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Prakash P, Erdjument-Bromage H, O'Dea MR, Munson CN, Labib D, Fossati V, Neubert TA, Liddelow SA. Proteomic profiling of interferon-responsive reactive astrocytes in rodent and human. Glia 2024; 72:625-642. [PMID: 38031883 PMCID: PMC10843807 DOI: 10.1002/glia.24494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023]
Abstract
Astrocytes are a heterogeneous population of central nervous system glial cells that respond to pathological insults and injury by undergoing a transformation called "reactivity." Reactive astrocytes exhibit distinct and context-dependent cellular, molecular, and functional state changes that can either support or disturb tissue homeostasis. We recently identified a reactive astrocyte sub-state defined by interferon-responsive genes like Igtp, Ifit3, Mx1, and others, called interferon-responsive reactive astrocytes (IRRAs). To further this transcriptomic definition of IRRAs, we wanted to define the proteomic changes that occur in this reactive sub-state. We induced IRRAs in immunopanned rodent astrocytes and human iPSC-differentiated astrocytes using TNF, IL1α, C1Q, and IFNβ and characterized their proteomic profile (both cellular and secreted) using unbiased quantitative proteomics. We identified 2335 unique cellular proteins, including IFIT2/3, IFITM3, OASL1/2, MX1/2/3, and STAT1. We also report that rodent and human IRRAs secrete PAI1, a serine protease inhibitor which may influence reactive states and functions of nearby cells. Finally, we evaluated how IRRAs are distinct from neurotoxic reactive astrocytes (NRAs). While NRAs are described by expression of the complement protein C3, it was not upregulated in IRRAs. Instead, we found ~90 proteins unique to IRRAs not identified in NRAs, including OAS1A, IFIT3, and MX1. Interferon signaling in astrocytes is critical for the antiviral immune response and for regulating synaptic plasticity and glutamate transport mechanisms. How IRRAs contribute to these functions is unknown. This study provides the basis for future experiments to define the functional roles of IRRAs in the context of neurodegenerative disorders.
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Affiliation(s)
- Priya Prakash
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
| | - Hediye Erdjument-Bromage
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Michael R O'Dea
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
| | - Christy N Munson
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
| | - David Labib
- The New York Stem Cell Foundation Research Institute, New York, New York, USA
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, New York, USA
| | - Thomas A Neubert
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, New York, USA
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, New York, USA
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, New York, USA
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, New York, USA
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Ren M, Xu Y, Phoon CKL, Erdjument-Bromage H, Neubert TA, Schlame M. Cardiolipin prolongs the lifetimes of respiratory proteins in Drosophila flight muscle. J Biol Chem 2023; 299:105241. [PMID: 37690688 PMCID: PMC10622840 DOI: 10.1016/j.jbc.2023.105241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023] Open
Abstract
Respiratory complexes and cardiolipins have exceptionally long lifetimes. The fact that they co-localize in mitochondrial cristae raises the question of whether their longevities have a common cause and whether the longevity of OXPHOS proteins is dependent on cardiolipin. To address these questions, we developed a method to measure side-by-side the half-lives of proteins and lipids in wild-type Drosophila and cardiolipin-deficient mutants. We fed adult flies with stable isotope-labeled precursors (13C615N2-lysine or 13C6-glucose) and determined the relative abundance of heavy isotopomers in protein and lipid species by mass spectrometry. To minimize the confounding effects of tissue regeneration, we restricted our analysis to the thorax, the bulk of which consists of post-mitotic flight muscles. Analysis of 680 protein and 45 lipid species showed that the subunits of respiratory complexes I-V and the carriers for phosphate and ADP/ATP were among the longest-lived proteins (average half-life of 48 ± 16 days) while the molecular species of cardiolipin were the longest-lived lipids (average half-life of 27 ± 6 days). The remarkable longevity of these crista residents was not shared by all mitochondrial proteins, especially not by those residing in the matrix and the inner boundary membrane. Ablation of cardiolipin synthase, which causes replacement of cardiolipin by phosphatidylglycerol, and ablation of tafazzin, which causes partial replacement of cardiolipin by monolyso-cardiolipin, decreased the lifetimes of the respiratory complexes. Ablation of tafazzin also decreased the lifetimes of the remaining cardiolipin species. These data suggest that an important function of cardiolipin in mitochondria is to protect respiratory complexes from degradation.
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Affiliation(s)
- Mindong Ren
- Departments of Anesthesiology, Physiology, New York University Grossman School of Medicine, New York, New York, USA; Departments of Cell Biology, Physiology, New York University Grossman School of Medicine, New York, New York, USA.
| | - Yang Xu
- Departments of Anesthesiology, Physiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Colin K L Phoon
- Departments of Pediatrics, Physiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Hediye Erdjument-Bromage
- Departments of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Thomas A Neubert
- Departments of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Michael Schlame
- Departments of Anesthesiology, Physiology, New York University Grossman School of Medicine, New York, New York, USA; Departments of Cell Biology, Physiology, New York University Grossman School of Medicine, New York, New York, USA.
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3
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Im E, Jiang Y, Stavrides PH, Darji S, Erdjument-Bromage H, Neubert TA, Choi JY, Wegiel J, Lee JH, Nixon RA. Lysosomal dysfunction in Down syndrome and Alzheimer mouse models is caused by v-ATPase inhibition by Tyr 682-phosphorylated APP βCTF. Sci Adv 2023; 9:eadg1925. [PMID: 37494443 PMCID: PMC10371027 DOI: 10.1126/sciadv.adg1925] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
Lysosome dysfunction arises early and propels Alzheimer's disease (AD). Herein, we show that amyloid precursor protein (APP), linked to early-onset AD in Down syndrome (DS), acts directly via its β-C-terminal fragment (βCTF) to disrupt lysosomal vacuolar (H+)-adenosine triphosphatase (v-ATPase) and acidification. In human DS fibroblasts, the phosphorylated 682YENPTY internalization motif of APP-βCTF binds selectively within a pocket of the v-ATPase V0a1 subunit cytoplasmic domain and competitively inhibits association of the V1 subcomplex of v-ATPase, thereby reducing its activity. Lowering APP-βCTF Tyr682 phosphorylation restores v-ATPase and lysosome function in DS fibroblasts and in vivo in brains of DS model mice. Notably, lowering APP-βCTF Tyr682 phosphorylation below normal constitutive levels boosts v-ATPase assembly and activity, suggesting that v-ATPase may also be modulated tonically by phospho-APP-βCTF. Elevated APP-βCTF Tyr682 phosphorylation in two mouse AD models similarly disrupts v-ATPase function. These findings offer previously unknown insight into the pathogenic mechanism underlying faulty lysosomes in all forms of AD.
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Affiliation(s)
- Eunju Im
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Jiang
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Philip H. Stavrides
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Sandipkumar Darji
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Thomas A. Neubert
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Jun Yong Choi
- Department of Chemistry and Biochemistry, Queens College, Queens, NY 11367, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Jerzy Wegiel
- Department of Developmental Neurobiology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY 10314, USA
| | - Ju-Hyun Lee
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ralph A. Nixon
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
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4
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Frenster JD, Erdjument-Bromage H, Stephan G, Ravn-Boess N, Wang S, Liu W, Bready D, Wilcox J, Kieslich B, Jankovic M, Wilde C, Horn S, Sträter N, Liebscher I, Schöneberg T, Fenyo D, Neubert TA, Placantonakis DG. PTK7 is a positive allosteric modulator of GPR133 signaling in glioblastoma. Cell Rep 2023; 42:112679. [PMID: 37354459 PMCID: PMC10445595 DOI: 10.1016/j.celrep.2023.112679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 04/24/2023] [Accepted: 05/23/2023] [Indexed: 06/26/2023] Open
Abstract
The adhesion G-protein-coupled receptor GPR133 (ADGRD1) supports growth of the brain malignancy glioblastoma. How the extracellular interactome of GPR133 in glioblastoma modulates signaling remains unknown. Here, we use affinity proteomics to identify the transmembrane protein PTK7 as an extracellular binding partner of GPR133 in glioblastoma. PTK7 binds the autoproteolytically generated N-terminal fragment of GPR133 and its expression in trans increases GPR133 signaling. This effect requires the intramolecular cleavage of GPR133 and PTK7's anchoring in the plasma membrane. PTK7's allosteric action on GPR133 signaling is additive with but topographically distinct from orthosteric activation by soluble peptide mimicking the endogenous tethered Stachel agonist. GPR133 and PTK7 are expressed in adjacent cells in glioblastoma, where their knockdown phenocopies each other. We propose that this ligand-receptor interaction is relevant to the pathogenesis of glioblastoma and possibly other physiological processes in healthy tissues.
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Affiliation(s)
- Joshua D Frenster
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA; Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Gabriele Stephan
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Niklas Ravn-Boess
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Shuai Wang
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Devin Bready
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jordan Wilcox
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Björn Kieslich
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany; Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Manuel Jankovic
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany
| | - Caroline Wilde
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Susanne Horn
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - David Fenyo
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Thomas A Neubert
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA; Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dimitris G Placantonakis
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Brain and Spine Tumor Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA.
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5
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Rodina A, Xu C, Digwal CS, Joshi S, Patel Y, Santhaseela AR, Bay S, Merugu S, Alam A, Yan P, Yang C, Roychowdhury T, Panchal P, Shrestha L, Kang Y, Sharma S, Almodovar J, Corben A, Alpaugh ML, Modi S, Guzman ML, Fei T, Taldone T, Ginsberg SD, Erdjument-Bromage H, Neubert TA, Manova-Todorova K, Tsou MFB, Young JC, Wang T, Chiosis G. Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation. Nat Commun 2023; 14:3742. [PMID: 37353488 PMCID: PMC10290137 DOI: 10.1038/s41467-023-39241-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 06/05/2023] [Indexed: 06/25/2023] Open
Abstract
Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) cells and tissues are lacking. Herein, we take advantage of chemical binders of maladaptive scaffolding structures termed epichaperomes and develop an epichaperome-based 'omics platform, epichaperomics, to identify PPI alterations in disease. We provide multiple lines of evidence, at both biochemical and functional levels, demonstrating the importance of these probes to identify and study PPI network dysfunctions and provide mechanistically and therapeutically relevant proteome-wide insights. As proof-of-principle, we derive systems-level insight into PPI dysfunctions of cancer cells which enabled the discovery of a context-dependent mechanism by which cancer cells enhance the fitness of mitotic protein networks. Importantly, our systems levels analyses support the use of epichaperome chemical binders as therapeutic strategies aimed at normalizing PPI networks.
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Affiliation(s)
- Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chao Xu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chander S Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yogita Patel
- Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Anand R Santhaseela
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sadik Bay
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Swathi Merugu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Aftab Alam
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Pengrong Yan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chenghua Yang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Tanaya Roychowdhury
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Liza Shrestha
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yanlong Kang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Justina Almodovar
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Adriana Corben
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Maimonides Medical Center, Brooklyn, NY, USA
| | - Mary L Alpaugh
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Rowan University, Glassboro, NJ, USA
| | - Shanu Modi
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Monica L Guzman
- Department of Medicine, Division of Hematology Oncology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Tony Taldone
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Stephen D Ginsberg
- Departments of Psychiatry, Neuroscience & Physiology & the NYU Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, 10962, USA
| | - Hediye Erdjument-Bromage
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Thomas A Neubert
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Katia Manova-Todorova
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Meng-Fu Bryan Tsou
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jason C Young
- Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, QC, H3G 0B1, Canada
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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Carbonell AU, Freire-Cobo C, Deyneko IV, Dobariya S, Erdjument-Bromage H, Clipperton-Allen AE, Page DT, Neubert TA, Jordan BA. Comparing synaptic proteomes across five mouse models for autism reveals converging molecular similarities including deficits in oxidative phosphorylation and Rho GTPase signaling. Front Aging Neurosci 2023; 15:1152562. [PMID: 37255534 PMCID: PMC10225639 DOI: 10.3389/fnagi.2023.1152562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023] Open
Abstract
Specific and effective treatments for autism spectrum disorder (ASD) are lacking due to a poor understanding of disease mechanisms. Here we test the idea that similarities between diverse ASD mouse models are caused by deficits in common molecular pathways at neuronal synapses. To do this, we leverage the availability of multiple genetic models of ASD that exhibit shared synaptic and behavioral deficits and use quantitative mass spectrometry with isobaric tandem mass tagging (TMT) to compare their hippocampal synaptic proteomes. Comparative analyses of mouse models for Fragile X syndrome (Fmr1 knockout), cortical dysplasia focal epilepsy syndrome (Cntnap2 knockout), PTEN hamartoma tumor syndrome (Pten haploinsufficiency), ANKS1B syndrome (Anks1b haploinsufficiency), and idiopathic autism (BTBR+) revealed several common altered cellular and molecular pathways at the synapse, including changes in oxidative phosphorylation, and Rho family small GTPase signaling. Functional validation of one of these aberrant pathways, Rac1 signaling, confirms that the ANKS1B model displays altered Rac1 activity counter to that observed in other models, as predicted by the bioinformatic analyses. Overall similarity analyses reveal clusters of synaptic profiles, which may form the basis for molecular subtypes that explain genetic heterogeneity in ASD despite a common clinical diagnosis. Our results suggest that ASD-linked susceptibility genes ultimately converge on common signaling pathways regulating synaptic function and propose that these points of convergence are key to understanding the pathogenesis of this disorder.
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Affiliation(s)
- Abigail U. Carbonell
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Carmen Freire-Cobo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Ilana V. Deyneko
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Saunil Dobariya
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Hediye Erdjument-Bromage
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Amy E. Clipperton-Allen
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, United States
| | - Damon T. Page
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL, United States
| | - Thomas A. Neubert
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Bryen A. Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, United States
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7
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Ren M, Xu Y, Phoon CKL, Erdjument-Bromage H, Neubert TA, Schlame M. Knockout of cardiolipin synthase disrupts postnatal cardiac development by inhibiting the maturation of mitochondrial cristae. bioRxiv 2023:2023.03.09.531996. [PMID: 36945411 PMCID: PMC10029008 DOI: 10.1101/2023.03.09.531996] [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: 03/12/2023]
Abstract
Background Cardiomyocyte maturation requires a massive increase in respiratory enzymes and their assembly into long-lived complexes of oxidative phosphorylation (OXPHOS). The molecular mechanisms underlying the maturation of cardiac mitochondria have not been established. Methods To determine whether the mitochondria-specific lipid cardiolipin is involved in cardiac maturation, we created a cardiomyocyte-restricted knockout (KO) of cardiolipin synthase ( Crls1 ) in mice and studied the postnatal development of the heart. We also measured the turnover rates of proteins and lipids in cardiolipin-deficient flight muscle from Drosophila, a tissue that has mitochondria with high OXPHOS activity like the heart. Results Crls1KO mice survived the prenatal period but failed to accumulate OXPHOS proteins during postnatal maturation and succumbed to heart failure at the age of 2 weeks. Turnover measurements showed that the exceptionally long half-life of OXPHOS proteins is critically dependent on cardiolipin. Conclusions Cardiolipin is essential for the postnatal maturation of cardiomyocytes because it allows mitochondrial cristae to accumulate OXPHOS proteins to a high concentration and to shield them from degradation.
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8
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Beenken A, Cerutti G, Brasch J, Guo Y, Sheng Z, Erdjument-Bromage H, Aziz Z, Robbins-Juarez SY, Chavez EY, Ahlsen G, Katsamba PS, Neubert TA, Fitzpatrick AWP, Barasch J, Shapiro L. Structures of LRP2 reveal a molecular machine for endocytosis. Cell 2023; 186:821-836.e13. [PMID: 36750096 PMCID: PMC9993842 DOI: 10.1016/j.cell.2023.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/29/2022] [Accepted: 01/10/2023] [Indexed: 02/08/2023]
Abstract
The low-density lipoprotein (LDL) receptor-related protein 2 (LRP2 or megalin) is representative of the phylogenetically conserved subfamily of giant LDL receptor-related proteins, which function in endocytosis and are implicated in diseases of the kidney and brain. Here, we report high-resolution cryoelectron microscopy structures of LRP2 isolated from mouse kidney, at extracellular and endosomal pH. The structures reveal LRP2 to be a molecular machine that adopts a conformation for ligand binding at the cell surface and for ligand shedding in the endosome. LRP2 forms a homodimer, the conformational transformation of which is governed by pH-sensitive sites at both homodimer and intra-protomer interfaces. A subset of LRP2 deleterious missense variants in humans appears to impair homodimer assembly. These observations lay the foundation for further understanding the function and mechanism of LDL receptors and implicate homodimerization as a conserved feature of the LRP receptor subfamily.
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Affiliation(s)
- Andrew Beenken
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Julia Brasch
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Columbia University, New York, NY 10032, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University, New York, NY 10032, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Zainab Aziz
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | | | - Estefania Y Chavez
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Goran Ahlsen
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Thomas A Neubert
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Anthony W P Fitzpatrick
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Jonathan Barasch
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Columbia University George M. O'Brien Urology Center, New York, NY 10032, USA.
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Aaron Diamond AIDS Research Center, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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9
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Zhang G, Deinhardt K, Neubert TA. Stable Isotope Labeling by Amino Acids and Bioorthogonal Noncanonical Amino Acid Tagging in Cultured Primary Neurons. Methods Mol Biol 2023; 2603:163-171. [PMID: 36370278 PMCID: PMC10150910 DOI: 10.1007/978-1-0716-2863-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Cultured primary neurons are a well-established model for the study of neuronal function. Conventional stable isotope labeling with amino acids in cell culture (SILAC) requires nearly complete metabolic labeling of proteins and therefore is difficult to apply to cultured primary neurons, which do not divide in culture. In a multiplex SILAC strategy, two different sets of heavy amino acids are used for labeling cells for the different experimental conditions. This allows for straightforward SILAC quantitation using partially labeled cells because the two cell populations are always equally labeled. When combined with bioorthogonal noncanonical amino acid tagging (BONCAT), it allows for comparative proteomic analysis of de novo protein synthesis. Here we describe protocols that utilize the multiplex SILAC labeling strategy for primary cultured neurons to study steady-state and nascent proteomes.
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Affiliation(s)
- Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Katrin Deinhardt
- Institute for Life Sciences and Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Thomas A Neubert
- Department of Cell Biology and Kimmel Center for Molecular Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA.
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10
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D'Acunzo P, Ungania JM, Kim Y, Barreto BR, DeRosa S, Pawlik M, Canals‐Baker S, Erdjument‐Bromage H, Hashim A, Goulbourne CN, Neubert TA, Saito M, Sershen H, Levy E. Cocaine perturbs mitovesicle biology in the brain. J Extracell Vesicles 2023; 12:e12301. [PMID: 36691887 PMCID: PMC9871795 DOI: 10.1002/jev2.12301] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 08/02/2022] [Revised: 12/06/2022] [Accepted: 12/26/2022] [Indexed: 01/25/2023] Open
Abstract
Cocaine, an addictive psychostimulant, has a broad mechanism of action, including the induction of a wide range of alterations in brain metabolism and mitochondrial homeostasis. Our group recently identified a subpopulation of non-microvesicular, non-exosomal extracellular vesicles of mitochondrial origin (mitovesicles) and developed a method to isolate mitovesicles from brain parenchyma. We hypothesised that the generation and secretion of mitovesicles is affected by mitochondrial abnormalities induced by chronic cocaine exposure. Mitovesicles from the brain extracellular space of cocaine-administered mice were enlarged and more numerous when compared to controls, supporting a model in which mitovesicle biogenesis is enhanced in the presence of mitochondrial alterations. This interrelationship was confirmed in vitro. Moreover, cocaine affected mitovesicle protein composition, causing a functional alteration in mitovesicle ATP production capacity. These data suggest that mitovesicles are previously unidentified players in the biology of cocaine addiction and that target therapies to fine-tune brain mitovesicle functionality may be beneficial to mitigate the effects of chronic cocaine exposure.
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Affiliation(s)
- Pasquale D'Acunzo
- Center for Dementia ResearchNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
- Department of PsychiatryNew York University Grossman School of MedicineNew YorkNew YorkUSA
| | - Jonathan M. Ungania
- Center for Dementia ResearchNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
| | - Yohan Kim
- Center for Dementia ResearchNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
- Department of PsychiatryNew York University Grossman School of MedicineNew YorkNew YorkUSA
| | - Bryana R. Barreto
- Center for Dementia ResearchNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
| | - Steven DeRosa
- Center for Dementia ResearchNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
| | - Monika Pawlik
- Center for Dementia ResearchNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
| | - Stefanie Canals‐Baker
- Division of NeurochemistryNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
| | - Hediye Erdjument‐Bromage
- Department of Cell BiologyNew York University Grossman School of MedicineNew YorkNew YorkUSA
- Kimmel Center for Biology and Medicine at the Skirball InstituteNew York University Grossman School of MedicineNew YorkNew YorkUSA
| | - Audrey Hashim
- Division of NeurochemistryNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
| | - Chris N. Goulbourne
- Center for Dementia ResearchNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
| | - Thomas A. Neubert
- Department of Cell BiologyNew York University Grossman School of MedicineNew YorkNew YorkUSA
- Kimmel Center for Biology and Medicine at the Skirball InstituteNew York University Grossman School of MedicineNew YorkNew YorkUSA
| | - Mariko Saito
- Department of PsychiatryNew York University Grossman School of MedicineNew YorkNew YorkUSA
- Division of NeurochemistryNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
| | - Henry Sershen
- Department of PsychiatryNew York University Grossman School of MedicineNew YorkNew YorkUSA
- Division of NeurochemistryNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
| | - Efrat Levy
- Center for Dementia ResearchNathan S. Kline Institute for Psychiatric ResearchOrangeburgNew YorkUSA
- Department of PsychiatryNew York University Grossman School of MedicineNew YorkNew YorkUSA
- Department of Biochemistry & Molecular PharmacologyNew York University Grossman School of MedicineNew YorkNew YorkUSA
- NYU Neuroscience InstituteNew York University Grossman School of MedicineNew YorkNew YorkUSA
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11
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Ren M, Xu Y, Phoon CKL, Erdjument-Bromage H, Neubert TA, Rajan S, Hussain MM, Schlame M. Condensed Mitochondria Assemble Into the Acrosomal Matrix During Spermiogenesis. Front Cell Dev Biol 2022; 10:867175. [PMID: 35531097 PMCID: PMC9068883 DOI: 10.3389/fcell.2022.867175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
Mammalian spermatogenesis is associated with the transient appearance of condensed mitochondria, a singularity of germ cells with unknown function. Using proteomic analysis, respirometry, and electron microscopy with tomography, we studied the development of condensed mitochondria. Condensed mitochondria arose from orthodox mitochondria during meiosis by progressive contraction of the matrix space, which was accompanied by an initial expansion and a subsequent reduction of the surface area of the inner membrane. Compared to orthodox mitochondria, condensed mitochondria respired more actively, had a higher concentration of respiratory enzymes and supercomplexes, and contained more proteins involved in protein import and expression. After the completion of meiosis, the abundance of condensed mitochondria declined, which coincided with the onset of the biogenesis of acrosomes. Immuno-electron microscopy and the analysis of sub-cellular fractions suggested that condensed mitochondria or their fragments were translocated into the lumen of the acrosome. Thus, it seems condensed mitochondria are formed from orthodox mitochondria by extensive transformations in order to support the formation of the acrosomal matrix.
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Affiliation(s)
- Mindong Ren
- Departments of Anesthesiology, New York, NY, United States
- Department of Cell Biology, New York, NY, United States
| | - Yang Xu
- Departments of Anesthesiology, New York, NY, United States
| | | | - Hediye Erdjument-Bromage
- Department of Cell Biology, New York, NY, United States
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, United States
| | - Thomas A. Neubert
- Department of Cell Biology, New York, NY, United States
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, United States
| | - Sujith Rajan
- Department of Foundations of Medicine, NYU Long Island School of Medicine, Mineola, NY, United States
| | - M. Mahmood Hussain
- Department of Foundations of Medicine, NYU Long Island School of Medicine, Mineola, NY, United States
| | - Michael Schlame
- Departments of Anesthesiology, New York, NY, United States
- Department of Cell Biology, New York, NY, United States
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12
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Joshi S, Gomes ED, Wang T, Corben A, Taldone T, Gandu S, Xu C, Sharma S, Buddaseth S, Yan P, Chan LYL, Gokce A, Rajasekhar VK, Shrestha L, Panchal P, Almodovar J, Digwal CS, Rodina A, Merugu S, Pillarsetty N, Miclea V, Peter RI, Wang W, Ginsberg SD, Tang L, Mattar M, de Stanchina E, Yu KH, Lowery M, Grbovic-Huezo O, O’Reilly EM, Janjigian Y, Healey JH, Jarnagin WR, Allen PJ, Sander C, Erdjument-Bromage H, Neubert TA, Leach SD, Chiosis G. Pharmacologically controlling protein-protein interactions through epichaperomes for therapeutic vulnerability in cancer. Commun Biol 2021; 4:1333. [PMID: 34824367 PMCID: PMC8617294 DOI: 10.1038/s42003-021-02842-3] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 11/03/2021] [Indexed: 12/03/2022] Open
Abstract
Cancer cell plasticity due to the dynamic architecture of interactome networks provides a vexing outlet for therapy evasion. Here, through chemical biology approaches for systems level exploration of protein connectivity changes applied to pancreatic cancer cell lines, patient biospecimens, and cell- and patient-derived xenografts in mice, we demonstrate interactomes can be re-engineered for vulnerability. By manipulating epichaperomes pharmacologically, we control and anticipate how thousands of proteins interact in real-time within tumours. Further, we can essentially force tumours into interactome hyperconnectivity and maximal protein-protein interaction capacity, a state whereby no rebound pathways can be deployed and where alternative signalling is supressed. This approach therefore primes interactomes to enhance vulnerability and improve treatment efficacy, enabling therapeutics with traditionally poor performance to become highly efficacious. These findings provide proof-of-principle for a paradigm to overcome drug resistance through pharmacologic manipulation of proteome-wide protein-protein interaction networks.
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Affiliation(s)
- Suhasini Joshi
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Erica DaGama Gomes
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Tai Wang
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Adriana Corben
- grid.51462.340000 0001 2171 9952Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Tony Taldone
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Srinivasa Gandu
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Chao Xu
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Sahil Sharma
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Salma Buddaseth
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Pengrong Yan
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Lon Yin L. Chan
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Askan Gokce
- grid.51462.340000 0001 2171 9952Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Vinagolu K. Rajasekhar
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Lisa Shrestha
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Palak Panchal
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Justina Almodovar
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Chander S. Digwal
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Anna Rodina
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Swathi Merugu
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - NagaVaraKishore Pillarsetty
- grid.51462.340000 0001 2171 9952Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Vlad Miclea
- grid.6827.b0000000122901764Faculty of Automation and Computer Science, Technical University of Cluj-Napoca, Cluj-Napoca, CJ 400114 Romania
| | - Radu I. Peter
- grid.6827.b0000000122901764Faculty of Automation and Computer Science, Technical University of Cluj-Napoca, Cluj-Napoca, CJ 400114 Romania
| | - Wanyan Wang
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Stephen D. Ginsberg
- grid.250263.00000 0001 2189 4777Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962 USA ,grid.240324.30000 0001 2109 4251Departments of Psychiatry, Neuroscience & Physiology, and the NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016 USA
| | - Laura Tang
- grid.51462.340000 0001 2171 9952Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Marissa Mattar
- grid.51462.340000 0001 2171 9952Antitumour Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Elisa de Stanchina
- grid.51462.340000 0001 2171 9952Antitumour Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA ,grid.51462.340000 0001 2171 9952Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Kenneth H. Yu
- grid.51462.340000 0001 2171 9952David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Maeve Lowery
- grid.51462.340000 0001 2171 9952David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Olivera Grbovic-Huezo
- grid.51462.340000 0001 2171 9952David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Eileen M. O’Reilly
- grid.51462.340000 0001 2171 9952David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Yelena Janjigian
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY 10065 USA
| | - John H. Healey
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - William R. Jarnagin
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Peter J. Allen
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA ,grid.26009.3d0000 0004 1936 7961Department of Surgery, Duke University School of Medicine, Durham, NC 27710 USA
| | - Chris Sander
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Cell Biology, Harvard Medical School, Boston, MA 02115 USA
| | - Hediye Erdjument-Bromage
- grid.240324.30000 0001 2109 4251Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016 USA ,grid.137628.90000 0004 1936 8753Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY 10016 USA
| | - Thomas A. Neubert
- grid.240324.30000 0001 2109 4251Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016 USA ,grid.137628.90000 0004 1936 8753Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY 10016 USA
| | - Steven D. Leach
- grid.51462.340000 0001 2171 9952David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA ,grid.254880.30000 0001 2179 2404Dartmouth Geisel School of Medicine and Norris Cotton Cancer Center, Lebanon, NH 03766 USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. .,Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, 10065, USA.
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13
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Hanamura K, Washburn HR, Sheffler-Collins SI, Xia NL, Henderson N, Tillu DV, Hassler S, Spellman DS, Zhang G, Neubert TA, Price TJ, Dalva MB. Correction: Extracellular phosphorylation of a receptor tyrosine kinase controls synaptic localization of NMDA receptors and regulates pathological pain. PLoS Biol 2021; 19:e3001452. [PMID: 34752444 PMCID: PMC8577777 DOI: 10.1371/journal.pbio.3001452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Xu Y, Erdjument-Bromage H, Phoon CKL, Neubert TA, Ren M, Schlame M. Cardiolipin remodeling enables protein crowding in the inner mitochondrial membrane. EMBO J 2021; 40:e108428. [PMID: 34661298 DOI: 10.15252/embj.2021108428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial cristae are extraordinarily crowded with proteins, which puts stress on the bilayer organization of lipids. We tested the hypothesis that the high concentration of proteins drives the tafazzin-catalyzed remodeling of fatty acids in cardiolipin, thereby reducing bilayer stress in the membrane. Specifically, we tested whether protein crowding induces cardiolipin remodeling and whether the lack of cardiolipin remodeling prevents the membrane from accumulating proteins. In vitro, the incorporation of large amounts of proteins into liposomes altered the outcome of the remodeling reaction. In yeast, the concentration of proteins involved in oxidative phosphorylation (OXPHOS) correlated with the cardiolipin composition. Genetic ablation of either remodeling or biosynthesis of cardiolipin caused a substantial drop in the surface density of OXPHOS proteins in the inner membrane of the mouse heart and Drosophila flight muscle mitochondria. Our data suggest that OXPHOS protein crowding induces cardiolipin remodelling and that remodeled cardiolipin supports the high concentration of these proteins in the inner mitochondrial membrane.
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Affiliation(s)
- Yang Xu
- Department of Anesthesiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Hediye Erdjument-Bromage
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
| | - Colin K L Phoon
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
| | - Mindong Ren
- Department of Anesthesiology, New York University Grossman School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
| | - Michael Schlame
- Department of Anesthesiology, New York University Grossman School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
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15
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Wang J, Anastasia A, Bains H, Giza JI, Clossey DG, Deng J, Neubert TA, Rice WJ, Lee FS, Hempstead BL, Bracken C. Zinc induced structural changes in the intrinsically disordered BDNF Met prodomain confer synaptic elimination. Metallomics 2021; 12:1208-1219. [PMID: 32744273 DOI: 10.1039/d0mt00108b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human brain derived neurotrophic factor (BDNF) encodes a protein product consisting of a C-terminal mature domain (mature BDNF) and an N-terminal prodomain, which is an intrinsically disordered protein. A common single nucleotide polymorphism in humans results in a methionine substitution for valine at position 66 of the prodomain, and is associated with memory deficits, depression and anxiety disorders. The BDNF Met66 prodomain, but not the Val66 prodomain, promotes rapid structural remodeling of hippocampal neurons' growth cones and dendritic spines by interacting directly with the SorCS2 receptor. While it has been reported that the Met66 and Val66 prodomains exhibit only modest differences in structural propensities in the apo state, here we show that Val66 and Met66 prodomains differentially bind zinc (Zn). Zn2+ binds with higher affinity and more broadly impacts residues on the Met66 prodomain compared to the Val66 prodomain as shown by NMR and ITC. Zn2+ binding to the Met66 and Val66 prodomains results in distinct conformational and macroscopic differences observed by NMR, light scattering and cryoEM. To determine if Zn2+ mediated conformational change in the Met66 prodomain is required for biological effect, we mutated His40, a Zn2+ binding site, and observed a loss of Met66 prodomain bioactivity. As the His40 site is distant from the known region of the prodomain involved in receptor binding, we suggest that Met66 prodomain bioactivity involves His40 mediated stabilization of the multimeric structure. Our results point to the necessity of a Zn2+-mediated higher order molecular assembly of the Met66 prodomain to mediate neuronal remodeling.
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Affiliation(s)
- Jing Wang
- Weill Cornell Medicine, Department of Biochemistry, New York, NY, USA.
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16
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Elder MK, Erdjument-Bromage H, Oliveira MM, Mamcarz M, Neubert TA, Klann E. Age-dependent shift in the de novo proteome accompanies pathogenesis in an Alzheimer's disease mouse model. Commun Biol 2021; 4:823. [PMID: 34193971 PMCID: PMC8245541 DOI: 10.1038/s42003-021-02324-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is an age-related neurodegenerative disorder associated with memory loss, but the AD-associated neuropathological changes begin years before memory impairments. Investigation of the early molecular abnormalities in AD might offer innovative opportunities to target memory impairment prior to onset. Decreased protein synthesis plays a fundamental role in AD, yet the consequences of this dysregulation for cellular function remain unknown. We hypothesize that alterations in the de novo proteome drive early metabolic alterations in the hippocampus that persist throughout AD progression. Using a combinatorial amino acid tagging approach to selectively label and enrich newly synthesized proteins, we found that the de novo proteome is disturbed in young APP/PS1 mice prior to symptom onset, affecting the synthesis of multiple components of the synaptic, lysosomal, and mitochondrial pathways. Furthermore, the synthesis of large clusters of ribosomal subunits were affected throughout development. Our data suggest that large-scale changes in protein synthesis could underlie cellular dysfunction in AD.
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Affiliation(s)
- Megan K Elder
- Center for Neural Science, New York University, New York, NY, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | | | - Maggie Mamcarz
- Center for Neural Science, New York University, New York, NY, USA
| | - Thomas A Neubert
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY, USA.
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
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17
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Karajannis MA, Mauguen A, Maloku E, Xu Q, Dunbar EM, Plotkin SR, Yaffee A, Wang S, Roland JT, Sen C, Placantonakis DG, Golfinos JG, Allen JC, Vitanza NA, Chiriboga LA, Schneider RJ, Deng J, Neubert TA, Goldberg JD, Zagzag D, Giancotti FG, Blakeley JO. Phase 0 Clinical Trial of Everolimus in Patients with Vestibular Schwannoma or Meningioma. Mol Cancer Ther 2021; 20:1584-1591. [PMID: 34224367 DOI: 10.1158/1535-7163.mct-21-0143] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/18/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022]
Abstract
Inhibition of mTORC1 signaling has been shown to diminish growth of meningiomas and schwannomas in preclinical studies, and clinical data suggest that everolimus, an orally administered mTORC1 inhibitor, may slow tumor progression in a subset of patients with neurofibromatosis type 2 (NF2) with vestibular schwannoma. To assess the pharmacokinetics, pharmacodynamics, and potential mechanisms of treatment resistance, we performed a presurgical (phase 0) clinical trial of everolimus in patients undergoing elective surgery for vestibular schwannoma or meningiomas. Eligible patients with meningioma or vestibular schwannoma requiring tumor resection enrolled on study received everolimus 10 mg daily for 10 days immediately prior to surgery. Everolimus blood levels were determined immediately before and after surgery. Tumor samples were collected intraoperatively. Ten patients completed protocol therapy. Median pre- and postoperative blood levels of everolimus were found to be in a high therapeutic range (17.4 ng/mL and 9.4 ng/mL, respectively). Median tumor tissue drug concentration determined by mass spectrometry was 24.3 pg/mg (range, 9.2-169.2). We observed only partial inhibition of phospho-S6 in the treated tumors, indicating incomplete target inhibition compared with control tissues from untreated patients (P = 0.025). Everolimus led to incomplete inhibition of mTORC1 and downstream signaling. These data may explain the limited antitumor effect of everolimus observed in clinical studies for patients with NF2 and will inform the design of future preclinical and clinical studies targeting mTORC1 in meningiomas and schwannomas.
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Affiliation(s)
- Matthias A Karajannis
- Pediatric Neuro-Oncology Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Audrey Mauguen
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ekrem Maloku
- Division of Neuropathology, Department of Pathology, NYU Langone Health, New York, New York
| | - Qingwen Xu
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, Texas
| | - Erin M Dunbar
- Neuro-Oncology, Piedmont Brain Tumor Center, Atlanta, Georgia
| | - Scott R Plotkin
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Anna Yaffee
- Department of Pediatrics, NYU Langone Health, New York, New York
| | - Shiyang Wang
- Department of Pediatrics, NYU Langone Health, New York, New York
| | - J Thomas Roland
- Department of Otolaryngology, NYU Langone Health, New York, New York.,Department of Neurosurgery, NYU Langone Health, New York, New York
| | - Chandranath Sen
- Department of Neurosurgery, NYU Langone Health, New York, New York
| | | | - John G Golfinos
- Department of Neurosurgery, NYU Langone Health, New York, New York
| | - Jeffrey C Allen
- Department of Pediatrics, NYU Langone Health, New York, New York
| | | | | | | | - Jingjing Deng
- Department of Cell Biology and Skirball Institute, NYU Langone Health, New York, New York
| | - Thomas A Neubert
- Department of Cell Biology and Skirball Institute, NYU Langone Health, New York, New York
| | - Judith D Goldberg
- Department of Population Health, NYU Langone Health, New York, New York
| | - David Zagzag
- Division of Neuropathology, Department of Pathology, NYU Langone Health, New York, New York.,Department of Neurosurgery, NYU Langone Health, New York, New York
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18
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Ginsberg SD, Neubert TA, Sharma S, Digwal CS, Yan P, Timbus C, Wang T, Chiosis G. Disease-specific interactome alterations via epichaperomics: the case for Alzheimer's disease. FEBS J 2021; 289:2047-2066. [PMID: 34028172 DOI: 10.1111/febs.16031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/23/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022]
Abstract
The increasingly appreciated prevalence of complicated stressor-to-phenotype associations in human disease requires a greater understanding of how specific stressors affect systems or interactome properties. Many currently untreatable diseases arise due to variations in, and through a combination of, multiple stressors of genetic, epigenetic, and environmental nature. Unfortunately, how such stressors lead to a specific disease phenotype or inflict a vulnerability to some cells and tissues but not others remains largely unknown and unsatisfactorily addressed. Analysis of cell- and tissue-specific interactome networks may shed light on organization of biological systems and subsequently to disease vulnerabilities. However, deriving human interactomes across different cell and disease contexts remains a challenge. To this end, this opinion article links stressor-induced protein interactome network perturbations to the formation of pathologic scaffolds termed epichaperomes, revealing a viable and reproducible experimental solution to obtaining rigorous context-dependent interactomes. This article presents our views on how a specialized 'omics platform called epichaperomics may complement and enhance the currently available conventional approaches and aid the scientific community in defining, understanding, and ultimately controlling interactome networks of complex diseases such as Alzheimer's disease. Ultimately, this approach may aid the transition from a limited single-alteration perspective in disease to a comprehensive network-based mindset, which we posit will result in precision medicine paradigms for disease diagnosis and treatment.
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Affiliation(s)
- Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, USA.,Departments of Psychiatry, Neuroscience & Physiology, The NYU Neuroscience Institute, New York University Grossman School of Medicine, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY, USA
| | - Sahil Sharma
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Chander S Digwal
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Pengrong Yan
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Calin Timbus
- Department of Mathematics, Technical University of Cluj-Napoca, CJ, Romania
| | - Tai Wang
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Gabriela Chiosis
- Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA.,Breast Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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19
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Yan P, Patel HJ, Sharma S, Corben A, Wang T, Panchal P, Yang C, Sun W, Araujo TL, Rodina A, Joshi S, Robzyk K, Gandu S, White JR, de Stanchina E, Modi S, Janjigian YY, Hill EG, Liu B, Erdjument-Bromage H, Neubert TA, Que NLS, Li Z, Gewirth DT, Taldone T, Chiosis G. Molecular Stressors Engender Protein Connectivity Dysfunction through Aberrant N-Glycosylation of a Chaperone. Cell Rep 2021; 31:107840. [PMID: 32610141 PMCID: PMC7372946 DOI: 10.1016/j.celrep.2020.107840] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/04/2020] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
Stresses associated with disease may pathologically remodel the proteome by both increasing interaction strength and altering interaction partners, resulting in proteome-wide connectivity dysfunctions. Chaperones play an important role in these alterations, but how these changes are executed remains largely unknown. Our study unveils a specific N-glycosylation pattern used by a chaperone, Glucose-regulated protein 94 (GRP94), to alter its conformational fitness and stabilize a state most permissive for stable interactions with proteins at the plasma membrane. This "protein assembly mutation' remodels protein networks and properties of the cell. We show in cells, human specimens, and mouse xenografts that proteome connectivity is restorable by inhibition of the N-glycosylated GRP94 variant. In summary, we provide biochemical evidence for stressor-induced chaperone-mediated protein mis-assemblies and demonstrate how these alterations are actionable in disease.
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Affiliation(s)
- Pengrong Yan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hardik J Patel
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Adriana Corben
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Currently at Mount Sinai Hospital, New York, NY 10029, USA
| | - Tai Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chenghua Yang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Currently at Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Weilin Sun
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Thais L Araujo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kenneth Robzyk
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Srinivasa Gandu
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julie R White
- Comparative Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shanu Modi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elizabeth G Hill
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Bei Liu
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Thomas A Neubert
- Department of Cell Biology and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Nanette L S Que
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel T Gewirth
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Tony Taldone
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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20
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D'Acunzo P, Pérez-González R, Kim Y, Hargash T, Miller C, Alldred MJ, Erdjument-Bromage H, Penikalapati SC, Pawlik M, Saito M, Saito M, Ginsberg SD, Neubert TA, Goulbourne CN, Levy E. Mitovesicles are a novel population of extracellular vesicles of mitochondrial origin altered in Down syndrome. Sci Adv 2021; 7:7/7/eabe5085. [PMID: 33579698 PMCID: PMC7880603 DOI: 10.1126/sciadv.abe5085] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/23/2020] [Indexed: 05/03/2023]
Abstract
Mitochondrial dysfunction is an established hallmark of aging and neurodegenerative disorders such as Down syndrome (DS) and Alzheimer's disease (AD). Using a high-resolution density gradient separation of extracellular vesicles (EVs) isolated from murine and human DS and diploid control brains, we identify and characterize a previously unknown population of double-membraned EVs containing multiple mitochondrial proteins distinct from previously described EV subtypes, including microvesicles and exosomes. We term these newly identified mitochondria-derived EVs "mitovesicles." We demonstrate that brain-derived mitovesicles contain a specific subset of mitochondrial constituents and that their levels and cargo are altered during pathophysiological processes where mitochondrial dysfunction occurs, including in DS. The development of a method for the selective isolation of mitovesicles paves the way for the characterization in vivo of biological processes connecting EV biology and mitochondria dynamics and for innovative therapeutic and diagnostic strategies.
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Affiliation(s)
- Pasquale D'Acunzo
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
| | - Rocío Pérez-González
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
| | - Yohan Kim
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
| | - Tal Hargash
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Chelsea Miller
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Melissa J Alldred
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Sai C Penikalapati
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Monika Pawlik
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Mitsuo Saito
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
- Division of Analytical Psychopharmacology, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Mariko Saito
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
- Division of Neurochemistry, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Stephen D Ginsberg
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University School of Medicine, New York, NY 10016, USA
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY 10016, USA
| | - Thomas A Neubert
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Chris N Goulbourne
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Efrat Levy
- Center for Dementia Research, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA.
- Department of Psychiatry, New York University School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University School of Medicine, New York, NY 10016, USA
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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21
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Sweet ME, Zhang X, Erdjument-Bromage H, Dubey V, Khandelia H, Neubert TA, Pedersen BP, Stokes DL. Serine phosphorylation regulates the P-type potassium pump KdpFABC. eLife 2020; 9:55480. [PMID: 32955430 PMCID: PMC7535926 DOI: 10.7554/elife.55480] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 01/25/2020] [Accepted: 09/19/2020] [Indexed: 12/22/2022] Open
Abstract
KdpFABC is an ATP-dependent K+ pump that ensures bacterial survival in K+-deficient environments. Whereas transcriptional activation of kdpFABC expression is well studied, a mechanism for down-regulation when K+ levels are restored has not been described. Here, we show that KdpFABC is inhibited when cells return to a K+-rich environment. The mechanism of inhibition involves phosphorylation of Ser162 on KdpB, which can be reversed in vitro by treatment with serine phosphatase. Mutating Ser162 to Alanine produces constitutive activity, whereas the phosphomimetic Ser162Asp mutation inactivates the pump. Analyses of the transport cycle show that serine phosphorylation abolishes the K+-dependence of ATP hydrolysis and blocks the catalytic cycle after formation of the aspartyl phosphate intermediate (E1~P). This regulatory mechanism is unique amongst P-type pumps and this study furthers our understanding of how bacteria control potassium homeostasis to maintain cell volume and osmotic potential.
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Affiliation(s)
- Marie E Sweet
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
| | - Xihui Zhang
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
| | - Hediye Erdjument-Bromage
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
| | - Vikas Dubey
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Himanshu Khandelia
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Thomas A Neubert
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
| | - Bjørn P Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - David L Stokes
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
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22
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Klein ME, Younts TJ, Cobo CF, Buxbaum AR, Aow J, Erdjument-Bromage H, Richard S, Malinow R, Neubert TA, Singer RH, Castillo PE, Jordan BA. Sam68 Enables Metabotropic Glutamate Receptor-Dependent LTD in Distal Dendritic Regions of CA1 Hippocampal Neurons. Cell Rep 2020; 29:1789-1799.e6. [PMID: 31722197 PMCID: PMC6871770 DOI: 10.1016/j.celrep.2019.10.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 03/27/2018] [Revised: 08/15/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
The transport and translation of dendritic mRNAs by RNA-binding proteins (RBPs) allows for spatially restricted gene expression in neuronal processes. Although local translation in neuronal dendrites is now well documented, there is little evidence for corresponding effects on local synaptic function. Here, we report that the RBP Sam68 promotes the localization and translation of Arc mRNA preferentially in distal dendrites of rodent hippocampal CA1 pyramidal neurons. Consistent with Arc function in translation-dependent synaptic plasticity, we find that Sam68 knockout (KO) mice display impaired metabotropic glutamate-receptor-dependent long-term depression (mGluR-LTD) and impaired structural plasticity exclusively at distal Schaffer-collateral synapses. Moreover, by using quantitative proteomics, we find that the Sam68 interactome contains numerous regulators of mRNA translation and synaptic function. This work identifies an important player in Arc expression, provides a general framework for Sam68 regulation of protein synthesis, and uncovers a mechanism that enables the precise spatiotemporal expression of long-term plasticity throughout neurons.
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Affiliation(s)
- Matthew E Klein
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Thomas J Younts
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Carmen Freire Cobo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Adina R Buxbaum
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Jonathan Aow
- Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montréal, QC H3T 1E2, Canada
| | - Roberto Malinow
- Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Thomas A Neubert
- Department of Cell Biology and Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Robert H Singer
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
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23
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Wiseman RL, Chin KT, Haynes CM, Stanhill A, Xu CF, Roguev A, Krogan NJ, Neubert TA, Ron D. Correction: Thioredoxin-related protein 32 is an arsenite-regulated thiol reductase of the proteasome 19 S particle. J Biol Chem 2020; 295:9267. [PMID: 32620695 PMCID: PMC7335781 DOI: 10.1074/jbc.aac120.014712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023] Open
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24
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Li B, Suutari BS, Sun SD, Luo Z, Wei C, Chenouard N, Mandelberg NJ, Zhang G, Wamsley B, Tian G, Sanchez S, You S, Huang L, Neubert TA, Fishell G, Tsien RW. Neuronal Inactivity Co-opts LTP Machinery to Drive Potassium Channel Splicing and Homeostatic Spike Widening. Cell 2020; 181:1547-1565.e15. [PMID: 32492405 DOI: 10.1016/j.cell.2020.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 01/28/2020] [Accepted: 05/04/2020] [Indexed: 12/21/2022]
Abstract
Homeostasis of neural firing properties is important in stabilizing neuronal circuitry, but how such plasticity might depend on alternative splicing is not known. Here we report that chronic inactivity homeostatically increases action potential duration by changing alternative splicing of BK channels; this requires nuclear export of the splicing factor Nova-2. Inactivity and Nova-2 relocation were connected by a novel synapto-nuclear signaling pathway that surprisingly invoked mechanisms akin to Hebbian plasticity: Ca2+-permeable AMPA receptor upregulation, L-type Ca2+ channel activation, enhanced spine Ca2+ transients, nuclear translocation of a CaM shuttle, and nuclear CaMKIV activation. These findings not only uncover commonalities between homeostatic and Hebbian plasticity but also connect homeostatic regulation of synaptic transmission and neuronal excitability. The signaling cascade provides a full-loop mechanism for a classic autoregulatory feedback loop proposed ∼25 years ago. Each element of the loop has been implicated previously in neuropsychiatric disease.
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Affiliation(s)
- Boxing Li
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510810, China; Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA.
| | - Benjamin S Suutari
- Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA; Center for Neural Science, New York University, New York, NY 10003, USA
| | - Simón(e) D. Sun
- Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA; Center for Neural Science, New York University, New York, NY 10003, USA
| | - Zhengyi Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510120, China
| | - Chuanchuan Wei
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510810, China
| | - Nicolas Chenouard
- Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA
| | - Nataniel J Mandelberg
- Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA
| | - Guoan Zhang
- Department of Biochemistry and Molecular Pharmacology and Skirball Institute, NYU Grossman Medical Center, New York, NY 10016, USA
| | - Brie Wamsley
- Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA; Stanley Center for Psychiatric Research, The Broad Institute, Cambridge, MA 02142, USA
| | - Guoling Tian
- Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA
| | - Sandrine Sanchez
- Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA
| | - Sikun You
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510810, China
| | - Lianyan Huang
- Neuroscience Program, Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510810, China
| | - Thomas A Neubert
- Department of Biochemistry and Molecular Pharmacology and Skirball Institute, NYU Grossman Medical Center, New York, NY 10016, USA
| | - Gordon Fishell
- Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA; Stanley Center for Psychiatric Research, The Broad Institute, Cambridge, MA 02142, USA
| | - Richard W Tsien
- Department of Neuroscience and Physiology, Neuroscience Institute, NYU Grossman Medical Center, New York, NY 10016, USA; Center for Neural Science, New York University, New York, NY 10003, USA.
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25
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Ghiso J, Cabrera E, Neubert TA, Rostagno A. N‐ and C‐Terminal Alzheimer’s Aβ Heterogeneity Modulates the Balance Between Brain Clearance and Amyloid Formation. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.02002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Chen L, Marsiglia WM, Chen H, Katigbak J, Erdjument-Bromage H, Kemble DJ, Fu L, Ma J, Sun G, Zhang Y, Liang G, Neubert TA, Li X, Traaseth NJ, Mohammadi M. Molecular basis for receptor tyrosine kinase A-loop tyrosine transphosphorylation. Nat Chem Biol 2020; 16:267-277. [PMID: 31959966 PMCID: PMC7040854 DOI: 10.1038/s41589-019-0455-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 12/05/2019] [Accepted: 12/13/2019] [Indexed: 12/11/2022]
Abstract
A long-standing mystery shrouds the mechanism by which catalytically repressed receptor tyrosine kinase domains accomplish transphosphorylation of activation loop (A-loop) tyrosines. Here we show that this reaction proceeds via an asymmetric complex that is thermodynamically disadvantaged because of an electrostatic repulsion between enzyme and substrate kinases. Under physiological conditions, the energetic gain resulting from ligand-induced dimerization of extracellular domains overcomes this opposing clash, stabilizing the A-loop-transphosphorylating dimer. A unique pathogenic fibroblast growth factor receptor gain-of-function mutation promotes formation of the complex responsible for phosphorylation of A-loop tyrosines by eliminating this repulsive force. We show that asymmetric complex formation induces a more phosphorylatable A-loop conformation in the substrate kinase, which in turn promotes the active state of the enzyme kinase. This explains how quantitative differences in the stability of ligand-induced extracellular dimerization promotes formation of the intracellular A-loop-transphosphorylating asymmetric complex to varying extents, thereby modulating intracellular kinase activity and signaling intensity.
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MESH Headings
- AAA Domain/genetics
- AAA Domain/physiology
- Catalytic Domain
- Dimerization
- Enzyme Activation
- Humans
- Ligands
- Phosphorylation
- Protein Binding
- Protein Conformation
- Protein-Tyrosine Kinases/metabolism
- Protein-Tyrosine Kinases/physiology
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptor Protein-Tyrosine Kinases/physiology
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Signal Transduction
- Structure-Activity Relationship
- Tyrosine/chemistry
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Affiliation(s)
- Lingfeng Chen
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | | | - Huaibin Chen
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Joseph Katigbak
- Department of Chemistry, New York University, New York, NY, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - David J Kemble
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Lili Fu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jinghong Ma
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Gongqin Sun
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, USA
| | - Guang Liang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Thomas A Neubert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Xiaokun Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | | | - Moosa Mohammadi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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Sweet M, Erdjument-Bromage H, Neubert TA, Stokes DL. Action and Inactivation of the Bacterial Potassium Pump KdpFABC. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Schlame M, Xu Y, Erdjument-Bromage H, Neubert TA, Ren M. Lipidome-wide 13C flux analysis: a novel tool to estimate the turnover of lipids in organisms and cultures. J Lipid Res 2020; 61:95-104. [PMID: 31712250 PMCID: PMC6939592 DOI: 10.1194/jlr.d119000318] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/07/2019] [Indexed: 01/12/2023] Open
Abstract
Lipid metabolism plays an important role in the regulation of cellular homeostasis. However, because it is difficult to measure the actual rates of synthesis and degradation of individual lipid species, lipid compositions are often used as a surrogate to evaluate lipid metabolism even though they provide only static snapshots of the lipodome. Here, we designed a simple method to determine the turnover rate of phospholipid and acylglycerol species based on the incorporation of 13C6-glucose combined with LC-MS/MS. We labeled adult Drosophila melanogaster with 13C6-glucose that incorporates into the entire lipidome, derived kinetic parameters from mass spectra, and studied effects of deletion of CG6718, the fly homolog of the calcium-independent phospholipase A2β, on lipid metabolism. Although 13C6-glucose gave rise to a complex pattern of 13C incorporation, we were able to identify discrete isotopomers in which 13C atoms were confined to the glycerol group. With these isotopomers, we calculated turnover rate constants, half-life times, and fluxes of the glycerol backbone of multiple lipid species. To perform these calculations, we estimated the fraction of labeled molecules in glycerol-3-phosphate, the lipid precursor, by mass isotopomer distribution analysis of the spectra of phosphatidylglycerol. When we applied this method to D. melanogaster, we found a range of lipid half-lives from 2 to 200 days, demonstrated tissue-specific fluxes of individual lipid species, and identified a novel function of CG6718 in triacylglycerol metabolism. This method provides fluxomics-type data with significant potential to improve the understanding of complex lipid regulation in a variety of research models.
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Affiliation(s)
- Michael Schlame
- Departments of Anesthesiology, New York University School of Medicine, New York, NY 10016; Cell Biology, New York University School of Medicine, New York, NY 10016.
| | - Yang Xu
- Departments of Anesthesiology, New York University School of Medicine, New York, NY 10016
| | - Hediye Erdjument-Bromage
- Cell Biology, New York University School of Medicine, New York, NY 10016; Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016
| | - Thomas A Neubert
- Cell Biology, New York University School of Medicine, New York, NY 10016; Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016
| | - Mindong Ren
- Departments of Anesthesiology, New York University School of Medicine, New York, NY 10016; Cell Biology, New York University School of Medicine, New York, NY 10016
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Karajannis M, Goldberg J, Thomas Roland J, Sen C, Placantonakis D, Golfinos J, Allen J, Dunbar E, Plotkin S, Akshintala S, Schneider R, Deng J, Neubert TA, Giancotti F, Zagzag D, O Blakeley J. ACTR-09. A PHASE 0 PHARMACODYNAMIC AND PHARMACOKINETIC STUDY OF EVEROLIMUS IN VESTIBULAR SCHWANNOMA (VS) AND MENINGIOMA PATIENTS. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
BACKGROUND
Inhibition of mTORC1 signaling has been shown to diminish growth of NF2 deficient tumors in preclinical studies, and clinical data suggest that everolimus, an orally administered mTORC1 inhibitor, may slow tumor progression in a subset of adult and pediatric NF2 patients with VS. To assess the pharmacokinetics, pharmacodynamics and potential mechanisms of treatment resistance, we performed a pre-surgical (“phase 0”) clinical trial of everolimus in patients undergoing surgery for VS or meningiomas.
METHODS
Eligible patients with meningioma or VS requiring tumor resection received everolimus 10 mg daily for 10 days immediately prior to surgery. Everolimus blood levels were determined immediately prior to and after surgery. Tumor samples were collected intraoperatively.
RESULTS
Ten patients completed protocol therapy, including 5 patients with NF2-related meningioma, 3 patients with sporadic meningioma, and 2 patients with NF2-related VS. Median pre- and post-operative plasma levels of everolimus were found to be in a high therapeutic range (17.4 ng/ml and 9.4 ng/ml, respectively). Median tumor tissue drug concentration determined by mass spectrometry was 24.3 ng/g (range 9.2–169.2), and median tumor tissue to post-operative plasma drug concentration ratio was 0.39. We observed only partial inhibition of phospho-S6 in the treated tumors, indicating incomplete target inhibition compared to matched control tissues from untreated patients (p = 0.005). Consistent with prior observations that inhibition of mTORC1 may lead to MAPK pathway activation through a PI3K-dependent feedback loop, we observed a statistically significant increase of phospho-ERK (p < 0.03) versus untreated controls.
CONCLUSIONS
In patients with meningioma or VS, treatment with everolimus leads to incomplete inhibition of mTORC1 signaling and upregulation phospho-ERK. These data may explain the limited anti-tumor effect of everolimus observed in clinical studies for NF2 patients and identify upregulation of phospho-ERK as a likely resistance mechanism that could be addressed with combination therapies.
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Oh Y, Lai JSY, Mills HJ, Erdjument-Bromage H, Giammarinaro B, Saadipour K, Wang JG, Abu F, Neubert TA, Suh GSB. A glucose-sensing neuron pair regulates insulin and glucagon in Drosophila. Nature 2019; 574:559-564. [PMID: 31645735 PMCID: PMC6857815 DOI: 10.1038/s41586-019-1675-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 09/16/2019] [Indexed: 01/08/2023]
Abstract
Although glucose-sensing neurons were identified more than 50 years ago, the physiological role of glucose sensing in metazoans remains unclear. Here we identify a pair of glucose-sensing neurons with bifurcated axons in the brain of Drosophila. One axon branch projects to insulin-producing cells to trigger the release of Drosophila insulin-like peptide 2 (dilp2) and the other extends to adipokinetic hormone (AKH)-producing cells to inhibit secretion of AKH, the fly analogue of glucagon. These axonal branches undergo synaptic remodelling in response to changes in their internal energy status. Silencing of these glucose-sensing neurons largely disabled the response of insulin-producing cells to glucose and dilp2 secretion, disinhibited AKH secretion in corpora cardiaca and caused hyperglycaemia, a hallmark feature of diabetes mellitus. We propose that these glucose-sensing neurons maintain glucose homeostasis by promoting the secretion of dilp2 and suppressing the release of AKH when haemolymph glucose levels are high.
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Affiliation(s)
- Yangkyun Oh
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA
| | - Jason Sih-Yu Lai
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA
- QPS-Qualitix Taiwan, Ren-Ai Road, Taipei, Taiwan
| | - Holly J Mills
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA
- Ascend Public Charter Schools, New York, NY, USA
| | - Hediye Erdjument-Bromage
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA
| | - Benno Giammarinaro
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA
- Vision Sciences Graduate Program, School of Optometry, UC Berkeley, Berkeley, CA, USA
| | - Khalil Saadipour
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA
| | - Justin G Wang
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Farhan Abu
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Thomas A Neubert
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA
| | - Greg S B Suh
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, Neuroscience Institute, New York University School of Medicine, New York, NY, USA.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
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Abstract
Key genes, such as Agrin, Lrp4, and MuSK, are required for the initial formation, subsequent maturation, and long-term stabilization of mammalian neuromuscular synapses. Additional molecules are thought to function selectively during the evolution and stabilization of these synapses, but these molecular players are largely unknown. Here, we used mass spectrometry to identify vezatin, a two-pass transmembrane protein, as an acetylcholine receptor (AChR)–associated protein, and we provide evidence that vezatin binds directly to AChRs. We show that vezatin is dispensable for the formation of synapses but plays a later role in the emergence of a topologically complex and branched shape of the synapse, as well as the stabilization of AChRs. In addition, neuromuscular synapses in vezatin mutant mice display premature signs of deterioration, normally found only during aging. Thus, vezatin has a selective role in the structural elaboration and postnatal maturation of murine neuromuscular synapses.
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Affiliation(s)
- Natasha Koppel
- Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
| | - Matthew B Friese
- Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
| | - Helene L Cardasis
- Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
| | - Thomas A Neubert
- Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
| | - Steven J Burden
- Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
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32
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Carbonell AU, Cho CH, Tindi JO, Counts PA, Bates JC, Erdjument-Bromage H, Cvejic S, Iaboni A, Kvint I, Rosensaft J, Banne E, Anagnostou E, Neubert TA, Scherer SW, Molholm S, Jordan BA. Haploinsufficiency in the ANKS1B gene encoding AIDA-1 leads to a neurodevelopmental syndrome. Nat Commun 2019; 10:3529. [PMID: 31388001 PMCID: PMC6684583 DOI: 10.1038/s41467-019-11437-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 12/21/2018] [Accepted: 07/13/2019] [Indexed: 12/23/2022] Open
Abstract
Neurodevelopmental disorders, including autism spectrum disorder, have complex polygenic etiologies. Single-gene mutations in patients can help define genetic factors and molecular mechanisms underlying neurodevelopmental disorders. Here we describe individuals with monogenic heterozygous microdeletions in ANKS1B, a predicted risk gene for autism and neuropsychiatric diseases. Affected individuals present with a spectrum of neurodevelopmental phenotypes, including autism, attention-deficit hyperactivity disorder, and speech and motor deficits. Neurons generated from patient-derived induced pluripotent stem cells demonstrate loss of the ANKS1B-encoded protein AIDA-1, a brain-specific protein highly enriched at neuronal synapses. A transgenic mouse model of Anks1b haploinsufficiency recapitulates a range of patient phenotypes, including social deficits, hyperactivity, and sensorimotor dysfunction. Identification of the AIDA-1 interactome using quantitative proteomics reveals protein networks involved in synaptic function and the etiology of neurodevelopmental disorders. Our findings formalize a link between the synaptic protein AIDA-1 and a rare, previously undefined genetic disease we term ANKS1B haploinsufficiency syndrome.
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Affiliation(s)
- Abigail U Carbonell
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Chang Hoon Cho
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Jaafar O Tindi
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Pamela A Counts
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Juliana C Bates
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, 10016, NY, USA
| | - Svetlana Cvejic
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Alana Iaboni
- Autism Research Centre, Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, M46 1R8, ON, Canada
| | - Ifat Kvint
- Pediatric Neurology Clinic, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Jenny Rosensaft
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Ehud Banne
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Evdokia Anagnostou
- Autism Research Centre, Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, M46 1R8, ON, Canada
| | - Thomas A Neubert
- Department of Cell Biology and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, 10016, NY, USA
- Department of Pharmacology, New York University School of Medicine, New York, 10016, NY, USA
| | - Stephen W Scherer
- Centre for Applied Genomics and McLaughlin Centre, Hospital for Sick Children and University of Toronto, Toronto, M56 0A4, ON, Canada
| | - Sophie Molholm
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA.
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, 10461, NY, USA.
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Patil KS, Basak I, Dalen I, Hoedt E, Lange J, Lunde KA, Liu Y, Tysnes OB, Forsgren L, Aarsland D, Neubert TA, Larsen JP, Alves G, Møller SG. Combinatory microRNA serum signatures as classifiers of Parkinson's disease. Parkinsonism Relat Disord 2019; 64:202-210. [PMID: 31003905 DOI: 10.1016/j.parkreldis.2019.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/22/2019] [Accepted: 04/10/2019] [Indexed: 12/29/2022]
Abstract
INTRODUCTION As current clinical diagnostic protocols for Parkinson's disease (PD) may be prone to inaccuracies there is a need to identify and validate molecular biomarkers, such as circulating microRNAs, which will complement current practices and increase diagnostic accuracy. This study identifies, verifies and validates combinatory serum microRNA signatures as diagnostic classifiers of PD across different patient cohorts. METHODS 370 PD (drug naïve) and control serum samples from the Norwegian ParkWest study were used for identification and verification of differential microRNA levels in PD which were validated in a blind study using 64 NY Parkinsonism in UMeå (NYPUM) study serum samples and tested for specificity in 48 Dementia Study of Western Norway (DemWest) study Alzheimer's disease (AD) serum samples using miRNA-microarrays, and quantitative (q) RT-PCR. Proteomic approaches identified potential molecular targets for these microRNAs. RESULTS Using Affymetrix GeneChip® miRNA 4.0 arrays and qRT-PCR we comprehensively analyzed serum microRNA levels and found that the microRNA (PARKmiR)-combinations, hsa-miR-335-5p/hsa-miR-3613-3p (95% CI, 0.87-0.94), hsa-miR-335-5p/hsa-miR-6865-3p (95% CI, 0.87-0.93), and miR-335-5p/miR-3613-3p/miR-6865-3p (95% CI, 0.87-0.94) show a high degree of discriminatory accuracy (AUC 0.9-1.0). The PARKmiR signatures were validated in an independent PD cohort (AUC ≤ 0.71) and analysis in AD serum samples showed PARKmiR signature specificity to PD. Proteomic analyses showed that the PARKmiRs regulate key PD-associated proteins, including alpha-synuclein and Leucine Rich Repeat Kinase 2. CONCLUSIONS Our study has identified and validated unique miRNA serum signatures that represent PD classifiers, which may complement and increase the accuracy of current diagnostic protocols.
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Affiliation(s)
- Ketan S Patil
- Department of Biological Sciences, St. John's University, New York, NY, USA
| | - Indranil Basak
- Department of Biological Sciences, St. John's University, New York, NY, USA
| | - Ingvild Dalen
- Norwegian Center for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
| | - Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Johannes Lange
- Norwegian Center for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
| | - Kristin A Lunde
- Norwegian Center for Movement Disorders, Stavanger University Hospital, Stavanger, Norway; Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Norway
| | - Ying Liu
- Department of Computer Science, Mathematics and Science, St. John's University, New York, NY, USA
| | - Ole-Bjørn Tysnes
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Lars Forsgren
- Department of Pharmacology and Clinical Neuroscience, University of Umeå, Umeå, Sweden
| | - Dag Aarsland
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King's College, London, UK; Centre for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Jan Petter Larsen
- Network for Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Guido Alves
- Norwegian Center for Movement Disorders, Stavanger University Hospital, Stavanger, Norway; Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Norway
| | - Simon Geir Møller
- Department of Biological Sciences, St. John's University, New York, NY, USA
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34
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Ren M, Xu Y, Erdjument-Bromage H, Donelian A, Phoon CKL, Terada N, Strathdee D, Neubert TA, Schlame M. Extramitochondrial cardiolipin suggests a novel function of mitochondria in spermatogenesis. J Cell Biol 2019; 218:1491-1502. [PMID: 30914420 PMCID: PMC6504895 DOI: 10.1083/jcb.201808131] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 08/21/2018] [Revised: 11/29/2018] [Accepted: 03/07/2019] [Indexed: 12/03/2022] Open
Abstract
The acrosome is a protease-rich organelle in sperm essential for fertilization but little is known about acrosome biogenesis. Ren et al. find that the mitochondrial lipid cardiolipin and some mitochondrial proteins translocate to the acrosome during spermatogenesis, suggesting that mitochondria directly contribute to the assembly of this sperm-specific organelle. Mitochondria contain cardiolipin (CL), an organelle-specific phospholipid that carries four fatty acids with a strong preference for unsaturated chains. Unsaturation is essential for the stability and for the function of mitochondrial CL. Surprisingly, we found tetrapalmitoyl-CL (TPCL), a fully saturated species, in the testes of humans and mice. TPCL was absent from other mouse tissues but was the most abundant CL species in testicular germ cells. Most intriguingly, TPCL was not localized in mitochondria but was in other cellular membranes even though mitochondrial CL was the substrate from which TPCL was synthesized. During spermiogenesis, TPCL became associated with the acrosome, a sperm-specific organelle, along with a subset of authentic mitochondrial proteins, including Ant4, Suox, and Spata18. Our data suggest that mitochondria-derived membranes are assembled into the acrosome, challenging the concept that this organelle is strictly derived from the Golgi apparatus and revealing a novel function of mitochondria.
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Affiliation(s)
- Mindong Ren
- Department of Anesthesiology, New York University School of Medicine, New York, NY .,Department of Cell Biology, New York University School of Medicine, New York, NY
| | - Yang Xu
- Department of Anesthesiology, New York University School of Medicine, New York, NY
| | - Hediye Erdjument-Bromage
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY
| | - Alec Donelian
- Department of Anesthesiology, New York University School of Medicine, New York, NY
| | - Colin K L Phoon
- Department of Pediatrics, New York University School of Medicine, New York, NY
| | - Naohiro Terada
- Department of Pathology, University of Florida College of Medicine, Gainesville, FL
| | - Douglas Strathdee
- Transgenic Technology Laboratory, Cancer Research UK Beatson Institute, Glasgow, UK
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY
| | - Michael Schlame
- Department of Anesthesiology, New York University School of Medicine, New York, NY .,Department of Cell Biology, New York University School of Medicine, New York, NY
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Congdon EE, Chukwu JE, Shamir DB, Deng J, Ujla D, Sait HBR, Neubert TA, Kong XP, Sigurdsson EM. Tau antibody chimerization alters its charge and binding, thereby reducing its cellular uptake and efficacy. EBioMedicine 2019; 42:157-173. [PMID: 30910484 PMCID: PMC6492224 DOI: 10.1016/j.ebiom.2019.03.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 09/21/2018] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 12/28/2022] Open
Abstract
Background Bringing antibodies from pre-clinical studies to human trials requires humanization, but this process may alter properties that are crucial for efficacy. Since pathological tau protein is primarily intraneuronal in Alzheimer's disease, the most efficacious antibodies should work both intra- and extracellularly. Thus, changes which impact uptake or antibody binding will affect antibody efficacy. Methods Initially, we examined four tau mouse monoclonal antibodies with naturally differing charges. We quantified their neuronal uptake, and efficacy in preventing toxicity and pathological seeding induced by human-derived pathological tau. Later, we generated a human chimeric 4E6 (h4E6), an antibody with well documented efficacy in multiple tauopathy models. We compared the uptake and efficacy of unmodified and chimeric antibodies in neuronal and differentiated neuroblastoma cultures. Further, we analyzed tau binding using ELISA assays. Findings Neuronal uptake of tau antibodies and their efficacy strongly depends on antibody charge. Additionally, their ability to prevent tau toxicity and seeding of tau pathology does not necessarily go together. Particularly, chimerization of 4E6 increased its charge from 6.5 to 9.6, which blocked its uptake into human and mouse cells. Furthermore, h4E6 had altered binding characteristics despite intact binding sites, compared to the mouse antibody. Importantly, these changes in uptake and binding substantially decreased its efficacy in preventing tau toxicity, although under certain conditions it did prevent pathological seeding of tau. Conclusions These results indicate that efficacy of chimeric/humanized tau antibodies should be thoroughly characterized prior to clinical trials, which may require further engineering to maintain or improve their therapeutic potential. Fund National Institutes of Health (NS077239, AG032611, R24OD18340, R24OD018339 and RR027990, Alzheimer's Association (2016-NIRG-397228) and Blas Frangione Foundation.
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Affiliation(s)
- Erin E Congdon
- New York University School of Medicine, Department of Neuroscience and Physiology, and The Neuroscience Institute, 435 E 30th St. SB1123, New York, NY 10016, United States of America
| | - Jessica E Chukwu
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, 550 First Ave, MSB 398, New York, NY 10016, United States of America
| | - Dov B Shamir
- New York University School of Medicine, Department of Neuroscience and Physiology, and The Neuroscience Institute, 435 E 30th St. SB1123, New York, NY 10016, United States of America
| | - Jingjing Deng
- New York University School of Medicine, Department of Cell Biology, 540 First Avenue, Skirball Institute Lab 5-18, New York, NY 10016, United States of America
| | - Devyani Ujla
- New York University School of Medicine, Department of Neuroscience and Physiology, and The Neuroscience Institute, 435 E 30th St. SB1123, New York, NY 10016, United States of America
| | - Hameetha B R Sait
- New York University School of Medicine, Department of Neuroscience and Physiology, and The Neuroscience Institute, 435 E 30th St. SB1123, New York, NY 10016, United States of America
| | - Thomas A Neubert
- New York University School of Medicine, Department of Cell Biology, 540 First Avenue, Skirball Institute Lab 5-18, New York, NY 10016, United States of America
| | - Xiang-Peng Kong
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, 550 First Ave, MSB 398, New York, NY 10016, United States of America
| | - Einar M Sigurdsson
- New York University School of Medicine, Department of Neuroscience and Physiology, and The Neuroscience Institute, 435 E 30th St. SB1123, New York, NY 10016, United States of America; New York University School of Medicine, Department of Psychiatry, 435 E 30th St. Science Building SB1115, New York, NY 10016, United States of America.
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36
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Oury J, Liu Y, Töpf A, Todorovic S, Hoedt E, Preethish-Kumar V, Neubert TA, Lin W, Lochmüller H, Burden SJ. MACF1 links Rapsyn to microtubule- and actin-binding proteins to maintain neuromuscular synapses. J Cell Biol 2019; 218:1686-1705. [PMID: 30842214 PMCID: PMC6504910 DOI: 10.1083/jcb.201810023] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 10/04/2018] [Revised: 01/07/2019] [Accepted: 02/07/2019] [Indexed: 12/20/2022] Open
Abstract
Oury et al. show that the scaffolding protein MACF1 links Rapsyn, which binds acetylcholine receptors, to the microtubule- and actin-network at neuromuscular synapses. MACF1 thereby plays a role in synaptic maturation in mice, and mutations of MACF1 are associated with congenital myasthenia in humans. Complex mechanisms are required to form neuromuscular synapses, direct their subsequent maturation, and maintain the synapse throughout life. Transcriptional and post-translational pathways play important roles in synaptic differentiation and direct the accumulation of the neurotransmitter receptors, acetylcholine receptors (AChRs), to the postsynaptic membrane, ensuring for reliable synaptic transmission. Rapsyn, an intracellular peripheral membrane protein that binds AChRs, is essential for synaptic differentiation, but how Rapsyn acts is poorly understood. We screened for proteins that coisolate with AChRs in a Rapsyn-dependent manner and show that microtubule actin cross linking factor 1 (MACF1), a scaffolding protein with binding sites for microtubules (MT) and actin, is concentrated at neuromuscular synapses, where it binds Rapsyn and serves as a synaptic organizer for MT-associated proteins, EB1 and MAP1b, and the actin-associated protein, Vinculin. MACF1 plays an important role in maintaining synaptic differentiation and efficient synaptic transmission in mice, and variants in MACF1 are associated with congenital myasthenia in humans.
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Affiliation(s)
- Julien Oury
- Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University Medical School, New York, NY
| | - Yun Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Slobodanka Todorovic
- Clinic for Neurology and Psychiatry for Children and Youth, Belgrade, Serbia and Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Esthelle Hoedt
- Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University Medical School, New York, NY
| | | | - Thomas A Neubert
- Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University Medical School, New York, NY
| | - Weichun Lin
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX
| | - Hanns Lochmüller
- Department of Neuropediatrics and Muscle Disorders, Medical Center, University of Freiburg, Faculty of Medicine, Freiburg, Germany.,Centro Nacional de Análisis Genómico, Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
| | - Steven J Burden
- Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University Medical School, New York, NY
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37
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Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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38
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Kishinevsky S, Wang T, Rodina A, Chung SY, Xu C, Philip J, Taldone T, Joshi S, Alpaugh ML, Bolaender A, Gutbier S, Sandhu D, Fattahi F, Zimmer B, Shah SK, Chang E, Inda C, Koren J, Saurat NG, Leist M, Gross SS, Seshan VE, Klein C, Tomishima MJ, Erdjument-Bromage H, Neubert TA, Henrickson RC, Chiosis G, Studer L. HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient-specific midbrain dopamine neurons. Nat Commun 2018; 9:4345. [PMID: 30341316 PMCID: PMC6195591 DOI: 10.1038/s41467-018-06486-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 04/24/2017] [Accepted: 08/29/2018] [Indexed: 12/21/2022] Open
Abstract
Environmental and genetic risk factors contribute to Parkinson’s Disease (PD) pathogenesis and the associated midbrain dopamine (mDA) neuron loss. Here, we identify early PD pathogenic events by developing methodology that utilizes recent innovations in human pluripotent stem cells (hPSC) and chemical sensors of HSP90-incorporating chaperome networks. We show that events triggered by PD-related genetic or toxic stimuli alter the neuronal proteome, thereby altering the stress-specific chaperome networks, which produce changes detected by chemical sensors. Through this method we identify STAT3 and NF-κB signaling activation as examples of genetic stress, and phospho-tyrosine hydroxylase (TH) activation as an example of toxic stress-induced pathways in PD neurons. Importantly, pharmacological inhibition of the stress chaperome network reversed abnormal phospho-STAT3 signaling and phospho-TH-related dopamine levels and rescued PD neuron viability. The use of chemical sensors of chaperome networks on hPSC-derived lineages may present a general strategy to identify molecular events associated with neurodegenerative diseases. The early molecular events that ultimately lead to neuronal cell death in pathologies such as Parkinson’s disease are poorly understood. Here the authors use pluripotent stem-cell-derived human midbrain neurons and chemical biology tools to gain molecular level insight into the events induced by toxic and genetic stresses that mimic those occurring during neurodegeneration.
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Affiliation(s)
- Sarah Kishinevsky
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.,Neuroscience Graduate Program of Weill Cornell Graduate School of Biomedical Sciences, Weill Cornell Medical College, 1300 York Avenue, Box 65, New York, NY, 10065, USA
| | - Tai Wang
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Anna Rodina
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Sun Young Chung
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
| | - Chao Xu
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - John Philip
- Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Tony Taldone
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Suhasini Joshi
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Mary L Alpaugh
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.,Department of Molecular and Cellular Biosciences, Rowan University, 1275 York Avenue, Glassboro, NJ, 08028, USA
| | - Alexander Bolaender
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Simon Gutbier
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, 78464, Germany
| | - Davinder Sandhu
- Department of Pharmacology, Weill Cornell College of Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Faranak Fattahi
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
| | - Bastian Zimmer
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
| | - Smit K Shah
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Elizabeth Chang
- Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Carmen Inda
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.,Hostos Community College, City University of New York, Bronx, NY, 10453, USA
| | - John Koren
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.,Department of Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Nathalie G Saurat
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
| | - Marcel Leist
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, 78464, Germany
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell College of Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10017, USA
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, 23538, Germany
| | - Mark J Tomishima
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,SKI Stem Cell Research Facility, 1275 York Avenue, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, NYU School of Medicine, New York, NY, 10016, USA.,Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY, 10016, USA
| | - Thomas A Neubert
- Department of Cell Biology, NYU School of Medicine, New York, NY, 10016, USA.,Kimmel Center for Biology and Medicine at the Skirball Institute, NYU School of Medicine, New York, NY, 10016, USA
| | - Ronald C Henrickson
- Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Gabriela Chiosis
- Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Department of Medicine, Memorial Hospital, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| | - Lorenz Studer
- The Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 256, New York, NY, 10065, USA
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39
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Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) has become very popular as a quantitative proteomic method since it was firstly introduced by Matthias Mann's group in 2002. It is a metabolic labeling strategy in which isotope-labeled amino acids are metabolically incorporated in vivo into proteins during translation. After natural (light) or heavy amino acid incorporation, differentially labeled samples are mixed immediately after cell lysis and before any further processing, which minimizes quantitative errors caused by handling different samples in parallel. In this unit, we describe protocols for basic duplex SILAC, triplex SILAC for use in nondividing cells such as neurons, and for measuring amounts of newly synthesized proteins. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jingjing Deng
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, New York
| | - Hediye Erdjument-Bromage
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, New York
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, New York
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40
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Hernandez C, Wang Z, Ramazanov B, Tang Y, Mehta S, Dambrot C, Lee YW, Tessema K, Kumar I, Astudillo M, Neubert TA, Guo S, Ivanova NB. Dppa2/4 Facilitate Epigenetic Remodeling during Reprogramming to Pluripotency. Cell Stem Cell 2018; 23:396-411.e8. [PMID: 30146411 DOI: 10.1016/j.stem.2018.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 06/04/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
Abstract
As somatic cells are converted into induced pluripotent stem cells (iPSCs), their chromatin is remodeled to a pluripotent configuration with unique euchromatin-to-heterochromatin ratios, DNA methylation patterns, and enhancer and promoter status. The molecular machinery underlying this process is largely unknown. Here, we show that embryonic stem cell (ESC)-specific factors Dppa2 and Dppa4 play a key role in resetting the epigenome to a pluripotent state. They are induced in reprogramming intermediates, function as a heterodimer, and are required for efficient reprogramming of mouse and human cells. When co-expressed with Oct4, Klf4, Sox2, and Myc (OKSM) factors, Dppa2/4 yield reprogramming efficiencies that exceed 80% and accelerate reprogramming kinetics, generating iPSCs in 2 to 4 days. When bound to chromatin, Dppa2/4 initiate global chromatin decompaction via the DNA damage response pathway and contribute to downregulation of somatic genes and activation of ESC enhancers, all of which enables an efficient transition to pluripotency. Our work provides critical insights into how the epigenome is remodeled during acquisition of pluripotency.
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Affiliation(s)
- Charles Hernandez
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Zheng Wang
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Bulat Ramazanov
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Yin Tang
- Department of Genetics, Yale University, New Haven, CT, USA
| | - Sameet Mehta
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Center for Genome Analysis, Yale University, New Haven, CT, USA
| | - Cheryl Dambrot
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Yu-Wei Lee
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Kaleab Tessema
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Ishan Kumar
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Michael Astudillo
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Shangqin Guo
- Yale Stem Cell Center, Yale University, New Haven, CT, USA; Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Natalia B Ivanova
- Department of Genetics, Yale University, New Haven, CT, USA; Yale Stem Cell Center, Yale University, New Haven, CT, USA.
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41
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McDonald-Hyman C, Muller JT, Loschi M, Thangavelu G, Saha A, Kumari S, Reichenbach DK, Smith MJ, Zhang G, Koehn BH, Lin J, Mitchell JS, Fife BT, Panoskaltsis-Mortari A, Feser CJ, Kirchmeier AK, Osborn MJ, Hippen KL, Kelekar A, Serody JS, Turka LA, Munn DH, Chi H, Neubert TA, Dustin ML, Blazar BR. The vimentin intermediate filament network restrains regulatory T cell suppression of graft-versus-host disease. J Clin Invest 2018; 128:4604-4621. [PMID: 30106752 DOI: 10.1172/jci95713] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/26/2018] [Indexed: 01/04/2023] Open
Abstract
Regulatory T cells (Tregs) are critical for maintaining immune homeostasis. However, current Treg immunotherapies do not optimally treat inflammatory diseases in patients. Understanding the cellular processes that control Treg function may allow for the augmentation of therapeutic efficacy. In contrast to activated conventional T cells, in which protein kinase C-θ (PKC-θ) localizes to the contact point between T cells and antigen-presenting cells, in human and mouse Tregs, PKC-θ localizes to the opposite end of the cell in the distal pole complex (DPC). Here, using a phosphoproteomic screen, we identified the intermediate filament vimentin as a PKC-θ phospho target and show that vimentin forms a DPC superstructure on which PKC-θ accumulates. Treatment of mouse Tregs with either a clinically relevant PKC-θ inhibitor or vimentin siRNA disrupted vimentin and enhanced Treg metabolic and suppressive activity. Moreover, vimentin-disrupted mouse Tregs were significantly better than controls at suppressing alloreactive T cell priming in graft-versus-host disease (GVHD) and GVHD lethality, using a complete MHC-mismatch mouse model of acute GVHD (C57BL/6 donor into BALB/c host). Interestingly, vimentin disruption augmented the suppressor function of PKC-θ-deficient mouse Tregs. This suggests that enhanced Treg activity after PKC-θ inhibition is secondary to effects on vimentin, not just PKC-θ kinase activity inhibition. Our data demonstrate that vimentin is a key metabolic and functional controller of Treg activity and provide proof of principle that disruption of vimentin is a feasible, translationally relevant method to enhance Treg potency.
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Affiliation(s)
- Cameron McDonald-Hyman
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.,The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - James T Muller
- Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Michael Loschi
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.,The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Govindarajan Thangavelu
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.,The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Asim Saha
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.,The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Sudha Kumari
- Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Dawn K Reichenbach
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.,The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Michelle J Smith
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.,The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Guoan Zhang
- Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Brent H Koehn
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.,The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Jiqiang Lin
- Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Jason S Mitchell
- The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA.,Division of Rheumatology, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Brian T Fife
- The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA.,Division of Rheumatology, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Angela Panoskaltsis-Mortari
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Colby J Feser
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew Kemal Kirchmeier
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mark J Osborn
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Keli L Hippen
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ameeta Kelekar
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, Division of Hematology/Oncology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Laurence A Turka
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David H Munn
- Department of Pediatrics, Georgia Health Sciences University, Augusta, Georgia, USA
| | - Hongbo Chi
- Department of Immunology, Saint Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Thomas A Neubert
- Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Bruce R Blazar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.,The Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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Modrek AS, Golub D, Khan T, Bready D, Prado J, Bowman C, Deng J, Zhang G, Rocha PP, Raviram R, Lazaris C, Stafford JM, LeRoy G, Kader M, Dhaliwal J, Bayin NS, Frenster JD, Serrano J, Chiriboga L, Baitalmal R, Nanjangud G, Chi AS, Golfinos JG, Wang J, Karajannis MA, Bonneau RA, Reinberg D, Tsirigos A, Zagzag D, Snuderl M, Skok JA, Neubert TA, Placantonakis DG. Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2. Cell Rep 2018; 21:1267-1280. [PMID: 29091765 DOI: 10.1016/j.celrep.2017.10.009] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/24/2017] [Accepted: 10/02/2017] [Indexed: 02/07/2023] Open
Abstract
Low-grade astrocytomas (LGAs) carry neomorphic mutations in isocitrate dehydrogenase (IDH) concurrently with P53 and ATRX loss. To model LGA formation, we introduced R132H IDH1, P53 shRNA, and ATRX shRNA into human neural stem cells (NSCs). These oncogenic hits blocked NSC differentiation, increased invasiveness in vivo, and led to a DNA methylation and transcriptional profile resembling IDH1 mutant human LGAs. The differentiation block was caused by transcriptional silencing of the transcription factor SOX2 secondary to disassociation of its promoter from a putative enhancer. This occurred because of reduced binding of the chromatin organizer CTCF to its DNA motifs and disrupted chromatin looping. Our human model of IDH mutant LGA formation implicates impaired NSC differentiation because of repression of SOX2 as an early driver of gliomagenesis.
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Affiliation(s)
- Aram S Modrek
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Danielle Golub
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Themasap Khan
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Devin Bready
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Jod Prado
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Christopher Bowman
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Jingjing Deng
- Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Guoan Zhang
- Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Pedro P Rocha
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Ramya Raviram
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Charalampos Lazaris
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Center, NYU School of Medicine, New York, NY 10016, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Gary LeRoy
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Michael Kader
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Joravar Dhaliwal
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - N Sumru Bayin
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Joshua D Frenster
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Jonathan Serrano
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Luis Chiriboga
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Rabaa Baitalmal
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Gouri Nanjangud
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew S Chi
- Department of Neurology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA
| | - John G Golfinos
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA
| | - Jing Wang
- Department of Anesthesiology, NYU School of Medicine, New York, NY 10016, USA
| | - Matthias A Karajannis
- Department of Pediatrics, NYU School of Medicine, New York, NY 10016, USA; Department of Otolaryngology, NYU School of Medicine, New York, NY 10016, USA
| | - Richard A Bonneau
- Department of Biology, New York University, New York, New York, 10003, USA; Department of Computer Science, New York University, New York, New York, 10003, USA; Simons Center for Data Analysis, New York, NY 10010, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Center, NYU School of Medicine, New York, NY 10016, USA
| | - David Zagzag
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA
| | - Matija Snuderl
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Department of Neurology, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA
| | - Jane A Skok
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Thomas A Neubert
- Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Dimitris G Placantonakis
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA; Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA.
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Wang Z, Gearhart MD, Lee YW, Kumar I, Ramazanov B, Zhang Y, Hernandez C, Lu AY, Neuenkirchen N, Deng J, Jin J, Kluger Y, Neubert TA, Bardwell VJ, Ivanova NB. A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs. Cell Stem Cell 2018; 22:235-251.e9. [PMID: 29337181 DOI: 10.1016/j.stem.2017.12.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/18/2017] [Accepted: 12/02/2017] [Indexed: 11/26/2022]
Abstract
Polycomb group proteins regulate self-renewal and differentiation in many stem cell systems. When assembled into two canonical complexes, PRC1 and PRC2, they sequentially deposit H3K27me3 and H2AK119ub histone marks and establish repressive chromatin, referred to as Polycomb domains. Non-canonical PRC1 complexes retain RING1/RNF2 E3-ubiquitin ligases but have unique sets of accessory subunits. How these non-canonical complexes recognize and regulate their gene targets remains poorly understood. Here, we show that the BCL6 co-repressor (BCOR), a member of the PRC1.1 complex, is critical for maintaining primed pluripotency in human embryonic stem cells (ESCs). BCOR depletion leads to the erosion of Polycomb domains at key developmental loci and the initiation of differentiation along endoderm and mesoderm lineages. The C terminus of BCOR regulates the assembly and targeting of the PRC1.1 complex, while the N terminus contributes to BCOR-PRC1.1 repressor function. Our findings advance understanding of Polycomb targeting and repression in ESCs and could apply broadly across developmental systems.
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Affiliation(s)
- Zheng Wang
- Department of Genetics, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, and the Masonic Cancer Center, Minneapolis, MN 55455, USA
| | - Yu-Wei Lee
- Department of Genetics, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Ishan Kumar
- Department of Genetics, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Bulat Ramazanov
- Department of Genetics, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Yan Zhang
- Department of Genetics, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Charles Hernandez
- Department of Genetics, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Alice Y Lu
- Department of Genetics, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Nils Neuenkirchen
- Department of Cell Biology, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Jingjing Deng
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY10016, USA
| | - Jiaqi Jin
- Department of Pathology, Yale University, New Haven, CT 06520, USA
| | - Yuval Kluger
- Department of Pathology, Yale University, New Haven, CT 06520, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY10016, USA
| | - Vivian J Bardwell
- Department of Genetics, Cell Biology and Development, University of Minnesota, and the Masonic Cancer Center, Minneapolis, MN 55455, USA
| | - Natalia B Ivanova
- Department of Genetics, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA.
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Daniels G, Zhang X, Zhong X, Santiago L, Wang LH, Wu X, Zhang JY, Liang F, Li X, Neubert TA, Steinke L, Shen Y, Basch R, Schneider R, Levy DE, Lee P. Cytoplasmic, full length and novel cleaved variant, TBLR1 reduces apoptosis in prostate cancer under androgen deprivation. Oncotarget 2018; 7:39556-39571. [PMID: 27127173 PMCID: PMC5129953 DOI: 10.18632/oncotarget.9005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 11/03/2015] [Accepted: 03/28/2016] [Indexed: 01/28/2023] Open
Abstract
TBLR1/TBL1XR1, a core component of the nuclear receptor corepressor (NCoR) complex critical for the regulation of multiple nuclear receptors, is a transcriptional coactivator of androgen receptor (AR) and functions as a tumor suppressor when expressed in the nucleus in prostate. Subcellular localization of a protein is critical for its function, and although TBLR1, as a transcriptional cofactor, has been primarily viewed as a nuclear protein, many cells also express variable levels of cytoplasmic TBLR1 and its cytoplasmic specific functions have not been studied. Prostate cancer (PCa) cells express moderately higher level of cytoplasmic TBLR1 compared to benign prostate cells. When comparing androgen-dependent (AD) to androgen-independent (AI) PCa, AI cells contain very high levels of TBLR1 cytoplasmic expression and low levels of nuclear expression. Overexpression of cytoplasmic TBLR1 in AD cells inhibits apoptosis induced by androgen deprivation therapy, either in an androgen free condition or in the presence of bicalutamide. Additionally, we identified a cytoplasmic specific isoform of TBLR1 (cvTBLR1) approximately 5 kDa lower in molecular weight, that is expressed at higher levels in AI PCa cells. By immunoprecipitation, we purified cvTBLR1 and using mass spectrometry analysis combined with N-terminal TMPP labeling and Edman degradation, we identified the cleavage site of cvTBLR1 at amino acid 89, truncating the first 88 amino acids of the N-terminus of the full length protein. Functionally, cvTBLR1 expressed in the cytoplasm reduced apoptosis in PCa cells and promoted growth, migration, and invasion. Finally, we identified a nuclear export signal sequence for TBLR1 cellular localization by deletion and site-directed mutagenesis. The roles of TBLR1 and cvTBLR1 provide novel insights into the mechanism of castration resistance and new strategies for PCa therapy.
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Affiliation(s)
- Garrett Daniels
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Xinmin Zhang
- Department of Pathology and Laboratory Medicine, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA
| | - Xuelin Zhong
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Larion Santiago
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Ling Hang Wang
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Xinyu Wu
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Jack Y Zhang
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Fengxia Liang
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Xin Li
- Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY, USA
| | - Thomas A Neubert
- Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Laurey Steinke
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ying Shen
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Ross Basch
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Robert Schneider
- Microbiology and Molecular Pathogenesis, New York University School of Medicine, New York, NY, USA
| | - David E Levy
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Peng Lee
- Department of Pathology, New York University School of Medicine, New York, NY, USA.,Department of Urology, New York University School of Medicine, New York, NY, USA.,NYU Cancer Institute, New York University School of Medicine, New York, NY, USA.,New York Harbor Healthcare System, New York University School of Medicine, New York, NY, USA
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Abstract
Mass spectrometry (MS)-based techniques have been finding utility as sensitive, high throughput metabolite analysis tools for complex biological samples. We describe here a nanoflow liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) system we developed and applied to metabolic profiling of human cells. Metabolites are extracted from cells using methanol, and filtered through a C18 StageTip to remove large particles. Metabolite samples are separated by HPLC at a flow rate of 400-500 nl/min, then analyzed in both positive and negative ion modes in an LTQ-Orbitrap MS. Metabolite identification and differential analysis are performed using commercial or open source software. Protocols outlined in this chapter describe how nano-LC-MS can be applied to investigate metabolic profiling with limited biomass amount.
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Affiliation(s)
- Jingjing Deng
- Department of Cell Biology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Department of Cell Biology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, USA.
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Erdjument-Bromage H, Huang FK, Neubert TA. Sample Preparation for Relative Quantitation of Proteins Using Tandem Mass Tags (TMT) and Mass Spectrometry (MS). Methods Mol Biol 2018; 1741:135-149. [PMID: 29392697 DOI: 10.1007/978-1-4939-7659-1_11] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quantitative proteome analysis allows comparisons of protein or phosphoprotein levels across multiple cell types or conditions. A number of experimental approaches have been described toward quantitative proteomics. In this chapter, we focus on Tandem Mass Tag (TMT) isobaric labeling of peptides for global, relative quantitation of proteins and phosphopeptides. To date, there has been no published protocol describing chemical labeling of small amounts of peptides specifically extracted from small tumor samples, for which rigorous sample preparation is necessary to ensure reproducible TMT labeling.
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Affiliation(s)
- Hediye Erdjument-Bromage
- Department of Cell Biology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Fang-Ke Huang
- Department of Cell Biology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.,NantOmics, Rockville, MD, USA
| | - Thomas A Neubert
- Department of Cell Biology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.
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Abstract
Amyloid β (Aβ) is the major constituent of the brain deposits found in parenchymal plaques and cerebral blood vessels of patients with Alzheimer's disease (AD). Besides classic full-length peptides, biochemical analyses of brain deposits have revealed high degree of Aβ heterogeneity likely resulting from the action of multiple proteolytic enzymes. This chapter describes a sequential extraction protocol allowing the differential fractionation of soluble and deposited Aβ species taking advantage of their differential solubility properties. Soluble Aβ is extracted by water-based buffers like phosphate-buffered saline-PBS-whereas pre-fibrillar and fibrillar deposits, usually poorly soluble in PBS, are extractable in detergent containing solutions or more stringent conditions as formic acid. The extraction procedure is followed by the biochemical identification of the extracted Aβ species using Western blot and a targeted proteomic analysis which combines immunoprecipitation with MALDI-ToF mass spectrometry. This approach revealed the presence of numerous C- and N-terminal truncated Aβ species in addition to Aβ1-40/42. Notably, the more soluble C-terminal cleaved fragments constitute a main part of PBS homogenates. On the contrary, N-terminal truncated species typically require more stringent conditions for the extraction in agreement with their lower solubility and enhanced aggregability. Detailed assessment of the molecular diversity of Aβ species composing interstitial fluid and amyloid deposits at different disease stages, as well as the evaluation of the truncation profile during various pharmacologic approaches will provide a comprehensive understanding of the still undefined contribution of Aβ truncations to AD pathogenesis and their potential as novel therapeutic targets.
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Affiliation(s)
- Agueda Rostagno
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Thomas A Neubert
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Jorge Ghiso
- Department of Pathology, New York University School of Medicine, New York, NY, USA.
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA.
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48
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Mitre M, Kranz TM, Marlin BJ, Schiavo JK, Erdjument-Bromage H, Zhang X, Minder J, Neubert TA, Hackett TA, Chao MV, Froemke RC. Sex-Specific Differences in Oxytocin Receptor Expression and Function for Parental Behavior. Gend Genome 2017; 1:142-166. [PMID: 32959027 PMCID: PMC7500123 DOI: 10.1089/gg.2017.0017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 01/17/2023] Open
Abstract
Parental care is among the most profound behavior expressed by humans and other animals. Despite intense interest in understanding the biological basis of parental behaviors, it remains unknown how much of parenting is encoded by the genome and which abilities instead are learned or can be refined by experience. One critical factor at the intersection between innate behaviors and experience-dependent learning is oxytocin, a neurohormone important for maternal physiology and neuroplasticity. Oxytocin acts throughout the body and brain to promote prosocial and maternal behaviors and modulates synaptic transmission to affect neural circuit dynamics. Recently we developed specific antibodies to mouse oxytocin receptors, found that oxytocin receptors are left lateralized in female auditory cortex, and examined how oxytocin enables maternal behavior by sensitizing the cortex to infant distress sounds. In this study we compare oxytocin receptor expression and function in male and female mice. Receptor expression is higher in adult female left auditory cortex than in right auditory cortex or males. Developmental profiles and mRNA expression were comparable between males and females. Behaviorally, male and female mice began expressing parental behavior similarly after cohousing with experienced females; however, oxytocin enhanced parental behavior onset in females but not males. This suggests that left lateralization of oxytocin receptor expression in females provides a mechanism for accelerating maternal behavior onset, although male mice can also effectively co-parent after experience with infants. The sex-specific pattern of oxytocin receptor expression might genetically predispose female cortex to respond to infant cues, which both males and females can also rapidly learn.
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Affiliation(s)
- Mariela Mitre
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York
- Neuroscience Institute, New York University School of Medicine, New York, New York
- Department of Otolaryngology, New York University School of Medicine, New York, New York
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, New York
- Department of Cell Biology, Psychiatry, New York University School of Medicine, New York, New York
| | - Thorsten M. Kranz
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York
- Neuroscience Institute, New York University School of Medicine, New York, New York
- Department of Otolaryngology, New York University School of Medicine, New York, New York
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, New York
- Department of Cell Biology, Psychiatry, New York University School of Medicine, New York, New York
| | - Bianca J. Marlin
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York
- Neuroscience Institute, New York University School of Medicine, New York, New York
- Department of Otolaryngology, New York University School of Medicine, New York, New York
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, New York
| | - Jennifer K. Schiavo
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York
- Neuroscience Institute, New York University School of Medicine, New York, New York
- Department of Otolaryngology, New York University School of Medicine, New York, New York
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, New York
| | - Hediye Erdjument-Bromage
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York
| | | | - Jess Minder
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York
- Neuroscience Institute, New York University School of Medicine, New York, New York
- Department of Otolaryngology, New York University School of Medicine, New York, New York
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, New York
| | - Thomas A. Neubert
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York
| | - Troy A. Hackett
- Department of Hearing and Speech Sciences, Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Moses V. Chao
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York
- Neuroscience Institute, New York University School of Medicine, New York, New York
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, New York
- Department of Cell Biology, Psychiatry, New York University School of Medicine, New York, New York
| | - Robert C. Froemke
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, New York
- Neuroscience Institute, New York University School of Medicine, New York, New York
- Department of Otolaryngology, New York University School of Medicine, New York, New York
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, New York
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49
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Stathopoulou A, Chhetri JB, Ambrose JC, Estève PO, Ji L, Erdjument-Bromage H, Zhang G, Neubert TA, Pradhan S, Herrero J, Schmitz RJ, Ooi SK. A novel requirement for DROSHA in maintenance of mammalian CG methylation. Nucleic Acids Res 2017; 45:9398-9412. [PMID: 28934503 PMCID: PMC5766157 DOI: 10.1093/nar/gkx695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/27/2017] [Indexed: 12/18/2022] Open
Abstract
In mammals, faithful inheritance of genomic methylation patterns ensures proper gene regulation and cell behaviour, impacting normal development and fertility. Following establishment, genomic methylation patterns are transmitted through S-phase by the maintenance methyltransferase Dnmt1. Using a protein interaction screen, we identify Microprocessor component DROSHA as a novel DNMT1-interactor. Drosha-deficient embryonic stem (ES) cells display genomic hypomethylation that is not accounted for by changes in the levels of DNMT proteins. DNMT1-mediated methyltransferase activity is also reduced in these cells. We identify two transcripts that are specifically upregulated in Drosha- but not Dicer-deficient ES cells. Regions within these transcripts predicted to form stem-loop structures are processed by Microprocessor and can inhibit DNMT1-mediated methylation in vitro. Our results highlight DROSHA as a novel regulator of mammalian DNA methylation and we propose that DROSHA-mediated processing of RNA is necessary to ensure full DNMT1 activity. This adds to the DROSHA repertoire of non-miRNA dependent functions as well as implicating RNA in regulating DNMT1 activity and correct levels of genomic methylation.
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Affiliation(s)
| | - Jyoti B. Chhetri
- Department of Cancer Biology, UCL Cancer Institute, London WC1E 6BT, UK
| | - John C. Ambrose
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | | | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA
| | - Hediye Erdjument-Bromage
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Guoqiang Zhang
- New England Biolabs, 240 Country Road, Ipswich, MA 01938, USA
| | - Thomas A. Neubert
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute, NYU School of Medicine, New York, NY 10016, USA
| | | | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6BT, UK
| | - Robert J. Schmitz
- Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA 30602, USA
| | - Steen K.T. Ooi
- Department of Cancer Biology, UCL Cancer Institute, London WC1E 6BT, UK
- To whom correspondence should be addressed. Tel: +44 2076 790717; Fax: +44 2076 796817;
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Gauthier SA, Pérez-González R, Sharma A, Huang FK, Alldred MJ, Pawlik M, Kaur G, Ginsberg SD, Neubert TA, Levy E. Enhanced exosome secretion in Down syndrome brain - a protective mechanism to alleviate neuronal endosomal abnormalities. Acta Neuropathol Commun 2017; 5:65. [PMID: 28851452 PMCID: PMC5576289 DOI: 10.1186/s40478-017-0466-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 08/17/2017] [Indexed: 12/18/2022] Open
Abstract
A dysfunctional endosomal pathway and abnormally enlarged early endosomes in neurons are an early characteristic of Down syndrome (DS) and Alzheimer's disease (AD). We have hypothesized that endosomal material can be released by endosomal multivesicular bodies (MVBs) into the extracellular space via exosomes to relieve neurons of accumulated endosomal contents when endosomal pathway function is compromised. Supporting this, we found that exosome secretion is enhanced in the brains of DS patients and a mouse model of the disease, and by DS fibroblasts. Furthermore, increased levels of the tetraspanin CD63, a regulator of exosome biogenesis, were observed in DS brains. Importantly, CD63 knockdown diminished exosome release and worsened endosomal pathology in DS fibroblasts. Taken together, these data suggest that increased CD63 expression enhances exosome release as an endogenous mechanism mitigating endosomal abnormalities in DS. Thus, the upregulation of exosome release represents a potential therapeutic goal for neurodegenerative disorders with endosomal pathology.
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