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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: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Tsegay KB, Adeyemi CM, Gniffke EP, Sather DN, Walker JK, Smith SEP. A Repurposed Drug Screen Identifies Compounds That Inhibit the Binding of the COVID-19 Spike Protein to ACE2. Front Pharmacol 2021; 12:685308. [PMID: 34194331 PMCID: PMC8236845 DOI: 10.3389/fphar.2021.685308] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/19/2021] [Indexed: 12/24/2022] Open
Abstract
Repurposed drugs that block the interaction between the SARS-CoV-2 spike protein and its receptor ACE2 could offer a rapid route to novel COVID-19 treatments or prophylactics. Here, we screened 2,701 compounds from a commercial library of drugs approved by international regulatory agencies for their ability to inhibit the binding of recombinant, trimeric SARS-CoV-2 spike protein to recombinant human ACE2. We identified 56 compounds that inhibited binding in a concentration-dependent manner, measured the IC50 of binding inhibition, and computationally modeled the docking of the best inhibitors to the Spike-ACE2 binding interface. The best candidates were Thiostrepton, Oxytocin, Nilotinib, and Hydroxycamptothecin with IC50's in the 4-9 μM range. These results highlight an effective screening approach to identify compounds capable of disrupting the Spike-ACE2 interaction, as well as identify several potential inhibitors of the Spike-ACE2 interaction.
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Affiliation(s)
- Kaleb B. Tsegay
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Christiana M. Adeyemi
- St. Louis University School of Medicine, Department of Pharmacology and Physiology, St. Louis, MO, United States
| | - Edward P. Gniffke
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - D. Noah Sather
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - John K. Walker
- St. Louis University School of Medicine, Department of Pharmacology and Physiology, St. Louis, MO, United States
- Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University St. Louis, Seattle, WA, United States
| | - Stephen E. P. Smith
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, United States
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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: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Tsegay KB, Adeyemi CM, Gniffke EP, Sather DN, Walker JK, Smith SEP. A repurposed drug screen identifies compounds that inhibit the binding of the COVID-19 spike protein to ACE2. bioRxiv 2021:2021.04.08.439071. [PMID: 33851160 PMCID: PMC8043450 DOI: 10.1101/2021.04.08.439071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Repurposed drugs that block the interaction between the SARS-CoV-2 spike protein and its receptor ACE2 could offer a rapid route to novel COVID-19 treatments or prophylactics. Here, we screened 2701 compounds from a commercial library of drugs approved by international regulatory agencies for their ability to inhibit the binding of recombinant, trimeric SARS-CoV-2 spike protein to recombinant human ACE2. We identified 56 compounds that inhibited binding by <90%, measured the EC 50 of binding inhibition, and computationally modeled the docking of the best inhibitors to both Spike and ACE2. These results highlight an effective screening approach to identify compounds capable of disrupting the Spike-ACE2 interaction as well as identifying several potential inhibitors that could serve as templates for future drug discovery efforts.
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Gniffke EP, Harrington WE, Dambrauskas N, Jiang Y, Trakhimets O, Vigdorovich V, Frenkel L, Sather DN, Smith SEP. Plasma From Recovered COVID-19 Patients Inhibits Spike Protein Binding to ACE2 in a Microsphere-Based Inhibition Assay. J Infect Dis 2020; 222:1965-1973. [PMID: 32798222 PMCID: PMC7454725 DOI: 10.1093/infdis/jiaa508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
We present a microsphere-based flow cytometry assay that quantifies the ability of plasma to inhibit the binding of spike protein to angiotensin-converting enzyme 2. Plasma from 22 patients who had recovered from mild coronavirus disease 2019 (COVID-19) and expressed anti–spike protein trimer immunoglobulin G inhibited angiotensin-converting enzyme 2–spike protein binding to a greater degree than controls. The degree of inhibition was correlated with anti–spike protein immunoglobulin G levels, neutralizing titers in a pseudotyped lentiviral assay, and the presence of fever during illness. This inhibition assay may be broadly useful to quantify the functional antibody response of patients recovered from COVID-19 or vaccine recipients in a cell-free assay system.
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Affiliation(s)
- Edward P Gniffke
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Whitney E Harrington
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Nicholas Dambrauskas
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Yonghou Jiang
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Olesya Trakhimets
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Lisa Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Stephen E P Smith
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Graduate Program in Neuroscience, University of Washington, Seattle, Washington, USA
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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