1
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Stamenkovic V, Lautz JD, Harsh FM, Smith SEP. SRC family kinase inhibition rescues molecular and behavioral phenotypes, but not protein interaction network dynamics, in a mouse model of Fragile X syndrome. Mol Psychiatry 2024; 29:1392-1405. [PMID: 38297084 DOI: 10.1038/s41380-024-02418-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 02/02/2024]
Abstract
Glutamatergic synapses encode information from extracellular inputs using dynamic protein interaction networks (PINs) that undergo widespread reorganization following synaptic activity, allowing cells to distinguish between signaling inputs and generate coordinated cellular responses. Here, we investigate how Fragile X Messenger Ribonucleoprotein (FMRP) deficiency disrupts signal transduction through a glutamatergic synapse PIN downstream of NMDA receptor or metabotropic glutamate receptor (mGluR) stimulation. In cultured cortical neurons or acute cortical slices from P7, P17 and P60 FMR1-/y mice, the unstimulated protein interaction network state resembled that of wildtype littermates stimulated with mGluR agonists, demonstrating resting state pre-activation of mGluR signaling networks. In contrast, interactions downstream of NMDAR stimulation were similar to WT. We identified the Src family kinase (SFK) Fyn as a network hub, because many interactions involving Fyn were pre-activated in FMR1-/y animals. We tested whether targeting SFKs in FMR1-/y mice could modify disease phenotypes, and found that Saracatinib (SCB), an SFK inhibitor, normalized elevated basal protein synthesis, novel object recognition memory and social behavior in FMR1-/y mice. However, SCB treatment did not normalize the PIN to a wild-type-like state in vitro or in vivo, but rather induced extensive changes to protein complexes containing Shank3, NMDARs and Fyn. We conclude that targeting abnormal nodes of a PIN can identify potential disease-modifying drugs, but behavioral rescue does not correlate with PIN normalization.
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Affiliation(s)
- Vera Stamenkovic
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Felicia M Harsh
- Center for Integrative Brain Research, Seattle Children's Research Institute, 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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2
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Ritmeester-Loy SA, Draper IH, Bueter EC, Lautz JD, Zhang-Wong Y, Gustafson JA, Wilson AL, Lin C, Gafken PR, Jensen MC, Orentas R, Smith SEP. Differential protein-protein interactions underlie signaling mediated by the TCR and a 4-1BB domain-containing CAR. Sci Signal 2024; 17:eadd4671. [PMID: 38442200 PMCID: PMC10986860 DOI: 10.1126/scisignal.add4671] [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: 06/13/2022] [Accepted: 01/09/2024] [Indexed: 03/07/2024]
Abstract
Cells rely on activity-dependent protein-protein interactions to convey biological signals. For chimeric antigen receptor (CAR) T cells containing a 4-1BB costimulatory domain, receptor engagement is thought to stimulate the formation of protein complexes similar to those stimulated by T cell receptor (TCR)-mediated signaling, but the number and type of protein interaction-mediating binding domains differ between CARs and TCRs. Here, we performed coimmunoprecipitation mass spectrometry analysis of a second-generation, CD19-directed 4-1BB:ζ CAR (referred to as bbζCAR) and identified 128 proteins that increased their coassociation after target engagement. We compared activity-induced TCR and CAR signalosomes by quantitative multiplex coimmunoprecipitation and showed that bbζCAR engagement led to the activation of two modules of protein interactions, one similar to TCR signaling that was more weakly engaged by bbζCAR as compared with the TCR and one composed of TRAF signaling complexes that was not engaged by the TCR. Batch-to-batch and interindividual variations in production of the cytokine IL-2 correlated with differences in the magnitude of protein network activation. Future CAR T cell manufacturing protocols could measure, and eventually control, biological variation by monitoring these signalosome activation markers.
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Affiliation(s)
- Samuel A. Ritmeester-Loy
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Isabella H. Draper
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Eric C. Bueter
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Yue Zhang-Wong
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Joshua A. Gustafson
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Seattle Children’s Therapeutics, Seattle Children’s Research Institute, Seattle, WA 98101 USA
| | - Ashley L. Wilson
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Seattle Children’s Therapeutics, Seattle Children’s Research Institute, Seattle, WA 98101 USA
| | - Chenwei Lin
- Proteomics and Metabolomics Facility, Fred Hutchinson Cancer Center, Seattle, WA 98101, USA
| | - Philip R. Gafken
- Proteomics and Metabolomics Facility, Fred Hutchinson Cancer Center, Seattle, WA 98101, USA
| | - Michael C. Jensen
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Seattle Children’s Therapeutics, Seattle Children’s Research Institute, Seattle, WA 98101 USA
- Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - Rimas Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - Stephen E. P. Smith
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA 98101, USA
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3
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Wehle DT, Bass CS, Sulc J, Mirzaa G, Smith SEP. Protein interaction network analysis of mTOR signaling reveals modular organization. J Biol Chem 2023; 299:105271. [PMID: 37741456 PMCID: PMC10594569 DOI: 10.1016/j.jbc.2023.105271] [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: 08/03/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023] Open
Abstract
The mammalian target of rapamycin (mTOR) is a serine-threonine kinase that acts as a central mediator of translation and plays important roles in cell growth, synaptic plasticity, cancer, and a wide range of developmental disorders. The signaling cascade linking lipid kinases (phosphoinositide 3-kinases), protein kinases (AKT), and translation initiation complexes (EIFs) to mTOR has been extensively modeled, but does not fully describe mTOR system behavior. Here, we use quantitative multiplex coimmunoprecipitation to monitor a protein interaction network (PIN) composed of 300+ binary interactions among mTOR-related proteins. Using a simple model system of serum-deprived or fresh-media-fed mouse 3T3 fibroblasts, we observed extensive PIN remodeling involving 27+ individual protein interactions after 1 h, despite phosphorylation changes observed after only 5 min. Using small molecule inhibitors of phosphoinositide 3-kinase, AKT, mTOR, MEK and ERK, we define subsets of the PIN, termed "modules", that respond differently to each inhibitor. Using primary fibroblasts from individuals with overgrowth disorders caused by pathogenic PIK3CA or MTOR variants, we find that hyperactivation of mTOR pathway components is reflected in a hyperactive PIN. Our data define a "modular" organization of the mTOR PIN in which coordinated groups of interactions respond to the activation or inhibition of distinct nodes, and demonstrate that kinase inhibitors affect the modular network architecture in a complex manner, inconsistent with simple linear models of signal transduction.
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Affiliation(s)
- Devin T Wehle
- Graduate Program in Neuroscience, University of Washington, Seattle, Washington, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Carter S Bass
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Josef Sulc
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Stephen E P Smith
- Graduate Program in Neuroscience, University of Washington, Seattle, Washington, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.
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4
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Wehle DT, Bass CS, Sulc J, Mirzaa G, Smith SEP. Protein interaction network analysis of mTOR signaling reveals modular organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552011. [PMID: 37577705 PMCID: PMC10418199 DOI: 10.1101/2023.08.04.552011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The mammalian target of rapamycin (mTOR) is a serine-threonine kinase that acts as a central mediator of translation, and plays important roles in cell growth, synaptic plasticity, cancer, and a wide range of developmental disorders. The signaling cascade linking lipid kinases (PI3Ks), protein kinases (AKT) and translation initiation complexes (EIFs) to mTOR has been extensively modeled, but does not fully describe mTOR system behavior. Here, we use quantitative multiplex co-immunoprecipitation to monitor a protein interaction network (PIN) composed of 300+ binary interactions among mTOR-related proteins. Using a simple model system of serum deprived or fresh-media-fed mouse 3T3 fibroblasts, we observed extensive PIN remodeling involving 27+ individual protein interactions after one hour, despite phosphorylation changes observed after only five minutes. Using small molecule inhibitors of PI3K, AKT, mTOR, MEK and ERK, we define subsets of the PIN, termed 'modules', that respond differently to each inhibitor. Using primary fibroblasts from individuals with overgrowth disorders caused by pathogenic PIK3CA or MTOR variants, we find that hyperactivation of mTOR pathway components is reflected in a hyperactive PIN. Our data define a "modular" organization of the mTOR PIN in which coordinated groups of interactions respond to activation or inhibition of distinct nodes, and demonstrate that kinase inhibitors affect the modular network architecture in a complex manner, inconsistent with simple linear models of signal transduction.
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Affiliation(s)
- Devin T Wehle
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Carter S Bass
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Josef Sulc
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Stephen E P Smith
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
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5
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Nanda H, Frye RE. Synchrony 2022: Catalyzing Research and Treatments to Benefit Individuals with Neurodevelopmental Disorders including Autism Spectrum Disorders. J Pers Med 2023; 13:jpm13030490. [PMID: 36983672 PMCID: PMC10053654 DOI: 10.3390/jpm13030490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
A unique translational medicine conference for research into treatments that can benefit individuals with neurodevelopmental disorders (NDD), including autism spectrum disorder (ASD), has been developed and hosted by The BRAIN Foundation (Pleasanton, CA, USA) since 2019 [...]
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Affiliation(s)
- Heer Nanda
- University of California, Berkeley, CA 94720, USA
| | - Richard E. Frye
- Autism Discovery and Treatment Foundation, Phoenix, AZ 85050, USA
- Rossignol Medical Center, Phoenix, AZ 85050, USA
- Southwest Autism Research and Resource Center, Phoenix, AZ 85006, USA
- Correspondence:
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6
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Purushotham SS, Reddy NMN, D'Souza MN, Choudhury NR, Ganguly A, Gopalakrishna N, Muddashetty R, Clement JP. A perspective on molecular signalling dysfunction, its clinical relevance and therapeutics in autism spectrum disorder. Exp Brain Res 2022; 240:2525-2567. [PMID: 36063192 DOI: 10.1007/s00221-022-06448-x] [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: 06/01/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022]
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are neurodevelopmental disorders that have become a primary clinical and social concern, with a prevalence of 2-3% in the population. Neuronal function and behaviour undergo significant malleability during the critical period of development that is found to be impaired in ID/ASD. Human genome sequencing studies have revealed many genetic variations associated with ASD/ID that are further verified by many approaches, including many mouse and other models. These models have facilitated the identification of fundamental mechanisms underlying the pathogenesis of ASD/ID, and several studies have proposed converging molecular pathways in ASD/ID. However, linking the mechanisms of the pathogenic genes and their molecular characteristics that lead to ID/ASD has progressed slowly, hampering the development of potential therapeutic strategies. This review discusses the possibility of recognising the common molecular causes for most ASD/ID based on studies from the available models that may enable a better therapeutic strategy to treat ID/ASD. We also reviewed the potential biomarkers to detect ASD/ID at early stages that may aid in diagnosis and initiating medical treatment, the concerns with drug failure in clinical trials, and developing therapeutic strategies that can be applied beyond a particular mutation associated with ASD/ID.
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Affiliation(s)
- Sushmitha S Purushotham
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Neeharika M N Reddy
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Michelle Ninochka D'Souza
- Centre for Brain Research, Indian Institute of Science Campus, CV Raman Avenue, Bangalore, 560 012, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - Nilpawan Roy Choudhury
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Anusa Ganguly
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Niharika Gopalakrishna
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Ravi Muddashetty
- Centre for Brain Research, Indian Institute of Science Campus, CV Raman Avenue, Bangalore, 560 012, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - James P Clement
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India.
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7
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Sun SY, Li XW, Cao R, Zhao Y, Sheng N, Tang AH. Correlative Assembly of Subsynaptic Nanoscale Organizations During Development. Front Synaptic Neurosci 2022; 14:748184. [PMID: 35685244 PMCID: PMC9171000 DOI: 10.3389/fnsyn.2022.748184] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/11/2022] [Indexed: 11/17/2022] Open
Abstract
Nanoscale organization of presynaptic proteins determines the sites of transmitter release, and its alignment with assemblies of postsynaptic receptors through nanocolumns is suggested to optimize the efficiency of synaptic transmission. However, it remains unknown how these nano-organizations are formed during development. In this study, we used super-resolution stochastic optical reconstruction microscopy (STORM) imaging technique to systematically analyze the evolvement of subsynaptic organization of three key synaptic proteins, namely, RIM1/2, GluA1, and PSD-95, during synapse maturation in cultured hippocampal neurons. We found that volumes of synaptic clusters and their subsynaptic heterogeneity increase as synapses get matured. Synapse sizes of presynaptic and postsynaptic compartments correlated well at all stages, while only more mature synapses demonstrated a significant correlation between presynaptic and postsynaptic nano-organizations. After a long incubation with an inhibitor of action potentials or AMPA receptors, both presynaptic and postsynaptic compartments showed increased synaptic cluster volume and subsynaptic heterogeneity; however, the trans-synaptic alignment was intact. Together, our results characterize the evolvement of subsynaptic protein architectures during development and demonstrate that the nanocolumn is organized more likely by an intrinsic mechanism and independent of synaptic activities.
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Affiliation(s)
- Shi-Yan Sun
- Chinese Academy of Sciences (CAS) Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Xiao-Wei Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ran Cao
- Chinese Academy of Sciences (CAS) Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yang Zhao
- Chinese Academy of Sciences (CAS) Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- State Key Laboratory of Genetic Resources and Evolution in Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Nengyin Sheng
- State Key Laboratory of Genetic Resources and Evolution in Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Nengyin Sheng
| | - Ai-Hui Tang
- Chinese Academy of Sciences (CAS) Key Laboratory of Brain Function and Disease, Ministry of Education Key Laboratory for Membrane-less Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- *Correspondence: Ai-Hui Tang
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8
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de Bartolomeis A, Barone A, Buonaguro EF, Tomasetti C, Vellucci L, Iasevoli F. The Homer1 family of proteins at the crossroad of dopamine-glutamate signaling: An emerging molecular "Lego" in the pathophysiology of psychiatric disorders. A systematic review and translational insight. Neurosci Biobehav Rev 2022; 136:104596. [PMID: 35248676 DOI: 10.1016/j.neubiorev.2022.104596] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 12/17/2022]
Abstract
Once considered only scaffolding proteins at glutamatergic postsynaptic density (PSD), Homer1 proteins are increasingly emerging as multimodal adaptors that integrate different signal transduction pathways within PSD, involved in motor and cognitive functions, with putative implications in psychiatric disorders. Regulation of type I metabotropic glutamate receptor trafficking, modulation of calcium signaling, tuning of long-term potentiation, organization of dendritic spines' growth, as well as meta- and homeostatic plasticity control are only a few of the multiple endocellular and synaptic functions that have been linked to Homer1. Findings from preclinical studies, as well as genetic studies conducted in humans, suggest that both constitutive (Homer1b/c) and inducible (Homer1a) isoforms of Homer1 play a role in the neurobiology of several psychiatric disorders, including psychosis, mood disorders, neurodevelopmental disorders, and addiction. On this background, Homer1 has been proposed as a putative novel target in psychopharmacological treatments. The aim of this review is to summarize and systematize the growing body of evidence on Homer proteins, highlighting the role of Homer1 in the pathophysiology and therapy of mental diseases.
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Affiliation(s)
- Andrea de Bartolomeis
- Laboratory of Translational and Molecular Psychiatry and Section of Psychiatry, Department of Neuroscience, University School of Medicine "Federico II", Naples, Italy.
| | - Annarita Barone
- Laboratory of Translational and Molecular Psychiatry and Section of Psychiatry, Department of Neuroscience, University School of Medicine "Federico II", Naples, Italy
| | - Elisabetta Filomena Buonaguro
- Laboratory of Translational and Molecular Psychiatry and Section of Psychiatry, Department of Neuroscience, University School of Medicine "Federico II", Naples, Italy
| | - Carmine Tomasetti
- Laboratory of Translational and Molecular Psychiatry and Section of Psychiatry, Department of Neuroscience, University School of Medicine "Federico II", Naples, Italy
| | - Licia Vellucci
- Laboratory of Translational and Molecular Psychiatry and Section of Psychiatry, Department of Neuroscience, University School of Medicine "Federico II", Naples, Italy
| | - Felice Iasevoli
- Laboratory of Translational and Molecular Psychiatry and Section of Psychiatry, Department of Neuroscience, University School of Medicine "Federico II", Naples, Italy
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9
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Stillman M, Lautz JD, Johnson RS, MacCoss MJ, Smith SEP. Activity dependent dissociation of the Homer1 interactome. Sci Rep 2022; 12:3207. [PMID: 35217690 PMCID: PMC8881602 DOI: 10.1038/s41598-022-07179-3] [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: 11/03/2021] [Accepted: 02/09/2022] [Indexed: 11/12/2022] Open
Abstract
Neurons encode information by rapidly modifying synaptic protein complexes, which changes the strength of specific synaptic connections. Homer1 is abundantly expressed at glutamatergic synapses, and is known to alter its binding to metabotropic glutamate receptor 5 (mGlu5) in response to synaptic activity. However, Homer participates in many additional known interactions whose activity-dependence is unclear. Here, we used co-immunoprecipitation and label-free quantitative mass spectrometry to characterize activity-dependent interactions in the cerebral cortex of wildtype and Homer1 knockout mice. We identified a small, high-confidence protein network consisting of mGlu5, Shank2 and 3, and Homer1–3, of which only mGlu5 and Shank3 were significantly reduced following neuronal depolarization. We identified several other proteins that reduced their co-association in an activity-dependent manner, likely mediated by Shank proteins. We conclude that Homer1 dissociates from mGlu5 and Shank3 following depolarization, but our data suggest that direct Homer1 interactions in the cortex may be more limited than expected.
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Affiliation(s)
- Mason Stillman
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Dartmouth-Hitchcock Medical Center Psychiatry Residency Program, Dartmouth, NH, USA
| | - Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, 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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10
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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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11
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Negraes PD, Trujillo CA, Yu NK, Wu W, Yao H, Liang N, Lautz JD, Kwok E, McClatchy D, Diedrich J, de Bartolome SM, Truong J, Szeto R, Tran T, Herai RH, Smith SEP, Haddad GG, Yates JR, Muotri AR. Altered network and rescue of human neurons derived from individuals with early-onset genetic epilepsy. Mol Psychiatry 2021; 26:7047-7068. [PMID: 33888873 PMCID: PMC8531162 DOI: 10.1038/s41380-021-01104-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 02/02/2023]
Abstract
Early-onset epileptic encephalopathies are severe disorders often associated with specific genetic mutations. In this context, the CDKL5 deficiency disorder (CDD) is a neurodevelopmental condition characterized by early-onset seizures, intellectual delay, and motor dysfunction. Although crucial for proper brain development, the precise targets of CDKL5 and its relation to patients' symptoms are still unknown. Here, induced pluripotent stem cells derived from individuals deficient in CDKL5 protein were used to generate neural cells. Proteomic and phosphoproteomic approaches revealed disruption of several pathways, including microtubule-based processes and cytoskeleton organization. While CDD-derived neural progenitor cells have proliferation defects, neurons showed morphological alterations and compromised glutamatergic synaptogenesis. Moreover, the electrical activity of CDD cortical neurons revealed hyperexcitability during development, leading to an overly synchronized network. Many parameters of this hyperactive network were rescued by lead compounds selected from a human high-throughput drug screening platform. Our results enlighten cellular, molecular, and neural network mechanisms of genetic epilepsy that could ultimately promote novel therapeutic opportunities for patients.
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Affiliation(s)
- Priscilla D Negraes
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Cleber A Trujillo
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
| | - Nam-Kyung Yu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wei Wu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Hang Yao
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Nicholas Liang
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
| | - Ellius Kwok
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McClatchy
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene Diedrich
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Justin Truong
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ryan Szeto
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Timothy Tran
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Roberto H Herai
- Experimental Multiuser Laboratory, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
| | - Gabriel G Haddad
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alysson R Muotri
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Kavli Institute for Brain and Mind, University of California San Diego, La Jolla, CA, USA.
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA, USA.
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12
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Heavner WE, Lautz JD, Speed HE, Gniffke EP, Immendorf KB, Welsh JP, Baertsch NA, Smith SEP. Remodeling of the Homer-Shank interactome mediates homeostatic plasticity. Sci Signal 2021; 14:14/681/eabd7325. [PMID: 33947797 DOI: 10.1126/scisignal.abd7325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurons maintain stable levels of excitability using homeostatic synaptic scaling, which adjusts the strength of a neuron's postsynaptic inputs to compensate for extended changes in overall activity. Here, we investigated whether prolonged changes in activity affect network-level protein interactions at the synapse. We assessed a glutamatergic synapse protein interaction network (PIN) composed of 380 binary associations among 21 protein members in mouse neurons. Manipulating the activation of cultured mouse cortical neurons induced widespread bidirectional PIN alterations that reflected rapid rearrangements of glutamate receptor associations involving synaptic scaffold remodeling. Sensory deprivation of the barrel cortex in live mice (by whisker trimming) caused specific PIN rearrangements, including changes in the association between the glutamate receptor mGluR5 and the kinase Fyn. These observations are consistent with emerging models of experience-dependent plasticity involving multiple types of homeostatic responses. However, mice lacking Homer1 or Shank3B did not undergo normal PIN rearrangements, suggesting that the proteins encoded by these autism spectrum disorder-linked genes serve as structural hubs for synaptic homeostasis. Our approach demonstrates how changes in the protein content of synapses during homeostatic plasticity translate into functional PIN alterations that mediate changes in neuron excitability.
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Affiliation(s)
- Whitney E Heavner
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Haley E Speed
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Edward P Gniffke
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karen B Immendorf
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - John P Welsh
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA.,University of Washington Autism Center, Seattle, WA 98195, USA.,Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195, USA
| | - Nathan A Baertsch
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA. .,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA.,Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195, USA
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13
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Trujillo CA, Rice ES, Schaefer NK, Chaim IA, Wheeler EC, Madrigal AA, Buchanan J, Preissl S, Wang A, Negraes PD, Szeto RA, Herai RH, Huseynov A, Ferraz MSA, Borges FS, Kihara AH, Byrne A, Marin M, Vollmers C, Brooks AN, Lautz JD, Semendeferi K, Shapiro B, Yeo GW, Smith SEP, Green RE, Muotri AR. Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment. Science 2021; 371:371/6530/eaax2537. [PMID: 33574182 DOI: 10.1126/science.aax2537] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 08/27/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1 Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.
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Affiliation(s)
- Cleber A Trujillo
- Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA
| | - Edward S Rice
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nathan K Schaefer
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Isaac A Chaim
- Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily C Wheeler
- Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Assael A Madrigal
- Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin Buchanan
- Department of Cellular & Molecular Medicine, Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sebastian Preissl
- Department of Cellular & Molecular Medicine, Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Allen Wang
- Department of Cellular & Molecular Medicine, Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Priscilla D Negraes
- Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ryan A Szeto
- Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA
| | - Roberto H Herai
- Experimental Multiuser Laboratory (LEM), Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR 80215-901, Brazil
| | - Alik Huseynov
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Mariana S A Ferraz
- Laboratório de Neurogenética, Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-070, Brazil
| | - Fernando S Borges
- Laboratório de Neurogenética, Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-070, Brazil
| | - Alexandre H Kihara
- Laboratório de Neurogenética, Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP 09606-070, Brazil
| | - Ashley Byrne
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Maximillian Marin
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jonathan D Lautz
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Pediatrics and Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195, USA
| | - Katerina Semendeferi
- Department of Anthropology, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gene W Yeo
- Department of Cellular & Molecular Medicine, Center for Epigenomics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.,Department of Pediatrics and Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alysson R Muotri
- Department of Pediatrics and Department of Cellular & Molecular Medicine, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92037, USA.
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14
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Sahasrabudhe A, Begum F, Guevara CA, Morrison C, Hsiao K, Kezunovic N, Bozdagi-Gunal O, Benson DL. Cyfip1 Regulates SynGAP1 at Hippocampal Synapses. Front Synaptic Neurosci 2021; 12:581714. [PMID: 33613257 PMCID: PMC7892963 DOI: 10.3389/fnsyn.2020.581714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
In humans, copy number variations in CYFIP1 appear to have sweeping physiological and structural consequences in the brain, either producing or altering the severity of intellectual disability, autism, and schizophrenia. Independently, SynGAP1 haploinsufficiency produces intellectual disability and, frequently, autism. Cyfip1 inhibits protein translation and promotes actin polymerization, and SynGAP1 is a synaptically localized Ras/Rap GAP. While these proteins are clearly distinct, studies investigating their functions in mice have shown that each regulates the maturation of synapses in the hippocampus and haploinsufficiency for either produces an exaggerated form of mGluR-dependent long-term depression, suggesting that some signaling pathways converge. In this study, we examined how Cyfip1 haploinsufficiency impacts SynGAP1 levels and localization, as well as potential sites for mechanistic interaction in mouse hippocampus. The data show that synaptic, but not total, levels of SynGAP1 in Cyfip1 +/- mice were abnormally low during early postnatal development and in adults. This may be in response to a shift in the balance of kinases that activate SynGAP1 as levels of Cdk5 were reduced and those of activated CaMKII were maintained in Cyfip1 +/- mice compared to wild-type mice. Alternatively, this could reflect altered actin dynamics as Rac1 activity in Cyfip1 +/- hippocampus was boosted significantly compared to wild-type mice, and levels of synaptic F-actin were generally enhanced due in part to an increase in the activity of the WAVE regulatory complex. Decreased synaptic SynGAP1 coupled with a CaMKII-mediated bias toward Rap1 inactivation at synapses is also consistent with increased levels of synaptic GluA2, increased AMPA receptor-mediated responses to stimulation, and increased levels of synaptic mGluR1/5 compared to wild-type mice. Collectively, our data suggest that Cyfip1 regulates SynGAP1 and the two proteins work coordinately at synapses to appropriately direct actin polymerization and GAP activity.
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Affiliation(s)
- Abhishek Sahasrabudhe
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, United States
| | - Fatema Begum
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, United States
| | - Christopher A Guevara
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, United States.,Graduate School of Biomedical Sciences, New York, NY, United States
| | - Chenel Morrison
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, United States
| | - Kuangfu Hsiao
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, United States
| | - Nebojsa Kezunovic
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, United States
| | - Ozlem Bozdagi-Gunal
- Department of Psychiatry, Rutgers New Jersey Medical School, Newark, NJ, United States
| | - Deanna L Benson
- Icahn School of Medicine at Mount Sinai, Nash Family Department of Neuroscience, Friedman Brain Institute, New York, NY, United States
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15
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Twenty Years of SynGAP Research: From Synapses to Cognition. J Neurosci 2020; 40:1596-1605. [PMID: 32075947 DOI: 10.1523/jneurosci.0420-19.2020] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
SynGAP is a potent regulator of biochemical signaling in neurons and plays critical roles in neuronal function. It was first identified in 1998, and has since been extensively characterized as a mediator of synaptic plasticity. Because of its involvement in synaptic plasticity, SynGAP has emerged as a critical protein for normal cognitive function. In recent years, mutations in the SYNGAP1 gene have been shown to cause intellectual disability in humans and have been linked to other neurodevelopmental disorders, such as autism spectrum disorders and schizophrenia. While the structure and biochemical function of SynGAP have been well characterized, a unified understanding of the various roles of SynGAP at the synapse and its contributions to neuronal function remains to be achieved. In this review, we summarize and discuss the current understanding of the multifactorial role of SynGAP in regulating neuronal function gathered over the last two decades.
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16
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Araki Y, Hong I, Gamache TR, Ju S, Collado-Torres L, Shin JH, Huganir RL. SynGAP isoforms differentially regulate synaptic plasticity and dendritic development. eLife 2020; 9:56273. [PMID: 32579114 PMCID: PMC7314543 DOI: 10.7554/elife.56273] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/07/2020] [Indexed: 11/14/2022] Open
Abstract
SynGAP is a synaptic Ras GTPase-activating protein (GAP) with four C-terminal splice variants: α1, α2, β, and γ. Although studies have implicated SYNGAP1 in several cognitive disorders, it is not clear which SynGAP isoforms contribute to disease. Here, we demonstrate that SynGAP isoforms exhibit unique spatiotemporal expression patterns and play distinct roles in neuronal and synaptic development in mouse neurons. SynGAP-α1, which undergoes liquid-liquid phase separation with PSD-95, is highly enriched in synapses and is required for LTP. In contrast, SynGAP-β, which does not bind PSD-95 PDZ domains, is less synaptically targeted and promotes dendritic arborization. A mutation in SynGAP-α1 that disrupts phase separation and synaptic targeting abolishes its ability to regulate plasticity and instead causes it to drive dendritic development like SynGAP-β. These results demonstrate that distinct intrinsic biochemical properties of SynGAP isoforms determine their function, and individual isoforms may differentially contribute to the pathogenesis of SYNGAP1-related cognitive disorders.
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Affiliation(s)
- Yoichi Araki
- Johns Hopkins University School of Medicine, Department of Neuroscience, Kavli Neuroscience Discovery Institute, Baltimore, United States
| | - Ingie Hong
- Johns Hopkins University School of Medicine, Department of Neuroscience, Kavli Neuroscience Discovery Institute, Baltimore, United States
| | - Timothy R Gamache
- Johns Hopkins University School of Medicine, Department of Neuroscience, Kavli Neuroscience Discovery Institute, Baltimore, United States
| | - Shaowen Ju
- Johns Hopkins University School of Medicine, Department of Neuroscience, Kavli Neuroscience Discovery Institute, Baltimore, United States
| | | | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, United States
| | - Richard L Huganir
- Johns Hopkins University School of Medicine, Department of Neuroscience, Kavli Neuroscience Discovery Institute, Baltimore, United States
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17
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Heavner WE, Smith SEP. Resolving the Synaptic versus Developmental Dichotomy of Autism Risk Genes. Trends Neurosci 2020; 43:227-241. [PMID: 32209454 DOI: 10.1016/j.tins.2020.01.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/21/2020] [Accepted: 01/30/2020] [Indexed: 12/28/2022]
Abstract
Genes that are mutated in Autism Spectrum Disorders (ASD) can be classified broadly as either synaptic or developmental. But what if this is a false distinction? A recent spate of publications has provided evidence for developmental mechanisms that rely on neural activity for proper cortical development. Conversely, a growing body of evidence indicates a role for developmental mechanisms, particularly chromatin remodeling, during learning or in response to neural activity. Here, we review these recent publications and propose a model in which genes that confer ASD risk operate in signal transduction networks critical for both cortical development and synaptic homeostasis.
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Affiliation(s)
- Whitney E Heavner
- Center for Integrative Brain Research, Seattle Children's Research Institute, 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 School of Medicine, Seattle, WA, USA; Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA.
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18
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Brown EA, Neier SC, Neuhauser C, Schrum AG, Smith SEP. Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation. J Vis Exp 2019. [PMID: 31498315 DOI: 10.3791/60029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Dynamic protein-protein interactions control cellular behavior, from motility to DNA replication to signal transduction. However, monitoring dynamic interactions among multiple proteins in a protein interaction network is technically difficult. Here, we present a protocol for Quantitative Multiplex Immunoprecipitation (QMI), which allows quantitative assessment of fold changes in protein interactions based on relative fluorescence measurements of Proteins in Shared Complexes detected by Exposed Surface epitopes (PiSCES). In QMI, protein complexes from cell lysates are immunoprecipitated onto microspheres, and then probed with a labeled antibody for a different protein in order to quantify the abundance of PiSCES. Immunoprecipitation antibodies are conjugated to different MagBead spectral regions, which allows a flow cytometer to differentiate multiple parallel immunoprecipitations and simultaneously quantify the amount of probe antibody associated with each. QMI does not require genetic tagging and can be performed using minimal biomaterial compared to other immunoprecipitation methods. QMI can be adapted for any defined group of interacting proteins, and has thus far been used to characterize signaling networks in T cells and neuronal glutamate synapses. Results have led to new hypothesis generation with potential diagnostic and therapeutic applications. This protocol includes instructions to perform QMI, from the initial antibody panel selection through to running assays and analyzing data. The initial assembly of a QMI assay involves screening antibodies to generate a panel, and empirically determining an appropriate lysis buffer. The subsequent reagent preparation includes covalently coupling immunoprecipitation antibodies to MagBeads, and biotinylating probe antibodies so they can be labeled by a streptavidin-conjugated fluorophore. To run the assay, lysate is mixed with MagBeads overnight, and then beads are divided and incubated with different probe antibodies, and then a fluorophore label, and read by flow cytometry. Two statistical tests are performed to identify PiSCES that differ significantly between experimental conditions, and results are visualized using heatmaps or node-edge diagrams.
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Affiliation(s)
- Emily A Brown
- Center for Integrative Brain Research, Seattle Children's Research Institute; Graduate Program in Neuroscience, University of Washington
| | - Steven C Neier
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School; Broad Institute of Harvard and MIT
| | | | - Adam G Schrum
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri; Department of Surgery, School of Medicine, University of Missouri; Department Bioengineering, College of Engineering, University of Missouri
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute; Graduate Program in Neuroscience, University of Washington; Department of Pediatrics, University of Washington;
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19
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Campbell BFN, Tyagarajan SK. Cellular Mechanisms Contributing to the Functional Heterogeneity of GABAergic Synapses. Front Mol Neurosci 2019; 12:187. [PMID: 31456660 PMCID: PMC6700328 DOI: 10.3389/fnmol.2019.00187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/19/2019] [Indexed: 11/24/2022] Open
Abstract
GABAergic inhibitory neurotransmission contributes to diverse aspects of brain development and adult plasticity, including the expression of complex cognitive processes. This is afforded for in part by the dynamic adaptations occurring at inhibitory synapses, which show great heterogeneity both in terms of upstream signaling and downstream effector mechanisms. Single-particle tracking and live imaging have revealed that complex receptor-scaffold interactions critically determine adaptations at GABAergic synapses. Super-resolution imaging studies have shown that protein interactions at synaptic sites contribute to nano-scale scaffold re-arrangements through post-translational modifications (PTMs), facilitating receptor and scaffold recruitment to synaptic sites. Additionally, plasticity mechanisms may be affected by the protein composition at individual synapses and the type of pre-synaptic input. This mini-review article examines recent discoveries of plasticity mechanisms that are operational within GABAergic synapses and discusses their contribution towards functional heterogeneity in inhibitory neurotransmission.
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Affiliation(s)
| | - Shiva K Tyagarajan
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
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20
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Lautz JD, Gniffke EP, Brown EA, Immendorf KB, Mendel RD, Smith SEP. Activity-dependent changes in synaptic protein complex composition are consistent in different detergents despite differential solubility. Sci Rep 2019; 9:10890. [PMID: 31350430 PMCID: PMC6659712 DOI: 10.1038/s41598-019-46690-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/03/2019] [Indexed: 12/02/2022] Open
Abstract
At the post-synaptic density (PSD), large protein complexes dynamically form and dissociate in response to synaptic activity, comprising the biophysical basis for learning and memory. The use of detergents to isolate the PSD and release its membrane-associated proteins complicates studies of these activity-dependent protein interaction networks, because detergents can simultaneously disrupt the very interactions under study. Despite widespread recognition that different detergents yield different experimental results, the effect of detergent on activity-dependent synaptic protein complexes has not been rigorously examined. Here, we characterize the effect of three detergents commonly used to study synaptic proteins on activity-dependent protein interactions. We first demonstrate that SynGAP-containing interactions are more abundant in 1% Deoxycholate (DOC), while Shank-, Homer- and mGluR5-containing interactions are more abundant in 1% NP-40 or Triton. All interactions were detected preferentially in high molecular weight complexes generated by size exclusion chromatography, although the detergent-specific abundance of proteins in high molecular weight fractions did not correlate with the abundance of detected interactions. Activity-dependent changes in protein complexes were consistent across detergent types, suggesting that detergents do not isolate distinct protein pools with unique behaviors. However, detection of activity-dependent changes is more or less feasible in different detergents due to baseline solubility. Collectively, our results demonstrate that detergents affect the solubility of individual proteins, but activity-dependent changes in protein interactions, when detectable, are consistent across detergent types.
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Affiliation(s)
- Jonathan D Lautz
- 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
| | - Emily A Brown
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
| | - Karen B Immendorf
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ryan D Mendel
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA. .,Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA. .,Department of Pediatrics, University of Washington, Seattle, WA, USA.
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21
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Rademacher N, Kuropka B, Kunde SA, Wahl MC, Freund C, Shoichet SA. Intramolecular domain dynamics regulate synaptic MAGUK protein interactions. eLife 2019; 8:41299. [PMID: 30864948 PMCID: PMC6438691 DOI: 10.7554/elife.41299] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 03/12/2019] [Indexed: 12/25/2022] Open
Abstract
PSD-95 MAGUK family scaffold proteins are multi-domain organisers of synaptic transmission that contain three PDZ domains followed by an SH3-GK domain tandem. This domain architecture allows coordinated assembly of protein complexes composed of neurotransmitter receptors, synaptic adhesion molecules and downstream signalling effectors. Here we show that binding of monomeric CRIPT-derived PDZ3 ligands to the third PDZ domain of PSD-95 induces functional changes in the intramolecular SH3-GK domain assembly that influence subsequent homotypic and heterotypic complex formation. We identify PSD-95 interactors that differentially bind to the SH3-GK domain tandem depending on its conformational state. Among these interactors, we further establish the heterotrimeric G protein subunit Gnb5 as a PSD-95 complex partner at dendritic spines of rat hippocampal neurons. The PSD-95 GK domain binds to Gnb5, and this interaction is triggered by CRIPT-derived PDZ3 ligands binding to the third PDZ domain of PSD-95, unraveling a hierarchical binding mechanism of PSD-95 complex formation.
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Affiliation(s)
- Nils Rademacher
- Neuroscience Research Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Stella-Amrei Kunde
- Neuroscience Research Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Markus C Wahl
- Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Freie Universität Berlin, Berlin, Germany.,Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | - Christian Freund
- Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Sarah A Shoichet
- Neuroscience Research Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
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22
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Brown EA, Lautz JD, Davis TR, Gniffke EP, VanSchoiack AAW, Neier SC, Tashbook N, Nicolini C, Fahnestock M, Schrum AG, Smith SEP. Clustering the autisms using glutamate synapse protein interaction networks from cortical and hippocampal tissue of seven mouse models. Mol Autism 2018; 9:48. [PMID: 30237867 PMCID: PMC6139139 DOI: 10.1186/s13229-018-0229-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/20/2018] [Indexed: 12/22/2022] Open
Abstract
Background Autism spectrum disorders (ASDs) are a heterogeneous group of behaviorally defined disorders and are associated with hundreds of rare genetic mutations and several environmental risk factors. Mouse models of specific risk factors have been successful in identifying molecular mechanisms associated with a given factor. However, comparisons among different models to elucidate underlying common pathways or to define clusters of biologically relevant disease subtypes have been complicated by different methodological approaches or different brain regions examined by the labs that developed each model. Here, we use a novel proteomic technique, quantitative multiplex co-immunoprecipitation or QMI, to make a series of identical measurements of a synaptic protein interaction network in seven different animal models. We aim to identify molecular disruptions that are common to multiple models. Methods QMI was performed on 92 hippocampal and cortical samples taken from seven mouse models of ASD: Shank3B, Shank3Δex4-9, Ube3a2xTG, TSC2, FMR1, and CNTNAP2 mutants, as well as E12.5 VPA (maternal valproic acid injection on day 12.5 post-conception). The QMI panel targeted a network of 16 interacting, ASD-linked, synaptic proteins, probing 240 potential co-associations. A custom non-parametric statistical test was used to call significant differences between ASD models and littermate controls, and Hierarchical Clustering by Principal Components was used to cluster the models using mean log2 fold change values. Results Each model displayed a unique set of disrupted interactions, but some interactions were disrupted in multiple models. These tended to be interactions that are known to change with synaptic activity. Clustering revealed potential relationships among models and suggested deficits in AKT signaling in Ube3a2xTG mice, which were confirmed by phospho-western blots. Conclusions These data highlight the great heterogeneity among models, but suggest that high-dimensional measures of a synaptic protein network may allow differentiation of subtypes of ASD with shared molecular pathology.
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Affiliation(s)
- Emily A Brown
- 1Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA USA
| | - Jonathan D Lautz
- 1Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA USA
| | - Tessa R Davis
- 2Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN USA.,3Present address: Department of Biomedical Engineering, UT Austin, Austin, TX USA
| | - Edward P Gniffke
- 1Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA USA
| | - Alison A W VanSchoiack
- 1Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA USA.,Present address: Nanostring, Seattle, WA USA
| | - Steven C Neier
- 2Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN USA.,5Present address: Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA.,6Present address: Department of Medicine, Harvard Medical School, Boston, MA USA.,7Present address: Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Noah Tashbook
- 1Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA USA
| | - Chiara Nicolini
- 8Department of Psychiatry & Behavioural Neurosciences, McMaster University, Hamilton, ON Canada
| | - Margaret Fahnestock
- 8Department of Psychiatry & Behavioural Neurosciences, McMaster University, Hamilton, ON Canada
| | - Adam G Schrum
- 9Departments of Molecular Microbiology & Immunology, Surgery and Bioengineering, University of Missouri, Columbia, MO USA
| | - Stephen E P Smith
- 1Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA USA.,10Department of Pediatrics and Graduate Program in Neuroscience, University of Washington, Seattle, WA USA
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Schweitzer B, Schulz JB. Open Science Badges in the Journal of Neurochemistry. J Neurochem 2018; 147:132-136. [PMID: 30069885 DOI: 10.1111/jnc.14536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 01/07/2023]
Abstract
The Open Science Framework (OSF) has the mission to increase openness, integrity, and reproducibility in research. The Journal of Neurochemistry became a signatory of their Transparency and Openness guidelines in 2016, which provides eight modular standards (Citation standards, Data Transparency, Analytic Methods/Code Transparency, Research Materials Transparency, Design and Analysis Transparency, Study Pre-registration, Analysis Plan Transparency, Replication) with increasing levels of stringency. Furthermore, OSF recommends and offers a collection of practices intended to make scientific processes and results more transparent and available in a standardized way for reuse to people outside the research team. It includes making research materials, data, and laboratory procedures freely accessible online to anyone. This editorial announces the decision of the Journal of Neurochemistry to introduce Open Science Badges, maintained by the Open Science Badges Committee and by the Center for Open Science (COS). The Open Science Badges, visual icons placed on publications, certify that an open practice was followed and signal to readers that an author has shared the corresponding research evidence, thus, allowing an independent researcher to understand how to reproduce the procedure.
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Affiliation(s)
- Barbara Schweitzer
- Department of Neurology, University Hospital RWTH Aachen, Aachen, Germany
| | - Jörg B Schulz
- Department of Neurology, University Hospital RWTH Aachen, Aachen, Germany.,Jülich Aachen Research Alliance (JARA), JARA-Institute Molecular Neuroscience and Neuroimaging, FZ Jülich and RWTH Aachen University, Aachen, Germany
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