenotypes in a non-additive synergistic manner. Our study reveals that multiple genes at a single GWAS risk locus mediate a compound effect on neural function, providing a mechanistic link between a non-coding risk variant and disease-related cellular phenotypes.
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Affiliation(s)
- Siwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Marc P. Forrest
- Department of Neuroscience, Northwestern University, Chicago, IL 60611, USA
- Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL 60611, USA
| | - Yifan Zhou
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Xiaotong Sun
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Vikram A. Bagchi
- Department of Neuroscience, Northwestern University, Chicago, IL 60611, USA
- Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL 60611, USA
| | - Alena Kozlova
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Marc Dos Santos
- Department of Neuroscience, Northwestern University, Chicago, IL 60611, USA
- Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL 60611, USA
| | - Nicolas H. Piguel
- Department of Neuroscience, Northwestern University, Chicago, IL 60611, USA
- Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL 60611, USA
| | - Leonardo E. Dionisio
- Department of Neuroscience, Northwestern University, Chicago, IL 60611, USA
- Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL 60611, USA
| | - Alan R. Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
| | - Zhiping P. Pang
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Peter Penzes
- Department of Neuroscience, Northwestern University, Chicago, IL 60611, USA
- Center for Autism and Neurodevelopment, Northwestern University, Chicago, IL 60611, USA
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
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17
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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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18
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Davies FCJ, Marshall GF, Pegram E, Gadd D, Abbott CM. Endogenous epitope tagging of eEF1A2 in mice reveals early embryonic expression of eEF1A2 and subcellular compartmentalisation of neuronal eEF1A1 and eEF1A2. Mol Cell Neurosci 2023; 126:103879. [PMID: 37429391 DOI: 10.1016/j.mcn.2023.103879] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
All vertebrate species express two independently-encoded forms of translation elongation factor eEF1A. In humans and mice eEF1A1 and eEF1A2 are 92 % identical at the amino acid level, but the well conserved developmental switch between the two variants in specific tissues suggests the existence of important functional differences. Heterozygous mutations in eEF1A2 result in neurodevelopmental disorders in humans; the mechanism of pathogenicity is unclear, but one hypothesis is that there is a dominant negative effect on eEF1A1 during development. The high degree of similarity between the eEF1A proteins has complicated expression analysis in the past; here we describe a gene edited mouse line in which we have introduced a V5 tag in the gene encoding eEF1A2. Expression analysis using anti-V5 and anti-eEF1A1 antibodies demonstrates that, in contrast to the prevailing view that eEF1A2 is only expressed postnatally, it is expressed from as early as E11.5 in the developing neural tube. Two colour immunofluorescence also reveals coordinated switching between eEF1A1 and eEF1A2 in different regions of postnatal brain. Completely reciprocal expression of the two variants is seen in post-weaning mouse brain with eEF1A1 expressed in oligodendrocytes and astrocytes and eEF1A2 in neuronal soma. Although eEF1A1 is absent from neuronal cell bodies after development, it is widely expressed in axons. This expression does not appear to coincide with myelin sheaths originating from oligodendrocytes but rather results from localised translation within the axon, suggesting that both variants are transcribed in neurons but show completely distinct subcellular localisation at the protein level. These findings will form an underlying framework for understanding how missense mutations in eEF1A2 result in neurodevelopmental disorders.
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Affiliation(s)
- Faith C J Davies
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
| | - Grant F Marshall
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom
| | - Eleanor Pegram
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom
| | - Danni Gadd
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom
| | - Catherine M Abbott
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, United Kingdom; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, United Kingdom.
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19
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Tong T, Chen Y, Hao C, Shen J, Chen W, Cheng W, Yan S, Li J, Li Y, Gulizhaerkezi T, Zeng J, Meng X. The effects of acupuncture on depression by regulating BDNF-related balance via lateral habenular nucleus BDNF/TrkB/CREB signaling pathway in rats. Behav Brain Res 2023; 451:114509. [PMID: 37244435 DOI: 10.1016/j.bbr.2023.114509] [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: 02/19/2023] [Revised: 05/08/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
Depression is a major mental disease worldwide, causing dysfunction of Lateral Habenular (LHb). As a non-invasive alternative, acupuncture (AP) has been widely used to treat depression in clinic, yet few basic studies have been focused on the effects and mechanism of acupuncture on synaptic plasticity in LHb. Therefore, this study aimed to explore the potential mechanism of the antidepressant effect of acupuncture. Male Sprague-Dawley (SD) rats were randomly divided into control, chronic unpredictable mild stress (CUMS), AP, fluoxetine (FLX), acupoint catgut embedding (ACE), sham-ACE groups (n = 9/group). Rats were given a 28-day treatment at the Shangxing (GV23) and Fengfu (GV16) acupoints with acupuncture, ACE, sham-ACE or fluoxetine (2.1 mg/kg). The results showed that AP, FLX and ACE suppressed the behavioral deficits, increased the level of the 5-hydroxytryptamine and FNDC5/IRISIN in serum, also reduced the expression of pro-BDNF impacted by CUMS. Both AP and FLX ameliorated the %area of IBA-1, GFAP, BrdU and DCX in the LHb and increased the expression of BDNF/TrkB/CREB, with non-significant difference between the two groups These findings suggest that AP therapy relieves depression-related manifestations in depressed rats, suggesting a potential mechanism via the BDNF/TrkB/CREB pathway in LHb.
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Affiliation(s)
- Tao Tong
- Department of Traditional Chinese Medicine, School of Medicine, Xiamen University, Xiamen, Fujian, P. R. China; Second Clinical College, Shanxi University of Traditional Chinese Medicine, Taiyuan, Shanxi, P. R. China
| | - Yiping Chen
- Department of Traditional Chinese Medicine, School of Medicine, Xiamen University, Xiamen, Fujian, P. R. China; Second Clinical College, Shanxi University of Traditional Chinese Medicine, Taiyuan, Shanxi, P. R. China
| | - Chonyao Hao
- Second Clinical College, Shanxi University of Traditional Chinese Medicine, Taiyuan, Shanxi, P. R. China
| | - Junliang Shen
- Department of Traditional Chinese Medicine, School of Medicine, Xiamen University, Xiamen, Fujian, P. R. China
| | - Wenjie Chen
- Department of Traditional Chinese Medicine, School of Medicine, Xiamen University, Xiamen, Fujian, P. R. China
| | - Wenjing Cheng
- Department of Rehabilitation Medicine, Ezhou Central Hospital, Ezhou, Hubei, P. R. China
| | - Simin Yan
- Department of Traditional Chinese Medicine, School of Medicine, Xiamen University, Xiamen, Fujian, P. R. China
| | - Jianguo Li
- Second Clinical College, Shanxi University of Traditional Chinese Medicine, Taiyuan, Shanxi, P. R. China
| | - Yuhan Li
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, P. R. China
| | - Tuergong Gulizhaerkezi
- Department of Traditional Chinese Medicine, School of Medicine, Xiamen University, Xiamen, Fujian, P. R. China
| | - Jingyu Zeng
- Department of Traditional Chinese Medicine, School of Medicine, Xiamen University, Xiamen, Fujian, P. R. China
| | - Xianjun Meng
- Department of Traditional Chinese Medicine, School of Medicine, Xiamen University, Xiamen, Fujian, P. R. China.
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20
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Liu X, Xu W, Leng F, Zhang P, Guo R, Zhang Y, Hao C, Ni X, Li W. NeuroCNVscore: a tissue-specific framework to prioritise the pathogenicity of CNVs in neurodevelopmental disorders. BMJ Paediatr Open 2023; 7:e001966. [PMID: 37407247 DOI: 10.1136/bmjpo-2023-001966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) are associated with altered development of the brain especially in childhood. Copy number variants (CNVs) play a crucial role in the genetic aetiology of NDDs by disturbing gene expression directly at linear sequence or remotely at three-dimensional genome level in a tissue-specific manner. Despite the substantial increase in NDD studies employing whole-genome sequencing, there is no specific tool for prioritising the pathogenicity of CNVs in the context of NDDs. METHODS Using an XGBoost classifier, we integrated 189 features that represent genomic sequences, gene information and functional/genomic segments for evaluating genome-wide CNVs in a neuro/brain-specific manner, to develop a new tool, neuroCNVscore. We used Human Phenotype Ontology to construct an independent NDD-related set. RESULTS Our neuroCNVscore framework (https://github.com/lxsbch/neuroCNVscore) achieved high predictive performance (precision recall=0.82; area under curve=0.85) and outperformed an existing reference method SVScore. Notably, the predicted pathogenic CNVs showed enrichment in known genes associated with autism. CONCLUSIONS NeuroCNVscore prioritises functional, deleterious and pathogenic CNVs in NDDs at whole genome-wide level, which is important for genetic studies and clinical genomic screening of NDDs as well as for providing novel biological insights into NDDs.
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Affiliation(s)
- Xuanshi Liu
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Wenjian Xu
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Fei Leng
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Peng Zhang
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Ruolan Guo
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Yue Zhang
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Chanjuan Hao
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
| | - Xin Ni
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- National Centre for Children's Health, Beijing, China
| | - Wei Li
- Beijing Children's Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, Beijing, China
- MOE Key Laboratory of Major Diseaseas in Children, Beijing, China
- Genetics and Birth Defects Control Centre, National Centre for Children's Health, Beijing, China
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21
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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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22
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Parisi MJ, Aimino MA, Mosca TJ. A conditional strategy for cell-type-specific labeling of endogenous excitatory synapses in Drosophila. CELL REPORTS METHODS 2023; 3:100477. [PMID: 37323572 PMCID: PMC10261928 DOI: 10.1016/j.crmeth.2023.100477] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/28/2023] [Accepted: 04/19/2023] [Indexed: 06/17/2023]
Abstract
Chemical neurotransmission occurs at specialized contacts where neurotransmitter release machinery apposes neurotransmitter receptors to underlie circuit function. A series of complex events underlies pre- and postsynaptic protein recruitment to neuronal connections. To better study synaptic development in individual neurons, we need cell-type-specific strategies to visualize endogenous synaptic proteins. Although presynaptic strategies exist, postsynaptic proteins remain less studied because of a paucity of cell-type-specific reagents. To study excitatory postsynapses with cell-type specificity, we engineered dlg1[4K], a conditionally labeled marker of Drosophila excitatory postsynaptic densities. With binary expression systems, dlg1[4K] labels central and peripheral postsynapses in larvae and adults. Using dlg1[4K], we find that distinct rules govern postsynaptic organization in adult neurons, multiple binary expression systems can concurrently label pre- and postsynapse in a cell-type-specific manner, and neuronal DLG1 can sometimes localize presynaptically. These results validate our strategy for conditional postsynaptic labeling and demonstrate principles of synaptic organization.
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Affiliation(s)
- Michael J. Parisi
- Department of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA 19107, USA
| | - Michael A. Aimino
- Department of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA 19107, USA
| | - Timothy J. Mosca
- Department of Neuroscience, Vickie and Jack Farber Institute of Neuroscience, Thomas Jefferson University, Bluemle Life Sciences Building, Philadelphia, PA 19107, USA
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23
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Aryal S, Bonanno K, Song B, Mani DR, Keshishian H, Carr SA, Sheng M, Dejanovic B. Deep proteomics identifies shared molecular pathway alterations in synapses of patients with schizophrenia and bipolar disorder and mouse model. Cell Rep 2023; 42:112497. [PMID: 37171958 DOI: 10.1016/j.celrep.2023.112497] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/10/2023] [Accepted: 04/26/2023] [Indexed: 05/14/2023] Open
Abstract
Synaptic dysfunction is implicated in the pathophysiology of schizophrenia (SCZ) and bipolar disorder (BP). We use quantitative mass spectrometry to carry out deep, unbiased proteomic profiling of synapses purified from the dorsolateral prefrontal cortex of 35 cases of SCZ, 35 cases of BP, and 35 controls. Compared with controls, SCZ and BP synapses show substantial and similar proteomic alterations. Network analyses reveal upregulation of proteins associated with autophagy and certain vesicle transport pathways and downregulation of proteins related to synaptic, mitochondrial, and ribosomal function in the synapses of individuals with SCZ or BP. Some of the same pathways are similarly dysregulated in the synaptic proteome of mutant mice deficient in Akap11, a recently discovered shared risk gene for SCZ and BP. Our work provides biological insights into molecular dysfunction at the synapse in SCZ and BP and serves as a resource for understanding the pathophysiology of these disorders.
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Affiliation(s)
- Sameer Aryal
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bonanno
- The Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bryan Song
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - D R Mani
- The Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hasmik Keshishian
- The Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- The Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Morgan Sheng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Borislav Dejanovic
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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24
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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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25
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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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26
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Droogers WJ, MacGillavry HD. Plasticity of postsynaptic nanostructure. Mol Cell Neurosci 2023; 124:103819. [PMID: 36720293 DOI: 10.1016/j.mcn.2023.103819] [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: 11/01/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
The postsynaptic density (PSD) of excitatory synapses is built from a wide variety of scaffolding proteins, receptors, and signaling molecules that collectively orchestrate synaptic transmission. Seminal work over the past decades has led to the identification and functional characterization of many PSD components. In contrast, we know far less about how these constituents are assembled within synapses, and how this organization contributes to synapse function. Notably, recent evidence from high-resolution microscopy studies and in silico models, highlights the importance of the precise subsynaptic structure of the PSD for controlling the strength of synaptic transmission. Even further, activity-driven changes in the distribution of glutamate receptors are acknowledged to contribute to long-term changes in synaptic efficacy. Thus, defining the mechanisms that drive structural changes within the PSD are important for a molecular understanding of synaptic transmission and plasticity. Here, we review the current literature on how the PSD is organized to mediate basal synaptic transmission and how synaptic activity alters the nanoscale organization of synapses to sustain changes in synaptic strength.
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Affiliation(s)
- W J Droogers
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, The Netherlands
| | - H D MacGillavry
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, The Netherlands.
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27
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Li Q, Xu X, Qian Y, Cai H, Zhao W, Zhu J, Yu Y. Resting-state brain functional alterations and their genetic mechanisms in drug-naive first-episode psychosis. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2023; 9:13. [PMID: 36841861 PMCID: PMC9968350 DOI: 10.1038/s41537-023-00338-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/07/2023] [Indexed: 02/27/2023]
Abstract
Extensive research has established the presence of resting-state brain functional damage in psychosis. However, the genetic mechanisms of such disease phenotype are yet to be unveiled. We investigated resting-state brain functional alterations in patients with drug-naive first-episode psychosis (DFP) by performing a neuroimaging meta-analysis of 8 original studies comprising 500 patients and 469 controls. Combined with the Allen Human Brain Atlas, we further conducted transcriptome-neuroimaging spatial correlations to identify genes whose expression levels were linked to brain functional alterations in DFP, followed by a range of gene functional characteristic analyses. Meta-analysis revealed a mixture of increased and decreased brain function in widespread areas including the default-mode, visual, motor, striatal, and cerebellar systems in DFP. Moreover, these brain functional alterations were spatially associated with the expression of 1662 genes, which were enriched for molecular functions, cellular components, and biological processes of the cerebral cortex, as well as psychiatric disorders including schizophrenia. Specific expression analyses demonstrated that these genes were specifically expressed in the brain tissue, in cortical neurons and immune cells, and during nearly all developmental periods. Concurrently, the genes could construct a protein-protein interaction network supported by hub genes and were linked to multiple behavioral domains including emotion, attention, perception, and motor. Our findings provide empirical evidence for the notion that brain functional damage in DFP involves a complex interaction of polygenes with various functional characteristics.
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Affiliation(s)
- Qian Li
- grid.459419.4Department of Radiology, Chaohu Hospital of Anhui Medical University, 238000 Hefei, China ,grid.412679.f0000 0004 1771 3402Department of Radiology, The First Affiliated Hospital of Anhui Medical University, 230022 Hefei, China ,Research Center of Clinical Medical Imaging, Anhui Province, 230032 Hefei, China ,Anhui Provincial Institute of Translational Medicine, 230032 Hefei, China
| | - Xiaotao Xu
- grid.412679.f0000 0004 1771 3402Department of Radiology, The First Affiliated Hospital of Anhui Medical University, 230022 Hefei, China ,Research Center of Clinical Medical Imaging, Anhui Province, 230032 Hefei, China ,Anhui Provincial Institute of Translational Medicine, 230032 Hefei, China
| | - Yinfeng Qian
- grid.412679.f0000 0004 1771 3402Department of Radiology, The First Affiliated Hospital of Anhui Medical University, 230022 Hefei, China ,Research Center of Clinical Medical Imaging, Anhui Province, 230032 Hefei, China ,Anhui Provincial Institute of Translational Medicine, 230032 Hefei, China
| | - Huanhuan Cai
- grid.412679.f0000 0004 1771 3402Department of Radiology, The First Affiliated Hospital of Anhui Medical University, 230022 Hefei, China ,Research Center of Clinical Medical Imaging, Anhui Province, 230032 Hefei, China ,Anhui Provincial Institute of Translational Medicine, 230032 Hefei, China
| | - Wenming Zhao
- grid.412679.f0000 0004 1771 3402Department of Radiology, The First Affiliated Hospital of Anhui Medical University, 230022 Hefei, China ,Research Center of Clinical Medical Imaging, Anhui Province, 230032 Hefei, China ,Anhui Provincial Institute of Translational Medicine, 230032 Hefei, China
| | - Jiajia Zhu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, 230022, Hefei, China. .,Research Center of Clinical Medical Imaging, Anhui Province, 230032, Hefei, China. .,Anhui Provincial Institute of Translational Medicine, 230032, Hefei, China.
| | - Yongqiang Yu
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, 230022, Hefei, China. .,Research Center of Clinical Medical Imaging, Anhui Province, 230032, Hefei, China. .,Anhui Provincial Institute of Translational Medicine, 230032, Hefei, China.
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28
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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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29
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Wang Y, Sun Z, He Q, Li J, Ni M, Yang M. Self-supervised graph representation learning integrates multiple molecular networks and decodes gene-disease relationships. PATTERNS (NEW YORK, N.Y.) 2022; 4:100651. [PMID: 36699743 PMCID: PMC9868676 DOI: 10.1016/j.patter.2022.100651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/19/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
Leveraging molecular networks to discover disease-relevant modules is a long-standing challenge. With the accumulation of interactomes, there is a pressing need for powerful computational approaches to handle the inevitable noise and context-specific nature of biological networks. Here, we introduce Graphene, a two-step self-supervised representation learning framework tailored to concisely integrate multiple molecular networks and adapted to gene functional analysis via downstream re-training. In practice, we first leverage GNN (graph neural network) pre-training techniques to obtain initial node embeddings followed by re-training Graphene using a graph attention architecture, achieving superior performance over competing methods for pathway gene recovery, disease gene reprioritization, and comorbidity prediction. Graphene successfully recapitulates tissue-specific gene expression across disease spectrum and demonstrates shared heritability of common mental disorders. Graphene can be updated with new interactomes or other omics features. Graphene holds promise to decipher gene function under network context and refine GWAS (genome-wide association study) hits and offers mechanistic insights via decoding diseases from genome to networks to phenotypes.
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Affiliation(s)
- Yi Wang
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Zijun Sun
- Computer Center, Peking University, Beijing, China
| | | | - Jiwei Li
- Department of Computer Science, Zhejiang University, Hangzhou, China
| | - Ming Ni
- MGI, BGI-Shenzhen, Shenzhen, China
- MGI-QingDao, BGI-Shenzhen, Qingdao, China
| | - Meng Yang
- MGI, BGI-Shenzhen, Shenzhen, China
- Corresponding author
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30
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Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder. Nat Commun 2022; 13:6463. [PMID: 36309498 PMCID: PMC9617891 DOI: 10.1038/s41467-022-34112-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 10/13/2022] [Indexed: 02/06/2023] Open
Abstract
Defining different genetic subtypes of autism spectrum disorder (ASD) can enable the prediction of developmental outcomes. Based on minor physical and major congenital anomalies, we categorize 325 Canadian children with ASD into dysmorphic and nondysmorphic subgroups. We develop a method for calculating a patient-level, genome-wide rare variant score (GRVS) from whole-genome sequencing (WGS) data. GRVS is a sum of the number of variants in morphology-associated coding and non-coding regions, weighted by their effect sizes. Probands with dysmorphic ASD have a significantly higher GRVS compared to those with nondysmorphic ASD (P = 0.03). Using the polygenic transmission disequilibrium test, we observe an over-transmission of ASD-associated common variants in nondysmorphic ASD probands (P = 2.9 × 10-3). These findings replicate using WGS data from 442 ASD probands with accompanying morphology data from the Simons Simplex Collection. Our results provide support for an alternative genomic classification of ASD subgroups using morphology data, which may inform intervention protocols.
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31
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Dissection of the long-range projections of specific neurons at the synaptic level in the whole mouse brain. Proc Natl Acad Sci U S A 2022; 119:e2202536119. [PMID: 36161898 PMCID: PMC9546530 DOI: 10.1073/pnas.2202536119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Through synaptic connections, long-range circuits transmit information among neurons and connect different brain regions to form functional motifs and execute specific functions. Tracing the synaptic distribution of specific neurons requires submicron-level resolution information. However, it is a great challenge to map the synaptic terminals completely because these fine structures span multiple regions, even in the whole brain. Here, we develop a pipeline including viral tracing, sample embedding, fluorescent micro-optical sectional tomography, and big data processing. We mapped the whole-brain distribution and architecture of long projections of the parvalbumin neurons in the basal forebrain at the synaptic level. These neurons send massive projections to multiple downstream regions with subregional preference. With three-dimensional reconstruction in the targeted areas, we found that synaptic degeneration was inconsistent with the accumulation of amyloid-β plaques but was preferred in memory-related circuits, such as hippocampal formation and thalamus, but not in most hypothalamic nuclei in 8-month-old mice with five familial Alzheimer's disease mutations. Our pipeline provides a platform for generating a whole-brain atlas of cell-type-specific synaptic terminals in the physiological and pathological brain, which can provide an important resource for the study of the organizational logic of specific neural circuits and the circuitry changes in pathological conditions.
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32
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Hsieh MY, Tuan LH, Chang HC, Wang YC, Chen CH, Shy HT, Lee LJ, Gau SSF. Altered synaptic protein expression, aberrant spine morphology, and impaired spatial memory in Dlgap2 mutant mice, a genetic model of autism spectrum disorder. Cereb Cortex 2022; 33:4779-4793. [PMID: 36169576 DOI: 10.1093/cercor/bhac379] [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: 05/24/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/14/2022] Open
Abstract
A microdeletion of approximately 2.4 Mb at the 8p23 terminal region has been identified in a Taiwanese autistic boy. Among the products transcribed/translated from genes mapped in this region, the reduction of DLGAP2, a postsynaptic scaffold protein, might be involved in the pathogenesis of autism spectrum disorder (ASD). DLGAP2 protein was detected in the hippocampus yet abolished in homozygous Dlgap2 knockout (Dlgap2 KO) mice. In this study, we characterized the hippocampal phenotypes in Dlgap2 mutant mice. Dlgap2 KO mice exhibited impaired spatial memory, indicating poor hippocampal function in the absence of DLGAP2. Aberrant expressions of postsynaptic proteins, including PSD95, SHANK3, HOMER1, GluN2A, GluR2, mGluR1, mGluR5, βCAMKII, ERK1/2, ARC, BDNF, were noticed in Dlgap2 mutant mice. Further, the spine density was increased in Dlgap2 KO mice, while the ratio of mushroom-type spines was decreased. We also observed a thinner postsynaptic density thickness in Dlgap2 KO mice at the ultrastructural level. These structural changes found in the hippocampus of Dlgap2 KO mice might be linked to impaired hippocampus-related cognitive functions such as spatial memory. Mice with Dlgap2 deficiency, showing signs of intellectual disability, a common co-occurring condition in patients with ASD, could be a promising animal model which may advance our understanding of ASD.
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Affiliation(s)
- Ming-Yen Hsieh
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Heng Tuan
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan.,School of Medicine, National Tsing Hua University, Hsinchu, Taiwan.,Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Ho-Ching Chang
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Chun Wang
- Department of Otolaryngology, Head and Neck Surgery, Chi-Mei Medical Center, Tainan, Taiwan
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan
| | - Horng-Tzer Shy
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Jen Lee
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan.,Institute of Brain and Mind Sciences, National Taiwan University College of Medicine, Taipei, Taiwan.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
| | - Susan Shur-Fen Gau
- Institute of Brain and Mind Sciences, National Taiwan University College of Medicine, Taipei, Taiwan.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan.,Department of Psychiatry, National Taiwan University Hospital, Taipei, Taiwan
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33
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Beyreli I, Karakahya O, Cicek AE. DeepND: Deep multitask learning of gene risk for comorbid neurodevelopmental disorders. PATTERNS 2022; 3:100524. [PMID: 35845835 PMCID: PMC9278518 DOI: 10.1016/j.patter.2022.100524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/11/2022] [Accepted: 05/09/2022] [Indexed: 01/24/2023]
Abstract
Autism spectrum disorder and intellectual disability are comorbid neurodevelopmental disorders with complex genetic architectures. Despite large-scale sequencing studies, only a fraction of the risk genes was identified for both. We present a network-based gene risk prioritization algorithm, DeepND, that performs cross-disorder analysis to improve prediction by exploiting the comorbidity of autism spectrum disorder (ASD) and intellectual disability (ID) via multitask learning. Our model leverages information from human brain gene co-expression networks using graph convolutional networks, learning which spatiotemporal neurodevelopmental windows are important for disorder etiologies and improving the state-of-the-art prediction in single- and cross-disorder settings. DeepND identifies the prefrontal and motor-somatosensory cortex (PFC-MFC) brain region and periods from early- to mid-fetal and from early childhood to young adulthood as the highest neurodevelopmental risk windows for ASD and ID. We investigate ASD- and ID-associated copy-number variation (CNV) regions and report our findings for several susceptibility gene candidates. DeepND can be generalized to analyze any combinations of comorbid disorders. DeepND can co-analyze comorbid neurodevelopmental disorders to discover risk genes The approach employs multitask learning to learn shared and disorder-specific weights DeepND uses graph convolution to process gene interactions in multiple networks The model includes a mixture-of-experts model to detect informative networks
While risk-gene-discovery algorithms have complemented exome/genome-sequencing studies of neurodevelopmental disorders, they are not capable of co-analyzing multiple comorbid conditions like autism and intellectual disability. A common approach is analyzing disorders one by one and comparing the outcomes. With this approach, the method does not utilize cross-disorder interactions and is bound by limited evidence per disorder. We address this gap with a technique, Deep Neurodevelopmental Disorders (DeepND), that uses multitask learning to co-analyze data from multiple disorders to learn shared and disorder-specific patterns. DeepND includes graph convolutional neural networks that process gene-interaction information from multiple networks. DeepND also learns which networks are important for disorder etiologies. Based on this, we propose an interpretable risk-gene-discovery algorithm for neuropsychiatric disorders.
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Affiliation(s)
- Ilayda Beyreli
- Department of Computer Engineering, Bilkent University, Ankara 06810, Turkey
| | - Oguzhan Karakahya
- Department of Computer Engineering, Bilkent University, Ankara 06810, Turkey
| | - A. Ercument Cicek
- Department of Computer Engineering, Bilkent University, Ankara 06810, Turkey
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, 15213 PA, USA
- Corresponding author
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34
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Ziani PR, Feiten JG, Goularte JF, Colombo R, Antqueviezc B, Géa LP, Rosa AR. Potential Candidates for Biomarkers in Bipolar Disorder: A Proteomic Approach through Systems Biology. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2022; 20:211-227. [PMID: 35466093 PMCID: PMC9048014 DOI: 10.9758/cpn.2022.20.2.211] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Paola Rampelotto Ziani
- Laboratory of Molecular Psychiatry, Hospital Clinic of Porto Alegre, Porto Alegre, Brasil
- Postgraduate Program in Biological Sciences: Pharmacology and Therapeutics - Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
| | - Jacson Gabriel Feiten
- Laboratory of Molecular Psychiatry, Hospital Clinic of Porto Alegre, Porto Alegre, Brasil
- Postgraduate Program in Psychiatry and Behavioral Sciences, Faculty of Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
| | | | - Rafael Colombo
- Laboratory of Molecular Psychiatry, Hospital Clinic of Porto Alegre, Porto Alegre, Brasil
- University of Caxias do Sul, Caxias do Sul, Brasil
| | - Bárbara Antqueviezc
- Laboratory of Molecular Psychiatry, Hospital Clinic of Porto Alegre, Porto Alegre, Brasil
| | - Luiza Paul Géa
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Adriane Ribeiro Rosa
- Laboratory of Molecular Psychiatry, Hospital Clinic of Porto Alegre, Porto Alegre, Brasil
- Postgraduate Program in Biological Sciences: Pharmacology and Therapeutics - Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
- Postgraduate Program in Psychiatry and Behavioral Sciences, Faculty of Medicine, Federal University of Rio Grande do Sul, Porto Alegre, Brasil
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35
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González-Calvo I, Cizeron M, Bessereau JL, Selimi F. Synapse Formation and Function Across Species: Ancient Roles for CCP, CUB, and TSP-1 Structural Domains. Front Neurosci 2022; 16:866444. [PMID: 35546877 PMCID: PMC9083331 DOI: 10.3389/fnins.2022.866444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
The appearance of synapses was a crucial step in the creation of the variety of nervous systems that are found in the animal kingdom. With increased complexity of the organisms came a greater number of synaptic proteins. In this review we describe synaptic proteins that contain the structural domains CUB, CCP, or TSP-1. These domains are found in invertebrates and vertebrates, and CUB and CCP domains were initially described in proteins belonging to the complement system of innate immunity. Interestingly, they are found in synapses of the nematode C. elegans, which does not have a complement system, suggesting an ancient function. Comparison of the roles of CUB-, CCP-, and TSP-1 containing synaptic proteins in various species shows that in more complex nervous systems, these structural domains are combined with other domains and that there is partial conservation of their function. These three domains are thus basic building blocks of the synaptic architecture. Further studies of structural domains characteristic of synaptic proteins in invertebrates such as C. elegans and comparison of their role in mammals will help identify other conserved synaptic molecular building blocks. Furthermore, this type of functional comparison across species will also identify structural domains added during evolution in correlation with increased complexity, shedding light on mechanisms underlying cognition and brain diseases.
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Affiliation(s)
- Inés González-Calvo
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Mélissa Cizeron
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5284, INSERM U-1314, MeLiS, Institut NeuroMyoGène, Lyon, France
| | - Jean-Louis Bessereau
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5284, INSERM U-1314, MeLiS, Institut NeuroMyoGène, Lyon, France
| | - Fekrije Selimi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
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Fenckova M, Muha V, Mariappa D, Catinozzi M, Czajewski I, Blok LER, Ferenbach AT, Storkebaum E, Schenck A, van Aalten DMF. Intellectual disability-associated disruption of O-GlcNAc cycling impairs habituation learning in Drosophila. PLoS Genet 2022; 18:e1010159. [PMID: 35500025 PMCID: PMC9140282 DOI: 10.1371/journal.pgen.1010159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 05/27/2022] [Accepted: 03/21/2022] [Indexed: 11/19/2022] Open
Abstract
O-GlcNAcylation is a reversible co-/post-translational modification involved in a multitude of cellular processes. The addition and removal of the O-GlcNAc modification is controlled by two conserved enzymes, O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (OGA). Mutations in OGT have recently been discovered to cause a novel Congenital Disorder of Glycosylation (OGT-CDG) that is characterized by intellectual disability. The mechanisms by which OGT-CDG mutations affect cognition remain unclear. We manipulated O-GlcNAc transferase and O-GlcNAc hydrolase activity in Drosophila and demonstrate an important role of O-GlcNAcylation in habituation learning and synaptic development at the larval neuromuscular junction. Introduction of patient-specific missense mutations into Drosophila O-GlcNAc transferase using CRISPR/Cas9 gene editing leads to deficits in locomotor function and habituation learning. The habituation deficit can be corrected by blocking O-GlcNAc hydrolysis, indicating that OGT-CDG mutations affect cognition-relevant habituation via reduced protein O-GlcNAcylation. This study establishes a critical role for O-GlcNAc cycling and disrupted O-GlcNAc transferase activity in cognitive dysfunction, and suggests that blocking O-GlcNAc hydrolysis is a potential strategy to treat OGT-CDG.
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Affiliation(s)
- Michaela Fenckova
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Villo Muha
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daniel Mariappa
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Marica Catinozzi
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Ignacy Czajewski
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Laura E. R. Blok
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Andrew T. Ferenbach
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Erik Storkebaum
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Daan M. F. van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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Broadhead MJ, Bonthron C, Waddington J, Smith WV, Lopez MF, Burley S, Valli J, Zhu F, Komiyama NH, Smith C, Grant SGN, Miles GB. Selective vulnerability of tripartite synapses in amyotrophic lateral sclerosis. Acta Neuropathol 2022; 143:471-486. [PMID: 35305541 PMCID: PMC8960590 DOI: 10.1007/s00401-022-02412-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/23/2022] [Accepted: 03/09/2022] [Indexed: 12/12/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder. Separate lines of evidence suggest that synapses and astrocytes play a role in the pathological mechanisms underlying ALS. Given that astrocytes make specialised contacts with some synapses, called tripartite synapses, we hypothesise that tripartite synapses could act as the fulcrum of disease in ALS. To test this hypothesis, we have performed an extensive microscopy-based investigation of synapses and tripartite synapses in the spinal cord of ALS model mice and post-mortem human tissue from ALS cases. We reveal widescale synaptic changes at the early symptomatic stages of the SOD1G93a mouse model. Super-resolution microscopy reveals that large complex postsynaptic structures are lost in ALS mice. Most surprisingly, tripartite synapses are selectively lost, while non-tripartite synapses remain in equal number to healthy controls. Finally, we also observe a similar selective loss of tripartite synapses in human post-mortem ALS spinal cords. From these data we conclude that tripartite synaptopathy is a key hallmark of ALS.
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38
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Machine Learning algorithm unveils glutamatergic alterations in the post-mortem schizophrenia brain. NPJ SCHIZOPHRENIA 2022; 8:8. [PMID: 35217646 PMCID: PMC8881508 DOI: 10.1038/s41537-022-00231-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/06/2021] [Indexed: 01/24/2023]
Abstract
Schizophrenia is a disorder of synaptic plasticity and aberrant connectivity in which a major dysfunction in glutamate synapse has been suggested. However, a multi-level approach tackling diverse clusters of interacting molecules of the glutamate signaling in schizophrenia is still lacking. We investigated in the post-mortem dorsolateral prefrontal cortex (DLPFC) and hippocampus of schizophrenia patients and non-psychiatric controls, the levels of neuroactive d- and l-amino acids (l-glutamate, d-serine, glycine, l-aspartate, d-aspartate) by HPLC. Moreover, by quantitative RT-PCR and western blotting we analyzed, respectively, the mRNA and protein levels of pre- and post-synaptic key molecules involved in the glutamatergic synapse functioning, including glutamate receptors (NMDA, AMPA, metabotropic), their interacting scaffolding proteins (PSD-95, Homer1b/c), plasma membrane and vesicular glutamate transporters (EAAT1, EAAT2, VGluT1, VGluT2), enzymes involved either in glutamate-dependent GABA neurotransmitter synthesis (GAD65 and 67), or in post-synaptic NMDA receptor-mediated signaling (CAMKIIα) and the pre-synaptic marker Synapsin-1. Univariable analyses revealed that none of the investigated molecules was differently represented in the post-mortem DLPFC and hippocampus of schizophrenia patients, compared with controls. Nonetheless, multivariable hypothesis-driven analyses revealed that the presence of schizophrenia was significantly affected by variations in neuroactive amino acid levels and glutamate-related synaptic elements. Furthermore, a Machine Learning hypothesis-free unveiled other discriminative clusters of molecules, one in the DLPFC and another in the hippocampus. Overall, while confirming a key role of glutamatergic synapse in the molecular pathophysiology of schizophrenia, we reported molecular signatures encompassing elements of the glutamate synapse able to discriminate patients with schizophrenia and normal individuals.
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Ji Y, Chen R, Wang Q, Wei Q, Tao R, Li B. Leveraging Gene-Level Prediction as Informative Covariate in Hypothesis Weighting Improves Power for Rare Variant Association Studies. Genes (Basel) 2022; 13:genes13020381. [PMID: 35205424 PMCID: PMC8872452 DOI: 10.3390/genes13020381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 02/05/2023] Open
Abstract
Gene-based rare variant association studies (RVASs) have low power due to the infrequency of rare variants and the large multiple testing burden. To correct for multiple testing, traditional false discovery rate (FDR) procedures which depend solely on P-values are often used. Recently, Independent Hypothesis Weighting (IHW) was developed to improve the detection power while maintaining FDR control by leveraging prior information for each hypothesis. Here, we present a framework to increase power of gene-based RVASs by incorporating prior information using IHW. We first build supervised machine learning models to assign each gene a prediction score that measures its disease risk, using the input of multiple biological features, fed with high-confidence risk genes and local background genes selected near GWAS significant loci as the training set. Then we use the prediction scores as covariates to prioritize RVAS results via IHW. We demonstrate the effectiveness of this framework through applications to RVASs in schizophrenia and autism spectrum disorder. We found sizeable improvements in the number of significant associations compared to traditional FDR approaches, and independent evidence supporting the relevance of the genes identified by our framework but not traditional FDR, demonstrating the potential of our framework to improve power of gene-based RVASs.
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Affiliation(s)
- Ying Ji
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Rui Chen
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Quan Wang
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Qiang Wei
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Ran Tao
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37203, USA
- Correspondence: (R.T.); (B.L.)
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
- Correspondence: (R.T.); (B.L.)
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40
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Christensen NR, Pedersen CP, Sereikaite V, Pedersen JN, Vistrup-Parry M, Sørensen AT, Otzen D, Teilum K, Madsen KL, Strømgaard K. Bidirectional protein-protein interactions control liquid-liquid phase separation of PSD-95 and its interaction partners. iScience 2022; 25:103808. [PMID: 35198873 PMCID: PMC8844826 DOI: 10.1016/j.isci.2022.103808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/29/2021] [Accepted: 01/20/2022] [Indexed: 01/08/2023] Open
Abstract
The organization of the postsynaptic density (PSD), a protein-dense semi-membraneless organelle, is mediated by numerous specific protein–protein interactions (PPIs) which constitute a functional postsynapse. The PSD protein 95 (PSD-95) interacts with a manifold of proteins, including the C-terminal of transmembrane AMPA receptor (AMPAR) regulatory proteins (TARPs). Here, we uncover the minimal essential peptide responsible for the Stargazin (TARP-γ2)-mediated liquid–liquid phase separation (LLPS) formation of PSD-95 and other key protein constituents of the PSD. Furthermore, we find that pharmacological inhibitors of PSD-95 can facilitate the formation of LLPS. We found that in some cases LLPS formation is dependent on multivalent interactions, while in other cases short, highly charged peptides are sufficient to promote LLPS in complex systems. This study offers a new perspective on PSD-95 interactions and their role in LLPS formation, while also considering the role of affinity over multivalency in LLPS systems. Charge and valency are important for LLPS formation, both for PSD-95 and the ePSD Peptide inhibitors may be used to induce LLPS formation for PSD-95 and the ePSD
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Affiliation(s)
- Nikolaj Riis Christensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.,Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Christian Parsbæk Pedersen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Vita Sereikaite
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Maria Vistrup-Parry
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Andreas Toft Sørensen
- Department of Neuroscience, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | | | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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41
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Lin GN, Song W, Wang W, Wang P, Yu H, Cai W, Jiang X, Huang W, Qian W, Chen Y, Chen M, Yu S, Xu T, Jiao Y, Liu Q, Zhang C, Yi Z, Fan Q, Chen J, Wang Z. De novo mutations identified by whole-genome sequencing implicate chromatin modifications in obsessive-compulsive disorder. SCIENCE ADVANCES 2022; 8:eabi6180. [PMID: 35020433 PMCID: PMC8754407 DOI: 10.1126/sciadv.abi6180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Obsessive-compulsive disorder (OCD) is a chronic anxiety disorder with a substantial genetic basis and a broadly undiscovered etiology. Recent studies of de novo mutation (DNM) exome-sequencing studies for OCD have reinforced the hypothesis that rare variation contributes to the risk. We performed, to our knowledge, the first whole-genome sequencing on 53 parent-offspring families with offspring affected with OCD to investigate all rare de novo variants and insertions/deletions. We observed higher mutation rates in promoter-anchored chromatin loops (empirical P = 0.0015) and regions with high frequencies of histone marks (empirical P = 0.0001). Mutations affecting coding regions were significantly enriched within coexpression modules of genes involved in chromatin modification during human brain development. Four genes—SETD5, KDM3B, ASXL3, and FBL—had strong aggregated evidence and functionally converged on transcription’s epigenetic regulation, suggesting an important OCD risk mechanism. Our data characterized different genome-wide DNMs and highlighted the contribution of chromatin modification in the etiology of OCD.
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Affiliation(s)
- Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
- Corresponding author. (G.N.L.); (Z.W.)
| | - Weichen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Weidi Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Pei Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Psychological and Behavioral Science, Shanghai Jiao Tong University, Shanghai, China
| | - Huan Yu
- Novogene Bioinformatics Institute, Beijing, China
| | - Wenxiang Cai
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Xue Jiang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wu Huang
- Novogene Bioinformatics Institute, Beijing, China
| | - Wei Qian
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yucan Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Miao Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shunying Yu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Tingting Xu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Psychological and Behavioral Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yumei Jiao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Liu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenghui Yi
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Fan
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Jue Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhen Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
- Institute of Psychological and Behavioral Science, Shanghai Jiao Tong University, Shanghai, China
- Corresponding author. (G.N.L.); (Z.W.)
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42
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Andrews B, Murphy AE, Stofella M, Maslen S, Almeida-Souza L, Skehel JM, Skene NG, Sobott F, Frank RAW. Multidimensional dynamics of the proteome in the neurodegenerative and aging mammalian brain. Mol Cell Proteomics 2021; 21:100192. [PMID: 34979241 PMCID: PMC8816717 DOI: 10.1016/j.mcpro.2021.100192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 12/03/2021] [Accepted: 12/29/2021] [Indexed: 11/18/2022] Open
Abstract
The amount of any given protein in the brain is determined by the rates of its synthesis and destruction, which are regulated by different cellular mechanisms. Here, we combine metabolic labeling in live mice with global proteomic profiling to simultaneously quantify both the flux and amount of proteins in mouse models of neurodegeneration. In multiple models, protein turnover increases were associated with increasing pathology. This method distinguishes changes in protein expression mediated by synthesis from those mediated by degradation. In the AppNL-F knockin mouse model of Alzheimer’s disease, increased turnover resulted from imbalances in both synthesis and degradation, converging on proteins associated with synaptic vesicle recycling (Dnm1, Cltc, Rims1) and mitochondria (Fis1, Ndufv1). In contrast to disease models, aging in wild-type mice caused a widespread decrease in protein recycling associated with a decrease in autophagic flux. Overall, this simple multidimensional approach enables a comprehensive mapping of proteome dynamics and identifies affected proteins in mouse models of disease and other live animal test settings. Multidimensional proteomic screen to detect imbalances in mouse models of disease. Increased proteome turnover in multiple symptomatic neurodegeneration mouse models. Healthy aging is associated with a global decrease in protein turnover.
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Affiliation(s)
- Byron Andrews
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alan E Murphy
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, W12 0BZ, UK
| | - Michele Stofella
- Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Leonardo Almeida-Souza
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; Helsinki Institute of Life Science - HiLIFE, Institute of Biotechnology and Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 5, 00790, Helsinki, Finland
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nathan G Skene
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, W12 0BZ, UK
| | - Frank Sobott
- Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - René A W Frank
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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43
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HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks. PLoS Comput Biol 2021; 17:e1009621. [PMID: 34843454 PMCID: PMC8659295 DOI: 10.1371/journal.pcbi.1009621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 12/09/2021] [Accepted: 11/08/2021] [Indexed: 12/03/2022] Open
Abstract
Signaling networks mediate many aspects of cellular function. The conventional, mechanistically motivated approach to modeling such networks is through mass-action chemistry, which maps directly to biological entities and facilitates experimental tests and predictions. However such models are complex, need many parameters, and are computationally costly. Here we introduce the HillTau form for signaling models. HillTau retains the direct mapping to biological observables, but it uses far fewer parameters, and is 100 to over 1000 times faster than ODE-based methods. In the HillTau formalism, the steady-state concentration of signaling molecules is approximated by the Hill equation, and the dynamics by a time-course tau. We demonstrate its use in implementing several biochemical motifs, including association, inhibition, feedforward and feedback inhibition, bistability, oscillations, and a synaptic switch obeying the BCM rule. The major use-cases for HillTau are system abstraction, model reduction, scaffolds for data-driven optimization, and fast approximations to complex cellular signaling. Chemical signals mediate many computations in cells, from housekeeping functions in all cells to memory and pattern selectivity in neurons. These signals form complex networks of interactions. Computer models are a powerful way to study how such networks behave, but it is hard to get all the chemical details for typical models, and it is slow to run them with standard numerical approaches to chemical kinetics. We introduce HillTau as a simplified way to model complex chemical networks. HillTau models condense multiple reaction steps into single steps defined by a small number of parameters for activation and settling time. As a result the models are simple, easy to find values for, and they run quickly. Remarkably, they fit the full chemical formulations rather well. We illustrate the utility of HillTau for modeling several signaling network functions, and for fitting complicated signaling networks.
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44
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Lautz JD, Tsegay KB, Zhu Z, Gniffke EP, Welsh JP, Smith SEP. Synaptic protein interaction networks encode experience by assuming stimulus-specific and brain-region-specific states. Cell Rep 2021; 37:110076. [PMID: 34852231 PMCID: PMC8722361 DOI: 10.1016/j.celrep.2021.110076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/01/2021] [Accepted: 11/09/2021] [Indexed: 11/02/2022] Open
Abstract
A core network of widely expressed proteins within the glutamatergic post-synapse mediates activity-dependent synaptic plasticity throughout the brain, but the specific proteomic composition of synapses differs between brain regions. Here, we address the question, how does proteomic composition affect activity-dependent protein-protein interaction networks (PINs) downstream of synaptic activity? Using quantitative multiplex co-immunoprecipitation, we compare the PIN response of in vivo or ex vivo neurons derived from different brain regions to activation by different agonists or different forms of eyeblink conditioning. We report that PINs discriminate between incoming stimuli using differential kinetics of overlapping and non-overlapping PIN parameters. Further, these "molecular logic rules" differ by brain region. We conclude that although the PIN of the glutamatergic post-synapse is expressed widely throughout the brain, its activity-dependent dynamics show remarkable stimulus-specific and brain-region-specific diversity. This diversity may help explain the challenges in developing molecule-specific drug therapies for neurological disorders.
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Affiliation(s)
- Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kaleb B Tsegay
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Zhiyi Zhu
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Edward P Gniffke
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - John P Welsh
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA.
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45
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Zhou J, Liang W, Wang J, Chen J, Liu D, Wang X, Wu Y, Zhang Q, Shen D. An epileptic encephalopathy associated GABRG2 missense mutation leads to pre- and postsynaptic defects in zebrafish. Hum Mol Genet 2021; 31:3216-3230. [PMID: 34957497 DOI: 10.1093/hmg/ddab338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Mutations in the γ-aminobutyric acid type A (GABAA) receptor γ2 subunit gene, GABRG2, have been associated with a variety of epilepsy syndromes. A de novo mutation (c.T1027C, p.F343L) in GABRG2 was identified in a patient with early onset epileptic encephalopathy. Zebrafish overexpressing mutant human GABRG2 (F343L) subunits displayed spontaneous seizure activity and convulsive behaviors. In this study, we demonstrated that Tg (hGABRG2F343L) zebrafish displayed hyperactivity during light phase with normal circadian rhythm, as well as increased drug-induced locomotor activity. Real-time quantitative PCR, whole mount in situ hybridization and western blotting showed that Tg(hGABRG2F343L) zebrafish had altered expression of GABAA receptor subunits. Furthermore, investigation of synaptic protein expression and synapse ultrastructure uncovered a robust synaptic phenotype that is causally linked to GABRG2(F343L) mutation. Strikingly, Tg(hGABRG2F343L) zebrafish not only had postsynaptic defects, but also displayed an unanticipated deficit at the presynaptic level. Overall, our Tg(hGABRG2F343L) overexpression zebrafish model has expanded the GABAergic paradigm in epileptic encephalopathy from channelopathy to synaptopathy.
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Affiliation(s)
- Jing Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Wenpeng Liang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Jie Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Juan Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Dong Liu
- School of Life Science, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Xin Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Youjia Wu
- Department of Pediatrics, Affiliated Hospital of Nantong University, Nantong, China
| | - Qi Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Dingding Shen
- Department of Neurology & Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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Electroacupuncture Ameliorates Depression-Like Behaviour in Rats by Enhancing Synaptic Plasticity via the GluN2B/CaMKII/CREB Signalling Pathway. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:2146001. [PMID: 34777532 PMCID: PMC8580672 DOI: 10.1155/2021/2146001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/11/2021] [Indexed: 12/27/2022]
Abstract
Background Hippocampal synaptic plasticity during the pathological process of depression has received increasing attention. Hippocampal neuron atrophy and the reduction in synaptic density induced by chronic stress are important pathological mechanisms of depression. Electroacupuncture (EA) exerts beneficial effects on depression, but the mechanism is unclear. This study explored the effect of EA on synaptic plasticity and the potential mechanism. Methods Forty-eight SD rats were randomly divided into the control, chronic unpredictable mild stress (CUMS), EA, and fluoxetine (FLX) groups, and each group consisted of 12 rats. The sucrose preference test, open field test, and forced swimming test were used for the evaluation of depression-like behaviour, and Golgi and Nissl staining were used for the assessment of synaptic plasticity. Western blotting and immunofluorescence were conducted to detect proteins related to synaptic plasticity and to determine their effects on signalling pathways. Results We found that CUMS led to depression-like behaviours, including a reduced preference for sucrose, a prolonged immobility time, and reduced exploration activity. The dendritic spine densities and neuron numbers and the protein levels of MAP-2, PSD-95, and SYN were decreased in the hippocampi of rats with CUMS-induced depression, and these trends were reversed by EA. The molecular mechanism regulating this plasticity may involve the GluN2B/CaMKII/CREB signalling pathway. Conclusion These results suggest that EA can improve depression-like behaviour and hippocampal plasticity induced by CUMS, and the mechanism may be related to the GluN2B/CaMKII/CREB pathway.
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Li Q, Wang Z, Zong L, Ye L, Ye J, Ou H, Jiang T, Guo B, Yang Q, Liang W, Zhang J, Long Y, Zheng X, Hou Y, Wu F, Zhou L, Li S, Huang X, Zhao C. Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function. Mol Psychiatry 2021; 26:6630-6642. [PMID: 33963283 DOI: 10.1038/s41380-021-01126-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/01/2021] [Accepted: 04/13/2021] [Indexed: 12/26/2022]
Abstract
The non-Mendelian features of phenotypic variations within monozygotic twins are likely complicated by environmental modifiers of genetic effects that have yet to be elucidated. Here, we performed methylome and genome analyses of blood DNA from psychiatric disorder-discordant monozygotic twins to study how allele-specific methylation (ASM) mediates phenotypic variations. We identified that thousands of genetic variants with ASM imbalances exhibit phenotypic variation-associated switching at regulatory loci. These ASMs have plausible causal associations with psychiatric disorders through effects on interactions between transcription factors, DNA methylations, and other epigenomic markers and then contribute to dysregulated gene expression, which eventually increases disease susceptibility. Moreover, we also experimentally validated the model that the rs4854158 alternative C allele at an ASM switching regulatory locus of EIPR1 encoding endosome-associated recycling protein-interacting protein 1, is associated with demethylation and higher RNA expression and shows lower TF binding affinities in unaffected controls. An epigenetic ASM switching induces C allele hypermethylation and then recruits repressive Polycomb repressive complex 2 (PRC2), reinforces trimethylation of lysine 27 on histone 3 and inhibits its transcriptional activity, thus leading to downregulation of EIPR1 in schizophrenia. Moreover, disruption of rs4854158 induces gain of EIPR1 function and promotes neural development and vesicle trafficking. Our study provides a powerful framework for identifying regulatory risk variants and contributes to our understanding of the interplay between genetic and epigenetic variants in mediating psychiatric disorder susceptibility.
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Affiliation(s)
- Qiyang Li
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhongju Wang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Lu Zong
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Linyan Ye
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Junping Ye
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Haiyan Ou
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Tingyun Jiang
- The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Bo Guo
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiong Yang
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Wenquan Liang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Yong Long
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Xianzhen Zheng
- Guangdong General Hospital, Guangdong Academy of Medical Science and Guangdong Mental Health Center, Guangzhou, China
| | - Yu Hou
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Fengchun Wu
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Lin Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China
| | - Shufen Li
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China
| | - Xingbing Huang
- Department of Psychiatry, the Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Cunyou Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, and Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Southern Medical University, Guangzhou, Guangdong, China. .,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, and Guangdong Province Key Laboratory of Psychiatric Disorders, Southern Medical University, Guangzhou, Guangdong, China.
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48
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Sluysmans S, Méan I, Xiao T, Boukhatemi A, Ferreira F, Jond L, Mutero A, Chang CJ, Citi S. PLEKHA5, PLEKHA6, and PLEKHA7 bind to PDZD11 to target the Menkes ATPase ATP7A to the cell periphery and regulate copper homeostasis. Mol Biol Cell 2021; 32:ar34. [PMID: 34613798 PMCID: PMC8693958 DOI: 10.1091/mbc.e21-07-0355] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 01/12/2023] Open
Abstract
Copper homeostasis is crucial for cellular physiology and development, and its dysregulation leads to disease. The Menkes ATPase ATP7A plays a key role in copper efflux, by trafficking from the Golgi to the plasma membrane upon cell exposure to elevated copper, but the mechanisms that target ATP7A to the cell periphery are poorly understood. PDZD11 interacts with the C-terminus of ATP7A, which contains sequences involved in ATP7A trafficking, but the role of PDZD11 in ATP7A localization is unknown. Here we identify PLEKHA5 and PLEKHA6 as new interactors of PDZD11 that bind to the PDZD11 N-terminus through their WW domains similarly to the junctional protein PLEKHA7. Using CRISPR-KO kidney epithelial cells, we show by immunofluorescence microscopy that WW-PLEKHAs (PLEKHA5, PLEKHA6, PLEKHA7) recruit PDZD11 to distinct plasma membrane localizations and that they are required for the efficient anterograde targeting of ATP7A to the cell periphery in elevated copper conditions. Pull-down experiments show that WW-PLEKHAs promote PDZD11 interaction with the C-terminus of ATP7A. However, WW-PLEKHAs and PDZD11 are not necessary for ATP7A Golgi localization in basal copper, ATP7A copper-induced exit from the Golgi, and ATP7A retrograde trafficking to the Golgi. Finally, measuring bioavailable and total cellular copper, metallothionein-1 expression, and cell viability shows that WW-PLEKHAs and PDZD11 are required for maintaining low intracellular copper levels when cells are exposed to elevated copper. These data indicate that WW-PLEKHAs-PDZD11 complexes regulate the localization and function of ATP7A to promote copper extrusion in elevated copper.
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Affiliation(s)
- Sophie Sluysmans
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Isabelle Méan
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Tong Xiao
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
| | - Amina Boukhatemi
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Flavio Ferreira
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Lionel Jond
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Annick Mutero
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Sandra Citi
- Department of Cell Biology, Faculty of Sciences, University of Geneva, CH-1205 Geneva, Switzerland
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Curran OE, Qiu Z, Smith C, Grant SGN. A single-synapse resolution survey of PSD95-positive synapses in twenty human brain regions. Eur J Neurosci 2021; 54:6864-6881. [PMID: 32492218 PMCID: PMC7615673 DOI: 10.1111/ejn.14846] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/24/2022]
Abstract
Mapping the molecular composition of individual excitatory synapses across the mouse brain reveals high synapse diversity with each brain region showing a distinct composition of synapse types. As a first step towards systematic mapping of synapse diversity across the human brain, we have labelled and imaged synapses expressing the excitatory synapse protein PSD95 in twenty human brain regions, including 13 neocortical, two subcortical, one hippocampal, one cerebellar and three brainstem regions, in four phenotypically normal individuals. We quantified the number, size and intensity of individual synaptic puncta and compared their regional distributions. We found that each region showed a distinct signature of synaptic puncta parameters. Comparison of brain regions showed that cortical and hippocampal structures are similar, and distinct from those of cerebellum and brainstem. Comparison of synapse parameters from human and mouse brain revealed conservation of parameters, hierarchical organization of brain regions and network architecture. This work illustrates the feasibility of generating a systematic single-synapse resolution atlas of the human brain, a potentially significant resource in studies of brain health and disease.
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Affiliation(s)
- Olimpia E Curran
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Zhen Qiu
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Colin Smith
- Academic Neuropathology, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, Chancellor's Building, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
- Simons Initiative for the Developing Brain (SIDB), Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, Edinburgh, UK
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50
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Carlyle BC, Kandigian SE, Kreuzer J, Das S, Trombetta BA, Kuo Y, Bennett DA, Schneider JA, Petyuk VA, Kitchen RR, Morris R, Nairn AC, Hyman BT, Haas W, Arnold SE. Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics. Neurobiol Aging 2021; 105:99-114. [PMID: 34052751 PMCID: PMC8338777 DOI: 10.1016/j.neurobiolaging.2021.04.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/18/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) is defined by the presence of abundant amyloid-β (Aβ) and tau neuropathology. While this neuropathology is necessary for AD diagnosis, it is not sufficient for causing cognitive impairment. Up to one third of community dwelling older adults harbor intermediate to high levels of AD neuropathology at death yet demonstrate no significant cognitive impairment. Conversely, there are individuals who exhibit dementia with no gross explanatory neuropathology. In prior studies, synapse loss correlated with cognitive impairment. To understand how synaptic composition changes in relation to neuropathology and cognition, multiplexed liquid chromatography mass-spectrometry was used to quantify enriched synaptic proteins from the parietal association cortex of 100 subjects with contrasting levels of AD pathology and cognitive performance. 123 unique proteins were significantly associated with diagnostic category. Functional analysis showed enrichment of serotonin release and oxidative phosphorylation categories in normal (cognitively unimpaired, low neuropathology) and "resilient" (unimpaired despite AD pathology) individuals. In contrast, frail individuals, (low pathology, impaired cognition) showed a metabolic shift towards glycolysis and increased presence of proteasome subunits.
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Affiliation(s)
- Becky C Carlyle
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Savannah E Kandigian
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Johannes Kreuzer
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Sudeshna Das
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Bianca A Trombetta
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Yikai Kuo
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Cardiology Division, Charlestown, MA, USA
| | | | | | | | - Robert R Kitchen
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Cardiology Division, Charlestown, MA, USA
| | - Robert Morris
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | | | - Bradley T Hyman
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Wilhelm Haas
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Steven E Arnold
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
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