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Yin JZ, Keszei AFA, Houliston S, Filandr F, Beenstock J, Daou S, Kitaygorodsky J, Schriemer DC, Mazhab-Jafari MT, Gingras AC, Sicheri F. The HisRS-like domain of GCN2 is a pseudoenzyme that can bind uncharged tRNA. Structure 2024:S0969-2126(24)00081-9. [PMID: 38531363 DOI: 10.1016/j.str.2024.02.021] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 01/09/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2α to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated with tRNA aminoacylation, led to the hypothesis that eIF2α kinase activity is regulated by the direct binding of this domain to uncharged tRNA. Here we solved the structure of the HisRS-like domain in the context of full-length GCN2 by cryoEM. Structure and function analysis shows the HisRS-like domain of GCN2 has lost histidine and ATP binding but retains tRNA binding abilities. Hydrogen deuterium exchange mass spectrometry, site-directed mutagenesis and computational docking experiments support a tRNA binding model that is partially shifted from that employed by bona fide HisRS enzymes. These results demonstrate that the HisRS-like domain of GCN2 is a pseudoenzyme and advance our understanding of GCN2 regulation and function.
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Affiliation(s)
- Jay Z Yin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jonah Beenstock
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Salima Daou
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Julia Kitaygorodsky
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mohammad T Mazhab-Jafari
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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2
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Maisonneuve P, Sahmi M, Bergeron-Labrecque F, Ma XI, Queguiner J, Arseneault G, Lefrançois M, Kurinov I, Fronzes R, Sicheri F, Therrien M. The CNK-HYP scaffolding complex promotes RAF activation by enhancing KSR-MEK interaction. Nat Struct Mol Biol 2024:10.1038/s41594-024-01233-6. [PMID: 38388830 DOI: 10.1038/s41594-024-01233-6] [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] [Received: 01/23/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
The RAS-MAPK pathway regulates cell proliferation, differentiation and survival, and its dysregulation is associated with cancer development. The pathway minimally comprises the small GTPase RAS and the kinases RAF, MEK and ERK. Activation of RAF by RAS is notoriously intricate and remains only partially understood. There are three RAF isoforms in mammals (ARAF, BRAF and CRAF) and two related pseudokinases (KSR1 and KSR2). RAS-mediated activation of RAF depends on an allosteric mechanism driven by the dimerization of its kinase domain. Recent work on human RAFs showed that MEK binding to KSR1 promotes KSR1-BRAF heterodimerization, which leads to the phosphorylation of free MEK molecules by BRAF. Similar findings were made with the single Drosophila RAF homolog. Here we show that the fly scaffold proteins CNK and HYP stabilize the KSR-MEK interaction, which in turn enhances RAF-KSR heterodimerization and RAF activation. The cryogenic electron microscopy structure of the minimal KSR-MEK-CNK-HYP complex reveals a ring-like arrangement of the CNK-HYP complex allowing CNK to simultaneously engage KSR and MEK, thus stabilizing the binary interaction. Together, these results illuminate how CNK contributes to RAF activation by stimulating the allosteric function of KSR and highlight the diversity of mechanisms impacting RAF dimerization as well as the regulatory potential of the KSR-MEK interaction.
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Affiliation(s)
- Pierre Maisonneuve
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, F-33600, Pessac, France.
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
| | - Malha Sahmi
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Fanny Bergeron-Labrecque
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Xianjie Iris Ma
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Juliette Queguiner
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Geneviève Arseneault
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Martin Lefrançois
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL, USA
| | - Rémi Fronzes
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS (UMR 5234), Pessac, France
| | - Frank Sicheri
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montréal, Quebec, Canada.
- Département de pathologie et biologie cellulaire, Université de Montréal, Montréal, Quebec, Canada.
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3
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Tessier TM, Chowdhury A, Stekel Z, Fux J, Sartori MA, Teyra J, Jarvik N, Chung J, Kurinov I, Sicheri F, Sidhu SS, Singer AU, Zhang W. Structural and functional validation of a highly specific Smurf2 inhibitor. Protein Sci 2024; 33:e4885. [PMID: 38147466 PMCID: PMC10823456 DOI: 10.1002/pro.4885] [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: 08/31/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/28/2023]
Abstract
Smurf1 and Smurf2 are two closely related member of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor-β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological processes. Generally, E3 ligases, of which over 800 exist in humans, are ideal targets for inhibition as they determine substrate specificity; however, there are few inhibitors with the ability to precisely target a particular E3 ligase of interest. In this work, we explored a panel of ubiquitin variants (UbVs) that were previously identified to bind Smurf1 or Smurf2. In vitro binding and ubiquitination assays identified a highly specific Smurf2 inhibitor, UbV S2.4, which was able to inhibit ligase activity with high potency in the low nanomolar range. Orthologous cellular assays further demonstrated high specificity of UbV S2.4 toward Smurf2 and no cross-reactivity toward Smurf1. Structural analysis of UbV S2.4 in complex with Smurf2 revealed its mechanism of inhibition was through targeting the E2 binding site. In summary, we investigated several protein-based inhibitors of Smurf1 and Smurf2 and identified a highly specific Smurf2 inhibitor that disrupts the E2-E3 protein interaction interface.
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Affiliation(s)
- Tanner M. Tessier
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Arvid Chowdhury
- Department of Molecular GeneticsUniversity of TorontoTorontoOntarioCanada
| | - Zane Stekel
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Julia Fux
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | | | | | - Nick Jarvik
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Jacky Chung
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Igor Kurinov
- NE‐CAT, Department of Chemistry and Chemical BiologyCornell UniversityArgonneIllinoisUSA
| | - Frank Sicheri
- Lunenfeld‐Tanenbaum Research Institute, Mount Sinai HospitalTorontoOntarioCanada
| | - Sachdev S. Sidhu
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Alex U. Singer
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Wei Zhang
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
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4
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Bruce HA, Singer AU, Filippova EV, Blazer LL, Adams JJ, Enderle L, Ben‐David M, Radley EH, Mao DYL, Pau V, Orlicky S, Sicheri F, Kurinov I, Atwell S, Kossiakoff AA, Sidhu SS. Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes. Protein Sci 2024; 33:e4824. [PMID: 37945533 PMCID: PMC10731619 DOI: 10.1002/pro.4824] [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: 08/11/2023] [Revised: 10/09/2023] [Accepted: 10/28/2023] [Indexed: 11/12/2023]
Abstract
The atomic-resolution structural information that X-ray crystallography can provide on the binding interface between a Fab and its cognate antigen is highly valuable for understanding the mechanism of interaction. However, many Fab:antigen complexes are recalcitrant to crystallization, making the endeavor a considerable effort with no guarantee of success. Consequently, there have been significant steps taken to increase the likelihood of Fab:antigen complex crystallization by altering the Fab framework. In this investigation, we applied the surface entropy reduction strategy coupled with phage-display technology to identify a set of surface substitutions that improve the propensity of a human Fab framework to crystallize. In addition, we showed that combining these surface substitutions with previously reported Crystal Kappa and elbow substitutions results in an extraordinary improvement in Fab and Fab:antigen complex crystallizability, revealing a strong synergistic relationship between these sets of substitutions. Through comprehensive Fab and Fab:antigen complex crystallization screenings followed by structure determination and analysis, we defined the roles that each of these substitutions play in facilitating crystallization and how they complement each other in the process.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Daniel Y. L. Mao
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoCanada
| | - Victor Pau
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoCanada
| | - Stephen Orlicky
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoCanada
| | - Frank Sicheri
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoCanada
- Departments of Biochemistry and Molecular GeneticsUniversity of TorontoOntarioCanada
| | | | | | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUSA
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5
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Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. High Accuracy Prediction of PROTAC Complex Structures. J Am Chem Soc 2023; 145:7123-7135. [PMID: 36961978 PMCID: PMC10240388 DOI: 10.1021/jacs.2c09387] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 03/26/2023]
Abstract
The design of PROteolysis-TArgeting Chimeras (PROTACs) requires bringing an E3 ligase into proximity with a target protein to modulate the concentration of the latter through its ubiquitination and degradation. Here, we present a method for generating high-accuracy structural models of E3 ligase-PROTAC-target protein ternary complexes. The method is dependent on two computational innovations: adding a "silent" convolution term to an efficient protein-protein docking program to eliminate protein poses that do not have acceptable linker conformations and clustering models of multiple PROTACs that use the same E3 ligase and target the same protein. Results show that the largest consensus clusters always have high predictive accuracy and that the ensemble of models can be used to predict the dissociation rate and cooperativity of the ternary complex that relate to the degrading activity of the PROTAC. The method is demonstrated by applications to known PROTAC structures and a blind test involving PROTACs against BRAF mutant V600E. The results confirm that PROTACs function by stabilizing a favorable interaction between the E3 ligase and the target protein but do not necessarily exploit the most energetically favorable geometry for interaction between the proteins.
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Affiliation(s)
- Mikhail Ignatov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Akhil Jindal
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 USA
- Acpharis Inc., Holliston, Massachusetts 01746, USA
| | - Ganna Posternak
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Xiaojing Tang
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
| | - Pierre Maisonneuve
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario L4K-M9W, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Frank Sicheri
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario L4K-M9W, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 USA
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
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6
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Alexander-Howden B, Zhang L, van der Sloot AM, Tollis S, St-Cyr DJ, Sicheri F, Bird AP, Tyers M, Lyst MJ. A screen for MeCP2-TBL1 interaction inhibitors using a luminescence-based assay. Sci Rep 2023; 13:3868. [PMID: 36890145 PMCID: PMC9995496 DOI: 10.1038/s41598-023-29915-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/13/2023] [Indexed: 03/10/2023] Open
Abstract
Understanding the molecular pathology of neurodevelopmental disorders should aid the development of therapies for these conditions. In MeCP2 duplication syndrome (MDS)-a severe autism spectrum disorder-neuronal dysfunction is caused by increased levels of MeCP2. MeCP2 is a nuclear protein that binds to methylated DNA and recruits the nuclear co-repressor (NCoR) complex to chromatin via an interaction with the WD repeat-containing proteins TBL1 and TBLR1. The peptide motif in MeCP2 that binds to TBL1/TBLR1 is essential for the toxicity of excess MeCP2 in animal models of MDS, suggesting that small molecules capable of disrupting this interaction might be useful therapeutically. To facilitate the search for such compounds, we devised a simple and scalable NanoLuc luciferase complementation assay for measuring the interaction of MeCP2 with TBL1/TBLR1. The assay allowed excellent separation between positive and negative controls, and had low signal variance (Z-factor = 0.85). We interrogated compound libraries using this assay in combination with a counter-screen based on luciferase complementation by the two subunits of protein kinase A (PKA). Using this dual screening approach, we identified candidate inhibitors of the interaction between MeCP2 and TBL1/TBLR1. This work demonstrates the feasibility of future screens of large compound collections, which we anticipate will enable the development of small molecule therapeutics to ameliorate MDS.
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Affiliation(s)
- Beatrice Alexander-Howden
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Li Zhang
- Institute for Research in Immunology and Cancer (IRIC), Department of Medicine, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
| | - Almer M van der Sloot
- Institute for Research in Immunology and Cancer (IRIC), Department of Medicine, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
- Mila - Quebec Artificial Intelligence Institute, 6666 Rue Saint-Urbain, Montréal, QC, H2S 3H1, Canada
| | - Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Daniel J St-Cyr
- Institute for Research in Immunology and Cancer (IRIC), Department of Medicine, Université de Montréal, Montréal, Québec, H3T 1J4, Canada
- X-Chem Inc, 7171 Frederick-Banting, Montréal, QC, H4S 1Z9, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Adrian P Bird
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK.
| | - Mike Tyers
- Institute for Research in Immunology and Cancer (IRIC), Department of Medicine, Université de Montréal, Montréal, Québec, H3T 1J4, Canada.
- The Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Matthew J Lyst
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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7
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O'Brien S, Kelso S, Steinhart Z, Orlicky S, Mis M, Kim Y, Lin S, Sicheri F, Angers S. SCF FBXW7 regulates G2-M progression through control of CCNL1 ubiquitination. EMBO Rep 2022; 23:e55044. [PMID: 36278408 PMCID: PMC9724663 DOI: 10.15252/embr.202255044] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/14/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
FBXW7, which encodes a substrate-specific receptor of an SCF E3 ligase complex, is a frequently mutated human tumor suppressor gene known to regulate the post-translational stability of various proteins involved in cellular proliferation. Here, using genome-wide CRISPR screens, we report a novel synthetic lethal genetic interaction between FBXW7 and CCNL1 and describe CCNL1 as a new substrate of the SCF-FBXW7 E3 ligase. Further analysis showed that the CCNL1-CDK11 complex is critical at the G2-M phase of the cell cycle since defective CCNL1 accumulation, resulting from FBXW7 mutation, leads to shorter mitotic time. Cells harboring FBXW7 loss-of-function mutations are hypersensitive to treatment with a CDK11 inhibitor, highlighting a genetic vulnerability that could be leveraged for cancer treatment.
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Affiliation(s)
- Siobhan O'Brien
- Department of BiochemistryUniversity of TorontoTorontoONCanada
- Donnelly Centre for Cellular and Biomolecular ResearchTorontoONCanada
| | - Susan Kelso
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoONCanada
| | - Zachary Steinhart
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
- Present address:
Gladstone InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Stephen Orlicky
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoONCanada
| | - Monika Mis
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
- Present address:
GenentechSouth San FranciscoCAUSA
| | - Yunhye Kim
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
| | - Sichun Lin
- Donnelly Centre for Cellular and Biomolecular ResearchTorontoONCanada
| | - Frank Sicheri
- Department of BiochemistryUniversity of TorontoTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoONCanada
| | - Stephane Angers
- Department of BiochemistryUniversity of TorontoTorontoONCanada
- Donnelly Centre for Cellular and Biomolecular ResearchTorontoONCanada
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
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8
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Kelso S, O'Brien S, Kurinov I, Angers S, Sicheri F. Crystal structure of the CDK11 kinase domain bound to the small-molecule inhibitor OTS964. Structure 2022; 30:1615-1625.e4. [PMID: 36327972 PMCID: PMC9722545 DOI: 10.1016/j.str.2022.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/06/2022] [Revised: 08/22/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
CDK11 is a cyclin-dependent kinase that controls proliferation by regulating transcription, RNA splicing, and the cell cycle. As its activity is increasingly associated with cancer, CDK11 is an attractive target for the development of small-molecule inhibitors. However, the development of CDK11 inhibitors with limited off-target effects against other CDKs poses a challenge based on the high conservation of sequence across family members. OTS964 is notable as it displays a measure of specificity for CDK11 in cells. To understand the basis for OTS964's specificity for CDK11, we solved a 2.6 Å crystal structure of the CDK11 kinase domain bound to OTS964. Despite the absence of cyclin, CDK11 adopts an active-like conformation when bound to OTS964. We identified amino acids likely to contribute to the specificity of OTS964 for CDK11 and assessed their contribution to OTS964 binding by isothermal titration calorimetry (ITC) in vitro and by resistance to OTS964 in cells.
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Affiliation(s)
- Susan Kelso
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siobhan O'Brien
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL 60439, USA
| | - Stephane Angers
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 1A8, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada.
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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9
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Bubenik M, Mader P, Mochirian P, Vallée F, Clark J, Truchon JF, Perryman AL, Pau V, Kurinov I, Zahn KE, Leclaire ME, Papp R, Mathieu MC, Hamel M, Duffy NM, Godbout C, Casas-Selves M, Falgueyret JP, Baruah PS, Nicolas O, Stocco R, Poirier H, Martino G, Fortin AB, Roulston A, Chefson A, Dorich S, St-Onge M, Patel P, Pellerin C, Ciblat S, Pinter T, Barabé F, Bakkouri ME, Parikh P, Gervais C, Sfeir A, Mamane Y, Morris SJ, Black WC, Sicheri F, Gallant M. Identification of RP-6685, an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Polθ. J Med Chem 2022; 65:13198-13215. [PMID: 36126059 PMCID: PMC9942948 DOI: 10.1021/acs.jmedchem.2c00998] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 11/29/2022]
Abstract
DNA polymerase theta (Polθ) is an attractive synthetic lethal target for drug discovery, predicted to be efficacious against breast and ovarian cancers harboring BRCA-mutant alleles. Here, we describe our hit-to-lead efforts in search of a selective inhibitor of human Polθ (encoded by POLQ). A high-throughput screening campaign of 350,000 compounds identified an 11 micromolar hit, giving rise to the N2-substituted fused pyrazolo series, which was validated by biophysical methods. Structure-based drug design efforts along with optimization of cellular potency and ADME ultimately led to the identification of RP-6685: a potent, selective, and orally bioavailable Polθ inhibitor that showed in vivo efficacy in an HCT116 BRCA2-/- mouse tumor xenograft model.
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Affiliation(s)
- Monica Bubenik
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Pavel Mader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada
| | - Philippe Mochirian
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Fréderic Vallée
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Jillian Clark
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Jean-François Truchon
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Alexander L. Perryman
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Victor Pau
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, USA
| | - Karl E. Zahn
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Marie-Eve Leclaire
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Robert Papp
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Marie-Claude Mathieu
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Martine Hamel
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Nicole M. Duffy
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Claude Godbout
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Matias Casas-Selves
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Jean-Pierre Falgueyret
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Prasamit S. Baruah
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Olivier Nicolas
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Rino Stocco
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Hugo Poirier
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Giovanni Martino
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | | | - Anne Roulston
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Amandine Chefson
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Stéphane Dorich
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Miguel St-Onge
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Purvish Patel
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Charles Pellerin
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
| | - Stéphane Ciblat
- Ventus Therapeutics 7150 Frederick-Banting suite 200, Montréal, Québec, H4S 2A1, Canada
- Paraza Pharma Inc., 2525 Ave. Marie Curie, Montréal, Québec, H4S 1Z9, Canada
| | - Thomas Pinter
- Paraza Pharma Inc., 2525 Ave. Marie Curie, Montréal, Québec, H4S 1Z9, Canada
| | - Francis Barabé
- Paraza Pharma Inc., 2525 Ave. Marie Curie, Montréal, Québec, H4S 1Z9, Canada
| | - Majida El Bakkouri
- Paraza Pharma Inc., 2525 Ave. Marie Curie, Montréal, Québec, H4S 1Z9, Canada
- National Research Council of Canada, 6100 Royalmount Ave, Montréal, Québec, H4P 2R2, Canada
| | - Paranjay Parikh
- Piramal Pharma Ltd., Plot No. 18, Village Matoda, Taluka: Sanand, Ahmedabad-382213, Gujarat, India
| | - Christian Gervais
- National Research Council of Canada, 6100 Royalmount Ave, Montréal, Québec, H4P 2R2, Canada
| | - Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, MSKCC, 430 E 67th Street, New York, NY 10065, USA
| | - Yael Mamane
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Stephen J. Morris
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - W. Cameron Black
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, M5G 1X5, Canada
| | - Michel Gallant
- Repare Therapeutics, 7171 Frederick-Banting, Building 2, H4S 1Z9, Montréal, Québec, Canada
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10
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Chana CK, Maisonneuve P, Posternak G, Grinberg NGA, Poirson J, Ona SM, Ceccarelli DF, Mader P, St-Cyr DJ, Pau V, Kurinov I, Tang X, Deng D, Cui W, Su W, Kuai L, Soll R, Tyers M, Röst HL, Batey RA, Taipale M, Gingras AC, Sicheri F. Discovery and Structural Characterization of Small Molecule Binders of the Human CTLH E3 Ligase Subunit GID4. J Med Chem 2022; 65:12725-12746. [PMID: 36117290 PMCID: PMC9574856 DOI: 10.1021/acs.jmedchem.2c00509] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Targeted protein
degradation (TPD) strategies exploit bivalent
small molecules to bridge substrate proteins to an E3 ubiquitin ligase
to induce substrate degradation. Few E3s have been explored as degradation
effectors due to a dearth of E3-binding small molecules. We show that
genetically induced recruitment to the GID4 subunit of the CTLH E3
complex induces protein degradation. An NMR-based fragment screen
followed by structure-guided analog elaboration identified two binders
of GID4, 16 and 67, with Kd values of 110 and 17 μM in vitro. A parallel DNA-encoded library (DEL) screen identified five binders
of GID4, the best of which, 88, had a Kd of 5.6 μM in vitro and an EC50 of 558 nM in cells with strong selectivity for GID4. X-ray
co-structure determination revealed the basis for GID4–small
molecule interactions. These results position GID4-CTLH as an E3 for
TPD and provide candidate scaffolds for high-affinity moieties that
bind GID4.
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Affiliation(s)
- Chetan K Chana
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Pierre Maisonneuve
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Ganna Posternak
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Nicolas G A Grinberg
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Juline Poirson
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Samara M Ona
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Derek F Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Pavel Mader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | | | - Victor Pau
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, United States
| | - Xiaojing Tang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Dongjing Deng
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Weiren Cui
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenji Su
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Letian Kuai
- WuXi AppTec, 55 Cambridge Parkway, 8th Floor, Cambridge, Massachusetts 02142, United States
| | - Richard Soll
- WuXi AppTec, 55 Cambridge Parkway, 8th Floor, Cambridge, Massachusetts 02142, United States
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montréal, Québec H3C 3J7, Canada
| | - Hannes L Röst
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada
| | - Robert A Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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11
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Szychowski J, Papp R, Dietrich E, Liu B, Vallée F, Leclaire MÈ, Fourtounis J, Martino G, Perryman AL, Pau V, Yun Yin S, Mader P, Roulston A, Truchon JF, Marshall CG, Diallo M, Duffy NM, Stocco R, Godbout C, Bonneau-Fortin A, Kryczka R, Bhaskaran V, Mao D, Orlicky S, Beaulieu P, Turcotte P, Kurinov I, Sicheri F, Mamane Y, Gallant M, Black WC. Discovery of an Orally Bioavailable and Selective PKMYT1 Inhibitor, RP-6306. J Med Chem 2022; 65:10251-10284. [PMID: 35880755 PMCID: PMC9837800 DOI: 10.1021/acs.jmedchem.2c00552] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/17/2023]
Abstract
PKMYT1 is a regulator of CDK1 phosphorylation and is a compelling therapeutic target for the treatment of certain types of DNA damage response cancers due to its established synthetic lethal relationship with CCNE1 amplification. To date, no selective inhibitors have been reported for this kinase that would allow for investigation of the pharmacological role of PKMYT1. To address this need compound 1 was identified as a weak PKMYT1 inhibitor. Introduction of a dimethylphenol increased potency on PKMYT1. These dimethylphenol analogs were found to exist as atropisomers that could be separated and profiled as single enantiomers. Structure-based drug design enabled optimization of cell-based potency. Parallel optimization of ADME properties led to the identification of potent and selective inhibitors of PKMYT1. RP-6306 inhibits CCNE1-amplified tumor cell growth in several preclinical xenograft models. The first-in-class clinical candidate RP-6306 is currently being evaluated in Phase 1 clinical trials for treatment of various solid tumors.
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Affiliation(s)
- Janek Szychowski
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Robert Papp
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Evelyne Dietrich
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Bingcan Liu
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Frédéric Vallée
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Marie-Ève Leclaire
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Jimmy Fourtounis
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Giovanni Martino
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Alexander L. Perryman
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Victor Pau
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Shou Yun Yin
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Pavel Mader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Anne Roulston
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Jean-Francois Truchon
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - C. Gary Marshall
- Repare Therapeutics, 1 Broadway, 15th Floor, Cambridge, MA 02142, USA
| | - Mohamed Diallo
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Nicole M. Duffy
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Rino Stocco
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Claude Godbout
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | | | - Rosie Kryczka
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Vivek Bhaskaran
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Daniel Mao
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Stephen Orlicky
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Patrick Beaulieu
- OmegaChem Inc., 480 Rue Perreault, Saint-Romuald, QC, G6W 7V6, Canada
| | - Pascal Turcotte
- AdMare BioInnovations, 7171 Frederick-Banting, Montréal, QC, H4S 1Z9, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Il 60439, USA
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Yael Mamane
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - Michel Gallant
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
| | - W. Cameron Black
- Repare Therapeutics, Inc., 7210 Frederick-Banting, Ville St-Laurent, QC, H4S 2A1, Canada
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12
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Martyn GD, Veggiani G, Kusebauch U, Morrone SR, Yates BP, Singer AU, Tong J, Manczyk N, Gish G, Sun Z, Kurinov I, Sicheri F, Moran MF, Moritz RL, Sidhu SS. Engineered SH2 Domains for Targeted Phosphoproteomics. ACS Chem Biol 2022; 17:1472-1484. [PMID: 35613471 DOI: 10.1021/acschembio.2c00051] [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: 11/30/2022]
Abstract
A comprehensive analysis of the phosphoproteome is essential for understanding molecular mechanisms of human diseases. However, current tools used to enrich phosphotyrosine (pTyr) are limited in their applicability and scope. Here, we engineered new superbinder Src-Homology 2 (SH2) domains that enrich diverse sets of pTyr-peptides. We used phage display to select a Fes-SH2 domain variant (superFes; sFes1) with high affinity for pTyr and solved its structure bound to a pTyr-peptide. We performed systematic structure-function analyses of the superbinding mechanisms of sFes1 and superSrc-SH2 (sSrc1), another SH2 superbinder. We grafted the superbinder motifs from sFes1 and sSrc1 into 17 additional SH2 domains and confirmed increased binding affinity for specific pTyr-peptides. Using mass spectrometry (MS), we demonstrated that SH2 superbinders have distinct specificity profiles and superior capabilities to enrich pTyr-peptides. Finally, using combinations of SH2 superbinders as affinity purification (AP) tools we showed that unique subsets of pTyr-peptides can be enriched with unparalleled depth and coverage.
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Affiliation(s)
- Gregory D. Martyn
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Ulrike Kusebauch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Seamus R. Morrone
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Bradley P. Yates
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Alex U. Singer
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Jiefei Tong
- Program in Cell biology, Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Gerald Gish
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, United States
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Michael F. Moran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Program in Cell biology, Hospital for Sick Children, Toronto M5G 0A4, Canada
- The Hospital for Sick Children, SPARC Biocentre, Toronto, Ontario M5G 0A4, Canada
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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13
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Chandler F, Walden M, Reddy PAN, Cassel J, Bell L, Campbell L, Foglizzo M, Sicheri F, Salvino JM, Greenberg RA, Zeqiraj E. First‐in‐class Deubiquitylase Inhibitors Reveal New Enzyme Conformations. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4428] [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]
Affiliation(s)
- Francesca Chandler
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeeds
| | - Miriam Walden
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeeds
| | | | - Joel Cassel
- The Wistar Cancer Center for Molecular ScreeningThe Wistar InstitutePhiladelphiaPA
| | - Lillie Bell
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeeds
| | - Lisa Campbell
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeeds
| | - Martina Foglizzo
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeeds
| | - Frank Sicheri
- Lunenfeld‐Tanenbaum Research Institute, Mount Sinai HospitalTorontoON
| | - Joseph M. Salvino
- The Wistar Cancer Center for Molecular ScreeningThe Wistar InstitutePhiladelphiaPA
| | - Roger A. Greenberg
- Department of Cancer BiologyBasser Center for BRCA, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaPA
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeeds
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14
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Veggiani G, Yates BP, Martyn GD, Manczyk N, Singer AU, Kurinov I, Sicheri F, Sidhu SS. Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs. ACS Chem Biol 2022; 17:941-956. [PMID: 35385646 PMCID: PMC9305627 DOI: 10.1021/acschembio.2c00089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ubiquitin (Ub)-binding domains embedded in intracellular proteins act as readers of the complex Ub code and contribute to regulation of numerous eukaryotic processes. Ub-interacting motifs (UIMs) are short α-helical modular recognition elements whose role in controlling proteostasis and signal transduction has been poorly investigated. Moreover, impaired or aberrant activity of UIM-containing proteins has been implicated in numerous diseases, but targeting modular recognition elements in proteins remains a major challenge. To overcome this limitation, we developed Ub variants (UbVs) that bind to 42 UIMs in the human proteome with high affinity and specificity. Structural analysis of a UbV:UIM complex revealed the molecular determinants of enhanced affinity and specificity. Furthermore, we showed that a UbV targeting a UIM in the cancer-associated Ub-specific protease 28 potently inhibited catalytic activity. Our work demonstrates the versatility of UbVs to target short α-helical Ub receptors with high affinity and specificity. Moreover, the UbVs provide a toolkit to investigate the role of UIMs in regulating and transducing Ub signals and establish a general strategy for the systematic development of probes for Ub-binding domains.
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Affiliation(s)
- Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Bradley P. Yates
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Gregory D. Martyn
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Alex U. Singer
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, NE-CAT, Cornell University, Argonne, Illinois 60439, United States
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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15
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Beenstock J, Sicheri F. The structural and functional workings of KEOPS. Nucleic Acids Res 2021; 49:10818-10834. [PMID: 34614169 PMCID: PMC8565320 DOI: 10.1093/nar/gkab865] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 07/30/2021] [Revised: 09/09/2021] [Accepted: 10/04/2021] [Indexed: 11/14/2022] Open
Abstract
KEOPS (Kinase, Endopeptidase and Other Proteins of Small size) is a five-subunit protein complex that is highly conserved in eukaryotes and archaea and is essential for the fitness of cells and for animal development. In humans, mutations in KEOPS genes underlie Galloway-Mowat syndrome, which manifests in severe microcephaly and renal dysfunction that lead to childhood death. The Kae1 subunit of KEOPS catalyzes the universal and essential tRNA modification N6-threonylcarbamoyl adenosine (t6A), while the auxiliary subunits Cgi121, the kinase/ATPase Bud32, Pcc1 and Gon7 play a supporting role. Kae1 orthologs are also present in bacteria and mitochondria but function in distinct complexes with proteins that are not related in structure or function to the auxiliary subunits of KEOPS. Over the past 15 years since its discovery, extensive study in the KEOPS field has provided many answers towards understanding the roles that KEOPS plays in cells and in human disease and how KEOPS carries out these functions. In this review, we provide an overview into recent advances in the study of KEOPS and illuminate exciting future directions.
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Affiliation(s)
- Jonah Beenstock
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Frank Sicheri
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, M5S 1A8, Canada.,Department of Biochemistry, University of Toronto, Ontario, M5S 1A8, Canada
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16
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St-Cyr D, Ceccarelli DF, Orlicky S, van der Sloot AM, Tang X, Kelso S, Moore S, James C, Posternak G, Coulombe-Huntington J, Bertomeu T, Marinier A, Sicheri F, Tyers M. Identification and optimization of molecular glue compounds that inhibit a noncovalent E2 enzyme-ubiquitin complex. Sci Adv 2021; 7:eabi5797. [PMID: 34705497 PMCID: PMC10763754 DOI: 10.1126/sciadv.abi5797] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Pharmacological control of the ubiquitin-proteasome system (UPS) is of intense interest in drug discovery. Here, we report the development of chemical inhibitors of the ubiquitin-conjugating (E2) enzyme CDC34A (also known as UBE2R1), which donates activated ubiquitin to the cullin-RING ligase (CRL) family of ubiquitin ligase (E3) enzymes. A FRET-based interaction assay was used to screen for novel compounds that stabilize the noncovalent complex between CDC34A and ubiquitin, and thereby inhibit the CDC34A catalytic cycle. An isonipecotamide hit compound was elaborated into analogs with ~1000-fold increased potency in stabilizing the CDC34A-ubiquitin complex. These analogs specifically inhibited CDC34A-dependent ubiquitination in vitro and stabilized an E2~ubiquitin thioester reaction intermediate in cells. The x-ray crystal structure of a CDC34A-ubiquitin-inhibitor complex uncovered the basis for analog structure-activity relationships. The development of chemical stabilizers of the CDC34A-ubiquitin complex illustrates a general strategy for de novo discovery of molecular glue compounds that stabilize weak protein interactions.
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Affiliation(s)
- Daniel St-Cyr
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Derek F. Ceccarelli
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Stephen Orlicky
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Almer M. van der Sloot
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Xiaojing Tang
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Susan Kelso
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Susan Moore
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Clint James
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Ganna Posternak
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Anne Marinier
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
- Department of Chemistry, University of Montreal, Montreal, Québec H3C 3J7, Canada
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Québec H3T 1J4, Canada
- Department of Medicine, University of Montreal, Montreal, Québec H3C 3J7, Canada
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17
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Abstract
Aurora A is a serine/threonine kinase essential for mitotic entry and spindle assembly. Recent molecular studies have revealed the existence of multiple, distinct mechanisms of Aurora A activation, each occurring at specific subcellular locations, optimized for cellular context, and primed by signaling events including phosphorylation and oxidation.
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Affiliation(s)
- Nicolas Tavernier
- Programme équipe Labellisée Ligue Contre le Cancer - Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, Paris, France
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Lionel Pintard
- Programme équipe Labellisée Ligue Contre le Cancer - Université de Paris, Centre National de la Recherche Scientifique, Institut Jacques Monod, Paris, France
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18
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Kelso S, Orlicky S, Beenstock J, Ceccarelli DF, Kurinov I, Gish G, Sicheri F. Bipartite binding of the N terminus of Skp2 to cyclin A. Structure 2021; 29:975-988.e5. [PMID: 33989513 DOI: 10.1016/j.str.2021.04.011] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/06/2021] [Accepted: 04/23/2021] [Indexed: 10/21/2022]
Abstract
Skp2 and cyclin A are cell-cycle regulators that control the activity of CDK2. Cyclin A acts as an activator and substrate recruitment factor of CDK2, while Skp2 mediates the ubiquitination and subsequent destruction of the CDK inhibitor protein p27. The N terminus of Skp2 can interact directly with cyclin A but is not required for p27 ubiquitination. To gain insight into this poorly understood interaction, we have solved the 3.2 Å X-ray crystal structure of the N terminus of Skp2 bound to cyclin A. The structure reveals a bipartite mode of interaction with two motifs in Skp2 recognizing two discrete surfaces on cyclin A. The uncovered binding mechanism allows for a rationalization of the inhibitory effect of Skp2 on CDK2-cyclin A kinase activity toward the RxL motif containing substrates and raises the possibility that other intermolecular regulators and substrates may use similar non-canonical modes of interaction for cyclin targeting.
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Affiliation(s)
- Susan Kelso
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, ON M5S 1A8, Canada
| | - Stephen Orlicky
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Jonah Beenstock
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Derek F Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL 60439, USA
| | - Gerald Gish
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, ON M5S 1A8, Canada.
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19
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Tavernier N, Thomas Y, Vigneron S, Maisonneuve P, Orlicky S, Mader P, Regmi SG, Van Hove L, Levinson NM, Gasmi-Seabrook G, Joly N, Poteau M, Velez-Aguilera G, Gavet O, Castro A, Dasso M, Lorca T, Sicheri F, Pintard L. Bora phosphorylation substitutes in trans for T-loop phosphorylation in Aurora A to promote mitotic entry. Nat Commun 2021; 12:1899. [PMID: 33771996 PMCID: PMC7997955 DOI: 10.1038/s41467-021-21922-w] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/19/2021] [Indexed: 12/16/2022] Open
Abstract
Polo-like kinase 1 (Plk1) is instrumental for mitotic entry and progression. Plk1 is activated by phosphorylation on a conserved residue Thr210 in its activation segment by the Aurora A kinase (AURKA), a reaction that critically requires the co-factor Bora phosphorylated by a CyclinA/B-Cdk1 kinase. Here we show that phospho-Bora is a direct activator of AURKA kinase activity. We localize the key determinants of phospho-Bora function to a 100 amino acid region encompassing two short Tpx2-like motifs and a phosphoSerine-Proline motif at Serine 112, through which Bora binds AURKA. The latter substitutes in trans for the Thr288 phospho-regulatory site of AURKA, which is essential for an active conformation of the kinase domain. We demonstrate the importance of these determinants for Bora function in mitotic entry both in Xenopus egg extracts and in human cells. Our findings unveil the activation mechanism of AURKA that is critical for mitotic entry.
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Affiliation(s)
- N Tavernier
- Centre for Systems Biology, Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Programme équipe Labellisée Ligue Contre le Cancer, Institut Jacques Monod, UMR7592, Université de Paris, CNRS, Paris, France
| | - Y Thomas
- Programme équipe Labellisée Ligue Contre le Cancer, Institut Jacques Monod, UMR7592, Université de Paris, CNRS, Paris, France
| | - S Vigneron
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237, Université de Montpellier, CNRS, Montpellier, France
| | - P Maisonneuve
- Centre for Systems Biology, Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - S Orlicky
- Centre for Systems Biology, Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - P Mader
- Centre for Systems Biology, Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - S G Regmi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - L Van Hove
- Programme équipe Labellisée Ligue Contre le Cancer, Institut Jacques Monod, UMR7592, Université de Paris, CNRS, Paris, France
| | - N M Levinson
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - G Gasmi-Seabrook
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - N Joly
- Programme équipe Labellisée Ligue Contre le Cancer, Institut Jacques Monod, UMR7592, Université de Paris, CNRS, Paris, France
| | - M Poteau
- Institut Gustave Roussy CNRS UMR9019, Villejuif, France
| | - G Velez-Aguilera
- Programme équipe Labellisée Ligue Contre le Cancer, Institut Jacques Monod, UMR7592, Université de Paris, CNRS, Paris, France
| | - O Gavet
- Institut Gustave Roussy CNRS UMR9019, Villejuif, France
| | - A Castro
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237, Université de Montpellier, CNRS, Montpellier, France
| | - M Dasso
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - T Lorca
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237, Université de Montpellier, CNRS, Montpellier, France
| | - F Sicheri
- Centre for Systems Biology, Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
| | - L Pintard
- Programme équipe Labellisée Ligue Contre le Cancer, Institut Jacques Monod, UMR7592, Université de Paris, CNRS, Paris, France.
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20
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Posternak G, Tang X, Maisonneuve P, Jin T, Lavoie H, Daou S, Orlicky S, Goullet de Rugy T, Caldwell L, Chan K, Aman A, Prakesch M, Poda G, Mader P, Wong C, Maier S, Kitaygorodsky J, Larsen B, Colwill K, Yin Z, Ceccarelli DF, Batey RA, Taipale M, Kurinov I, Uehling D, Wrana J, Durocher D, Gingras AC, Al-Awar R, Therrien M, Sicheri F. Functional characterization of a PROTAC directed against BRAF mutant V600E. Nat Chem Biol 2020; 16:1170-1178. [PMID: 32778845 PMCID: PMC7862923 DOI: 10.1038/s41589-020-0609-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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: 11/11/2019] [Accepted: 07/01/2020] [Indexed: 12/22/2022]
Abstract
The RAF family kinases function in the RAS-ERK pathway to transmit signals from activated RAS to the downstream kinases MEK and ERK. This pathway regulates cell proliferation, differentiation and survival, enabling mutations in RAS and RAF to act as potent drivers of human cancers. Drugs targeting the prevalent oncogenic mutant BRAF(V600E) have shown great efficacy in the clinic, but long-term effectiveness is limited by resistance mechanisms that often exploit the dimerization-dependent process by which RAF kinases are activated. Here, we investigated a proteolysis-targeting chimera (PROTAC) approach to BRAF inhibition. The most effective PROTAC, termed P4B, displayed superior specificity and inhibitory properties relative to non-PROTAC controls in BRAF(V600E) cell lines. In addition, P4B displayed utility in cell lines harboring alternative BRAF mutations that impart resistance to conventional BRAF inhibitors. This work provides a proof of concept for a substitute to conventional chemical inhibition to therapeutically constrain oncogenic BRAF.
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Affiliation(s)
- Ganna Posternak
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Xiaojing Tang
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Pierre Maisonneuve
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ting Jin
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Quebec, Montreal, Canada
| | - Hugo Lavoie
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Quebec, Montreal, Canada
| | - Salima Daou
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Stephen Orlicky
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Theo Goullet de Rugy
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Lauren Caldwell
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kin Chan
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Michael Prakesch
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Pavel Mader
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Cassandra Wong
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Stefan Maier
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Julia Kitaygorodsky
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brett Larsen
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Karen Colwill
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Zhe Yin
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Derek F Ceccarelli
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Robert A Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL, USA
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeff Wrana
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Durocher
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Quebec, Montreal, Canada.
- Département de Pathologie et Biologie Cellulaire, University of Montréal, Quebec, Montreal, Canada.
| | - Frank Sicheri
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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21
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Isho B, Abe KT, Zuo M, Jamal AJ, Rathod B, Wang JH, Li Z, Chao G, Rojas OL, Bang YM, Pu A, Christie-Holmes N, Gervais C, Ceccarelli D, Samavarchi-Tehrani P, Guvenc F, Budylowski P, Li A, Paterson A, Yue FY, Marin LM, Caldwell L, Wrana JL, Colwill K, Sicheri F, Mubareka S, Gray-Owen SD, Drews SJ, Siqueira WL, Barrios-Rodiles M, Ostrowski M, Rini JM, Durocher Y, McGeer AJ, Gommerman JL, Gingras AC. Persistence of serum and saliva antibody responses to SARS-CoV-2 spike antigens in COVID-19 patients. Sci Immunol 2020. [PMID: 33033173 DOI: 10.1101/2020.08.01.20166553] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
While the antibody response to SARS-CoV-2 has been extensively studied in blood, relatively little is known about the antibody response in saliva and its relationship to systemic antibody levels. Here, we profiled by enzyme-linked immunosorbent assays (ELISAs) IgG, IgA and IgM responses to the SARS-CoV-2 spike protein (full length trimer) and its receptor-binding domain (RBD) in serum and saliva of acute and convalescent patients with laboratory-diagnosed COVID-19 ranging from 3-115 days post-symptom onset (PSO), compared to negative controls. Anti-SARS-CoV-2 antibody responses were readily detected in serum and saliva, with peak IgG levels attained by 16-30 days PSO. Longitudinal analysis revealed that anti-SARS-CoV-2 IgA and IgM antibodies rapidly decayed, while IgG antibodies remained relatively stable up to 105 days PSO in both biofluids. Lastly, IgG, IgM and to a lesser extent IgA responses to spike and RBD in the serum positively correlated with matched saliva samples. This study confirms that serum and saliva IgG antibodies to SARS-CoV-2 are maintained in the majority of COVID-19 patients for at least 3 months PSO. IgG responses in saliva may serve as a surrogate measure of systemic immunity to SARS-CoV-2 based on their correlation with serum IgG responses.
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Affiliation(s)
- Baweleta Isho
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Kento T Abe
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michelle Zuo
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Alainna J Jamal
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Department of Microbiology, at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Bhavisha Rathod
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jenny H Wang
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Zhijie Li
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gary Chao
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Olga L Rojas
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Yeo Myong Bang
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Annie Pu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | | | - Christian Gervais
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, QC, Canada
| | - Derek Ceccarelli
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Payman Samavarchi-Tehrani
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Furkan Guvenc
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Patrick Budylowski
- Combined Containment Level 3 Unit, University of Toronto, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Angel Li
- Department of Microbiology, at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Aimee Paterson
- Department of Microbiology, at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Feng Yun Yue
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Lina M Marin
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lauren Caldwell
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Karen Colwill
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Molecular Diagnostics, Division of Microbiology, Sunnybrook Health Sciences Centre; Biological Sciences, Sunnybrook Research Institute; and Division of Infectious Diseases, Sunnybrook Health Sciences Centre, Toronto, ON, Canada; Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Combined Containment Level 3 Unit, University of Toronto, Toronto, ON, Canada
| | - Steven J Drews
- Canadian Blood Services, Edmonton, AB & Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Walter L Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Miriam Barrios-Rodiles
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Mario Ostrowski
- Department of Immunology, University of Toronto, Toronto, ON, Canada.,St. Michael's Hospital, Toronto, ON, Canada; Li Ka Shing Knowledge Institute.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - James M Rini
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Yves Durocher
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, QC, Canada
| | - Allison J McGeer
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.,Department of Microbiology, at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | | | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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22
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Isho B, Abe KT, Zuo M, Jamal AJ, Rathod B, Wang JH, Li Z, Chao G, Rojas OL, Bang YM, Pu A, Christie-Holmes N, Gervais C, Ceccarelli D, Samavarchi-Tehrani P, Guvenc F, Budylowski P, Li A, Paterson A, Yue FY, Marin LM, Caldwell L, Wrana JL, Colwill K, Sicheri F, Mubareka S, Gray-Owen SD, Drews SJ, Siqueira WL, Barrios-Rodiles M, Ostrowski M, Rini JM, Durocher Y, McGeer AJ, Gommerman JL, Gingras AC. Persistence of serum and saliva antibody responses to SARS-CoV-2 spike antigens in COVID-19 patients. Sci Immunol 2020; 5:5/52/eabe5511. [PMID: 33033173 PMCID: PMC8050884 DOI: 10.1126/sciimmunol.abe5511] [Citation(s) in RCA: 536] [Impact Index Per Article: 134.0] [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: 08/28/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022]
Abstract
While the antibody response to SARS-CoV-2 has been extensively studied in blood, relatively little is known about the antibody response in saliva and its relationship to systemic antibody levels. Here, we profiled by enzyme-linked immunosorbent assays (ELISAs) IgG, IgA and IgM responses to the SARS-CoV-2 spike protein (full length trimer) and its receptor-binding domain (RBD) in serum and saliva of acute and convalescent patients with laboratory-diagnosed COVID-19 ranging from 3-115 days post-symptom onset (PSO), compared to negative controls. Anti-SARS-CoV-2 antibody responses were readily detected in serum and saliva, with peak IgG levels attained by 16-30 days PSO. Longitudinal analysis revealed that anti-SARS-CoV-2 IgA and IgM antibodies rapidly decayed, while IgG antibodies remained relatively stable up to 105 days PSO in both biofluids. Lastly, IgG, IgM and to a lesser extent IgA responses to spike and RBD in the serum positively correlated with matched saliva samples. This study confirms that serum and saliva IgG antibodies to SARS-CoV-2 are maintained in the majority of COVID-19 patients for at least 3 months PSO. IgG responses in saliva may serve as a surrogate measure of systemic immunity to SARS-CoV-2 based on their correlation with serum IgG responses.
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Affiliation(s)
- Baweleta Isho
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Kento T Abe
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michelle Zuo
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Alainna J Jamal
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Department of Microbiology, at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Bhavisha Rathod
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jenny H Wang
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Zhijie Li
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gary Chao
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Olga L Rojas
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Yeo Myong Bang
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Annie Pu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | | | - Christian Gervais
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, QC, Canada
| | - Derek Ceccarelli
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Payman Samavarchi-Tehrani
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Furkan Guvenc
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Patrick Budylowski
- Combined Containment Level 3 Unit, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Angel Li
- Department of Microbiology, at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Aimee Paterson
- Department of Microbiology, at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Feng Yun Yue
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Lina M Marin
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lauren Caldwell
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Karen Colwill
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Molecular Diagnostics, Division of Microbiology, Sunnybrook Health Sciences Centre; Biological Sciences, Sunnybrook Research Institute; and Division of Infectious Diseases, Sunnybrook Health Sciences Centre, Toronto, ON, Canada; Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Combined Containment Level 3 Unit, University of Toronto, Toronto, ON, Canada
| | - Steven J Drews
- Canadian Blood Services, Edmonton, AB & Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Walter L Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Miriam Barrios-Rodiles
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Mario Ostrowski
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- St. Michael's Hospital, Toronto, ON, Canada; Li Ka Shing Knowledge Institute
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - James M Rini
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Yves Durocher
- Mammalian Cell Expression, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, QC, Canada
| | - Allison J McGeer
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Department of Microbiology, at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | | | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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23
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Wiechmann S, Maisonneuve P, Grebbin BM, Hoffmeister M, Kaulich M, Clevers H, Rajalingam K, Kurinov I, Farin HF, Sicheri F, Ernst A. Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids. J Biol Chem 2020; 295:4526-4540. [PMID: 32086379 DOI: 10.1074/jbc.ra119.011025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 09/11/2019] [Revised: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
The small GTPases H, K, and NRAS are molecular switches indispensable for proper regulation of cellular proliferation and growth. Several mutations in the genes encoding members of this protein family are associated with cancer and result in aberrant activation of signaling processes caused by a deregulated recruitment of downstream effector proteins. In this study, we engineered variants of the Ras-binding domain (RBD) of the C-Raf proto-oncogene, Ser/Thr kinase (CRAF). These variants bound with high affinity with the effector-binding site of Ras in an active conformation. Structural characterization disclosed how the newly identified RBD mutations cooperate and thereby enhance affinity with the effector-binding site in Ras compared with WT RBD. The engineered RBD variants closely mimicked the interaction mode of naturally occurring Ras effectors and acted as dominant-negative affinity reagents that block Ras signal transduction. Experiments with cancer cells showed that expression of these RBD variants inhibits Ras signaling, reducing cell growth and inducing apoptosis. Using these optimized RBD variants, we stratified patient-derived colorectal cancer organoids with known Ras mutational status according to their response to Ras inhibition. These results revealed that the presence of Ras mutations was insufficient to predict sensitivity to Ras inhibition, suggesting that not all of these tumors required Ras signaling for proliferation. In summary, by engineering the Ras/Raf interface of the CRAF-RBD, we identified potent and selective inhibitors of Ras in its active conformation that outcompete binding of Ras-signaling effectors.
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Affiliation(s)
- Svenja Wiechmann
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60596 Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Pierre Maisonneuve
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Britta M Grebbin
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt am Main, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Meike Hoffmeister
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60596 Frankfurt am Main, Germany.,Institute of Biochemistry, Brandenburg Medical School (MHB) Theodor Fontane, 14770 Brandenburg an der Havel, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60596 Frankfurt am Main, Germany.,Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands.,Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands.,Center for Molecular Medicine, Department of Genetics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | | | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439
| | - Henner F Farin
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt am Main, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60596 Frankfurt am Main, Germany .,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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24
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Hill S, Reichermeier K, Scott DC, Samentar L, Coulombe-Huntington J, Izzi L, Tang X, Ibarra R, Bertomeu T, Moradian A, Sweredoski MJ, Caberoy N, Schulman BA, Sicheri F, Tyers M, Kleiger G. Robust cullin-RING ligase function is established by a multiplicity of poly-ubiquitylation pathways. eLife 2019; 8:e51163. [PMID: 31868589 PMCID: PMC6975927 DOI: 10.7554/elife.51163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 08/17/2019] [Accepted: 12/22/2019] [Indexed: 12/24/2022] Open
Abstract
The cullin-RING ligases (CRLs) form the major family of E3 ubiquitin ligases. The prototypic CRLs in yeast, called SCF enzymes, employ a single E2 enzyme, Cdc34, to build poly-ubiquitin chains required for degradation. In contrast, six different human E2 and E3 enzyme activities, including Cdc34 orthologs UBE2R1 and UBE2R2, appear to mediate SCF-catalyzed substrate polyubiquitylation in vitro. The combinatorial interplay of these enzymes raises questions about genetic buffering of SCFs in human cells and challenges the dogma that E3s alone determine substrate specificity. To enable the quantitative comparisons of SCF-dependent ubiquitylation reactions with physiological enzyme concentrations, mass spectrometry was employed to estimate E2 and E3 levels in cells. In combination with UBE2R1/2, the E2 UBE2D3 and the E3 ARIH1 both promoted SCF-mediated polyubiquitylation in a substrate-specific fashion. Unexpectedly, UBE2R2 alone had negligible ubiquitylation activity at physiological concentrations and the ablation of UBE2R1/2 had no effect on the stability of SCF substrates in cells. A genome-wide CRISPR screen revealed that an additional E2 enzyme, UBE2G1, buffers against the loss of UBE2R1/2. UBE2G1 had robust in vitro chain extension activity with SCF, and UBE2G1 knockdown in cells lacking UBE2R1/2 resulted in stabilization of the SCF substrates p27 and CYCLIN E as well as the CUL2-RING ligase substrate HIF1α. The results demonstrate the human SCF enzyme system is diversified by association with multiple catalytic enzyme partners.
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Affiliation(s)
- Spencer Hill
- Department of Chemistry and BiochemistryUniversity of NevadaLas VegasUnited States
| | - Kurt Reichermeier
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Department of Discovery ProteomicsGenentech IncSouth San FranciscoUnited States
- Department of Discovery OncologyGenentech IncSouth San FranciscoUnited States
| | - Daniel C Scott
- Department of Structural BiologySt Jude Children's Research HospitalMemphisUnited States
| | - Lorena Samentar
- School of Life SciencesUniversity of NevadaLas VegasUnited States
- University of the PhilippinesIloiloPhilippines
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Luisa Izzi
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Xiaojing Tang
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
| | - Rebeca Ibarra
- Department of Chemistry and BiochemistryUniversity of NevadaLas VegasUnited States
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Annie Moradian
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman InstituteCalifornia Institute of TechnologyPasadenaUnited States
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman InstituteCalifornia Institute of TechnologyPasadenaUnited States
| | - Nora Caberoy
- School of Life SciencesUniversity of NevadaLas VegasUnited States
| | - Brenda A Schulman
- Max Planck Institute of Biochemistry, Molecular Machines and SignalingMartinsriedGermany
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Gary Kleiger
- Department of Chemistry and BiochemistryUniversity of NevadaLas VegasUnited States
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25
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Teyra J, Ernst A, Singer A, Sicheri F, Sidhu SS. Comprehensive analysis of all evolutionary paths between two divergent PDZ domain specificities. Protein Sci 2019; 29:433-442. [PMID: 31654425 DOI: 10.1002/pro.3759] [Citation(s) in RCA: 10] [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: 08/21/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
Abstract
To understand the molecular evolution of functional diversity in protein families, we comprehensively investigated the consequences of all possible mutation combinations separating two peptide-binding domains with highly divergent specificities. We analyzed the Erbin PDZ domain (Erbin-PDZ), which exhibits canonical type I specificity, and a synthetic Erbin-PDZ variant (E-14) that differs at six positions and exhibits an atypical specificity that closely resembles that of the natural Pdlim4 PDZ domain (Pdlim4-PDZ). We constructed a panel of 64 PDZ domains covering all possible transitions between Erbin-PDZ and E-14 (i.e., the panel contained variants with all possible combinations of either the Erbin-PDZ or E-14 sequence at the six differing positions). We assessed the specificity profiles of the 64 PDZ domains using a C-terminal phage-displayed peptide library containing all possible genetically encoded heptapeptides. The specificity profiles clustered into six distinct groups, showing that intermediate domains can be nodes for the evolution of divergent functions. Remarkably, three substitutions were sufficient to convert the specificity of Erbin-PDZ to that of Pdlim4-PDZ, whereas Pdlim4-PDZ contains 71 differences relative to Erbin-PDZ. X-ray crystallography revealed the structural basis for specificity transition: a single substitution in the center of the binding site, supported by contributions from auxiliary substitutions, altered the main chain conformation of the peptide ligand to resemble that of ligands bound to Pdlim4-PDZ. Our results show that a very small set of mutations can dramatically alter protein specificity, and these findings support the hypothesis whereby complex protein functions evolve by gene duplication followed by cumulative mutations.
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Affiliation(s)
- Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Andreas Ernst
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
| | - Alex Singer
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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26
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Assadieskandar A, Yu C, Maisonneuve P, Kurinov I, Sicheri F, Zhang C. Rigidification Dramatically Improves Inhibitor Selectivity for RAF Kinases. ACS Med Chem Lett 2019; 10:1074-1080. [PMID: 31312411 DOI: 10.1021/acsmedchemlett.9b00194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/04/2019] [Indexed: 12/18/2022] Open
Abstract
One effective means to achieve inhibitor specificity for RAF kinases, an important family of cancer drug targets, has been to target the monomeric inactive state conformation of the kinase domain, which, unlike most other kinases, can accommodate sulfonamide-containing drugs such as vemurafenib and dabrafenib because of the presence of a unique pocket specific to inactive RAF kinases. We previously reported an alternate strategy whereby rigidification of a nonselective pyrazolo[3,4-d]pyrimidine-based inhibitor through ring closure afforded moderate but appreciable increases in selectivity for RAF kinases. Here, we show that a further application of the rigidification strategy to a different pyrazolopyrimidine-based scaffold dramatically improved selectivity for RAF kinases. Crystal structure analysis confirmed our inhibitor design hypothesis revealing that 2l engages an active-like state conformation of BRAF normally associated with poorly discriminating inhibitors. When screened against a panel of distinct cancer cell lines, the optimized inhibitor 2l primarily inhibited the proliferation of the expected BRAFV600E-harboring cell lines consistent with its kinome selectivity profile. These results suggest that rigidification could be a general and powerful strategy for enhancing inhibitor selectivity against protein kinases, which may open up therapeutic opportunities not afforded by other approaches.
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Affiliation(s)
- Amir Assadieskandar
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Caiqun Yu
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Pierre Maisonneuve
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5 Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, United States
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5 Canada
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Chao Zhang
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, United States
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27
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Ceccarelli DF, Ivantsiv S, Mullin AA, Coyaud E, Manczyk N, Maisonneuve P, Kurinov I, Zhao L, Go C, Gingras AC, Raught B, Cordes S, Sicheri F. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Structure 2019; 27:1000-1012.e6. [PMID: 31056421 DOI: 10.1016/j.str.2019.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 11/07/2018] [Revised: 02/23/2019] [Accepted: 03/27/2019] [Indexed: 12/16/2022]
Abstract
Pseudoenzymes have been identified across a diverse range of enzyme classes and fulfill important cellular functions. Examples of pseudoenzymes exist within ubiquitin conjugating and deubiquitinase (DUB) protein families. Here we characterize FAM105A/OTULINL, the only putative pseudodeubiquitinase of the ovarian tumor protease (OTU domain) family in humans. The crystal structure of FAM105A revealed that the OTU domain possesses structural deficiencies in both active site and substrate-binding infrastructure predicted to impair normal DUB function. We confirmed the absence of catalytic function against all ubiquitin linkages and an inability of FAM105A to bind ubiquitin compared with catalytically active FAM105B/OTULIN. FAM105A co-localized with KDEL markers and Lamin B1 at the endoplasmic reticulum (ER) and nuclear envelope, respectively. Accordingly, the FAM105A interactome exhibited significant enrichment in proteins localized to the ER/outer nuclear, Golgi and vesicular membranes. In light of undetectable deubiquitinase activity, we posit that FAM105A/OTULINL functions through its ability to mediate protein-protein interactions.
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Affiliation(s)
- Derek F Ceccarelli
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Sofiia Ivantsiv
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amber Anne Mullin
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Noah Manczyk
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Pierre Maisonneuve
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL 60439, USA
| | - Liang Zhao
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Chris Go
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Sabine Cordes
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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28
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Manczyk N, Veggiani G, Gish GD, Yates BP, Ernst A, Sidhu SS, Sicheri F. Dimerization of a ubiquitin variant leads to high affinity interactions with a ubiquitin interacting motif. Protein Sci 2019; 28:848-856. [PMID: 30793400 DOI: 10.1002/pro.3593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 01/03/2019] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 11/06/2022]
Abstract
We previously described structural and functional characterization of the first ubiquitin variant (UbV), UbV.v27.1, engineered by phage display to bind with high affinity to a specific ubiquitin interacting motif (UIM). We identified two substitutions relative to ubiquitin (Gly10Val/His68Tyr) that were critical for enhancing binding affinity but could only rationalize the mechanism of action of the Tyr68 substitution. Here, we extend our characterization and uncover the mechanism by which the Val10 substitution enhances binding affinity. We show that Val10 in UbV.v27.1 drives UbV dimerization through an intermolecular β-strand exchange. Dimerization serves to increase the contact surface between the UIM and UbV and also affords direct contacts between two UIMs through an overall 2:2 binding stoichiometry. Our identification of the role of Val10 in UbV dimerization suggests a general means for the development of dimeric UbVs with improved affinity and specificity relative to their monomeric UbV counterparts. Statement: Previously, we used phage display to engineer a UbV that bound tightly and specifically to a UIM. Here, we discovered that tight binding is partly due to the dimerization of the UbV, which increases the contact surface between the UbV and UIM. We show that UbV dimerization is dependent on the Gly10Val substitution, and posit that dimerization may provide a general means for engineering UbVs with improved binding properties.
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Affiliation(s)
- Noah Manczyk
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Gianluca Veggiani
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, M5S 3E1 Toronto, Ontario, Canada
| | - Gerald D Gish
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Bradley P Yates
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, M5S 3E1 Toronto, Ontario, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Goethe University, Frankfurt am Main 60590, Germany
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, M5S 3E1 Toronto, Ontario, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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29
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Pascoe N, Seetharaman A, Teyra J, Manczyk N, Satori MA, Tjandra D, Makhnevych T, Schwerdtfeger C, Brasher BB, Moffat J, Costanzo M, Boone C, Sicheri F, Sidhu SS. Yeast Two-Hybrid Analysis for Ubiquitin Variant Inhibitors of Human Deubiquitinases. J Mol Biol 2019; 431:1160-1171. [PMID: 30763569 DOI: 10.1016/j.jmb.2019.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 07/25/2018] [Revised: 02/01/2019] [Accepted: 02/06/2019] [Indexed: 11/20/2022]
Abstract
We applied a yeast-two-hybrid (Y2H) analysis to screen for ubiquitin variant (UbV) inhibitors of a human deubiquitinase (DUB), ubiquitin-specific protease 2 (USP2). The Y2H screen used USP2 as the bait and a prey library consisting of UbVs randomized at four specific positions, which were known to interact with USP2 from phage display analysis. The screen yielded numerous UbVs that bound to USP2 both as a Y2H interaction in vivo and as purified proteins in vitro. The Y2H-derived UbVs inhibited the catalytic activity of USP2 in vitro with nanomolar-range potencies, and they bound and inhibited USP2 in human cells. Mutational and structural analysis showed that potent and selective inhibition could be achieved by just two substitutions in a UbV, which exhibited improved hydrophobic and hydrophilic contacts compared to the wild-type ubiquitin interaction with USP2. Our results establish Y2H as an effective platform for the development of UbV inhibitors of DUBs in vivo, providing an alternative strategy for the analysis of DUBs that are recalcitrant to phage display and other in vitro methods.
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Affiliation(s)
- Natasha Pascoe
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Ashwin Seetharaman
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Joan Teyra
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Maria Augusta Satori
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Donna Tjandra
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | - Taras Makhnevych
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada
| | | | - Bradley B Brasher
- Boston Biochem, a Bio-Techne Brand 840 Memorial Drive, Cambridge, MA 02139, USA
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON, M5G1Z8, Canada
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON, M5G1Z8, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Canadian Institute for Advanced Research, Toronto, ON, M5G1Z8, Canada
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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30
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Teyra J, Singer AU, Schmitges FW, Jaynes P, Kit Leng Lui S, Polyak MJ, Fodil N, Krieger JR, Tong J, Schwerdtfeger C, Brasher BB, Ceccarelli DFJ, Moffat J, Sicheri F, Moran MF, Gros P, Eichhorn PJA, Lenter M, Boehmelt G, Sidhu SS. Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Structure 2019; 27:590-605.e5. [PMID: 30713027 DOI: 10.1016/j.str.2019.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/23/2018] [Accepted: 12/31/2018] [Indexed: 12/12/2022]
Abstract
The multi-domain deubiquitinase USP15 regulates diverse eukaryotic processes and has been implicated in numerous diseases. We developed ubiquitin variants (UbVs) that targeted either the catalytic domain or each of three adaptor domains in USP15, including the N-terminal DUSP domain. We also designed a linear dimer (diUbV), which targeted the DUSP and catalytic domains, and exhibited enhanced specificity and more potent inhibition of catalytic activity than either UbV alone. In cells, the UbVs inhibited the deubiquitination of two USP15 substrates, SMURF2 and TRIM25, and the diUbV inhibited the effects of USP15 on the transforming growth factor β pathway. Structural analyses revealed that three distinct UbVs bound to the catalytic domain and locked the active site in a closed, inactive conformation, and one UbV formed an unusual strand-swapped dimer and bound two DUSP domains simultaneously. These inhibitors will enable the study of USP15 function in oncology, neurology, immunology, and inflammation.
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Affiliation(s)
- Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Alex U Singer
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frank W Schmitges
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sarah Kit Leng Lui
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Maria J Polyak
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Nassima Fodil
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Jonathan R Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jiefei Tong
- Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | | | - Bradley B Brasher
- Boston Biochem, a Bio-Techne Brand, 840 Memorial Drive, Cambridge, MA 02139, USA
| | - Derek F J Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael F Moran
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Pieter J A Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Martin Lenter
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | | | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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31
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Gayden T, Sepulveda FE, Khuong-Quang DA, Pratt J, Valera ET, Garrigue A, Kelso S, Sicheri F, Mikael LG, Hamel N, Bajic A, Dali R, Deshmukh S, Dervovic D, Schramek D, Guerin F, Taipale M, Nikbakht H, Majewski J, Moshous D, Charlebois J, Abish S, Bole-Feysot C, Nitschke P, Bader-Meunier B, Mitchell D, Thieblemont C, Battistella M, Gravel S, Nguyen VH, Conyers R, Diana JS, McCormack C, Prince HM, Besnard M, Blanche S, Ekert PG, Fraitag S, Foulkes WD, Fischer A, Neven B, Michonneau D, de Saint Basile G, Jabado N. Author Correction: Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome. Nat Genet 2018; 51:196. [PMID: 30429576 DOI: 10.1038/s41588-018-0304-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article originally published, the main-text sentence "In three patients of European ancestry, we identified the germline variant encoding p.Ile97Met in TIM-3, which was homozygous in two (P12 and P13) and heterozygous in one (P15) in the germline but with no TIM-3 plasma membrane expression in the tumor" misstated the identifiers of the two homozygous individuals, which should have been P13 and P14. The error has been corrected in the HTML, PDF and print versions of the paper.
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Affiliation(s)
- Tenzin Gayden
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Fernando E Sepulveda
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM U1163, Institut Imagine, and Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Dong-Anh Khuong-Quang
- Children's Cancer Center, The Royal Children's Hospital and Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Pediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Jonathan Pratt
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Elvis T Valera
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Alexandrine Garrigue
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM U1163, Institut Imagine, and Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Susan Kelso
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Leonie G Mikael
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Nancy Hamel
- Cancer Research Program, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Andrea Bajic
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Rola Dali
- Canadian Centre for Computational Genomics, Montreal, Quebec, Canada
| | - Shriya Deshmukh
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Dzana Dervovic
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Daniel Schramek
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frédéric Guerin
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM U1163, Institut Imagine, and Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hamid Nikbakht
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Canadian Centre for Computational Genomics, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Despina Moshous
- Department of Pediatric Immunology and Hematology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Janie Charlebois
- Division of Hematology and Oncology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Sharon Abish
- Division of Hematology and Oncology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Patrick Nitschke
- Plateforme de Bioinformatique, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
| | - Brigitte Bader-Meunier
- Department of Pediatric Immunology and Hematology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - David Mitchell
- Division of Hematology and Oncology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Catherine Thieblemont
- Hematology and Oncology Unit, Saint Louis Hospital, Paris, France.,Paris Diderot University, Université Sorbonne Paris Cité, Paris, France
| | - Maxime Battistella
- Paris Diderot University, Université Sorbonne Paris Cité, Paris, France.,Cytology and Pathology Laboratory, Saint Louis Hospital, Paris, France
| | - Simon Gravel
- McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Van-Hung Nguyen
- Department of Pathology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Rachel Conyers
- Children's Cancer Center, The Royal Children's Hospital and Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Pediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Jean-Sebastien Diana
- Department of Pediatric Immunology and Hematology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Chris McCormack
- Department of Surgical Oncology, Peter MacCallum Cancer Institute, University of Melbourne, Melbourne, Victoria, Australia.,Department of Dermatology, St. Vincent's Hospital, Fitzroy, Victoria, Australia
| | - H Miles Prince
- Epworth Healthcare, Melbourne, Victoria, Australia.,Department of Medical Oncology, Sir Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia
| | - Marianne Besnard
- Department of Neonatology, Centre Hospitalier de Polynésie Française, Papeete, French Polynesia
| | - Stephane Blanche
- Department of Pediatric Immunology and Hematology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Paul G Ekert
- Children's Cancer Center, The Royal Children's Hospital and Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Pediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Sylvie Fraitag
- Department of Anatomy and Cytology/Pathology, Centre Hospitalier Universitaire Paris, Hôpital Necker-Enfants Malades, Paris, France
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Alain Fischer
- Department of Pediatric Immunology and Hematology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,Collège de France, Paris, France.,INSERM U1163, Institut Imagine and Université Paris Descartes -Sorbonne Paris Cité, Paris, France
| | - Bénédicte Neven
- Department of Pediatric Immunology and Hematology, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,INSERM U1163, Institut Imagine and Université Paris Descartes -Sorbonne Paris Cité, Paris, France
| | - David Michonneau
- Paris Diderot University, Université Sorbonne Paris Cité, Paris, France.,Hematology and Transplantation Unit, Saint Louis Hospital, Paris, France
| | - Geneviève de Saint Basile
- Laboratory of Normal and Pathological Homeostasis of the Immune System, INSERM U1163, Institut Imagine, and Université Paris Descartes-Sorbonne Paris Cité, Paris, France. .,Centre d'Etudes des Déficits Immunitaires, Centre Hospitalier Universitaire Paris, Hôpital Necker-Enfants Malades, Paris, France.
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,Department of Pediatrics, McGill University, Montreal, Quebec, Canada. .,Research Institute, McGill University Health Centre, Montreal, Quebec, Canada.
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32
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Gayden T, Sepulveda FE, Khuong-Quang DA, Pratt J, Valera ET, Garrigue A, Kelso S, Sicheri F, Mikael LG, Hamel N, Bajic A, Dali R, Deshmukh S, Dervovic D, Schramek D, Guerin F, Taipale M, Nikbakht H, Majewski J, Moshous D, Charlebois J, Abish S, Bole-Feysot C, Nitschke P, Bader-Meunier B, Mitchell D, Thieblemont C, Battistella M, Gravel S, Nguyen VH, Conyers R, Diana JS, McCormack C, Prince HM, Besnard M, Blanche S, Ekert PG, Fraitag S, Foulkes WD, Fischer A, Neven B, Michonneau D, de Saint Basile G, Jabado N. Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome. Nat Genet 2018; 50:1650-1657. [DOI: 10.1038/s41588-018-0251-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
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33
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Daou S, Barbour H, Ahmed O, Masclef L, Baril C, Sen Nkwe N, Tchelougou D, Uriarte M, Bonneil E, Ceccarelli D, Mashtalir N, Tanji M, Masson JY, Thibault P, Sicheri F, Yang H, Carbone M, Therrien M, Affar EB. Monoubiquitination of ASXLs controls the deubiquitinase activity of the tumor suppressor BAP1. Nat Commun 2018; 9:4385. [PMID: 30349006 PMCID: PMC6197237 DOI: 10.1038/s41467-018-06854-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 12/18/2017] [Accepted: 09/19/2018] [Indexed: 12/21/2022] Open
Abstract
The tumor suppressor and deubiquitinase (DUB) BAP1 and its Drosophila ortholog Calypso assemble DUB complexes with the transcription regulators Additional sex combs-like (ASXL1, ASXL2, ASXL3) and Asx respectively. ASXLs and Asx use their DEUBiquitinase ADaptor (DEUBAD) domain to stimulate BAP1/Calypso DUB activity. Here we report that monoubiquitination of the DEUBAD is a general feature of ASXLs and Asx. BAP1 promotes DEUBAD monoubiquitination resulting in an increased stability of ASXL2, which in turn stimulates BAP1 DUB activity. ASXL2 monoubiquitination is directly catalyzed by UBE2E family of Ubiquitin-conjugating enzymes and regulates mammalian cell proliferation. Remarkably, Calypso also regulates Asx monoubiquitination and transgenic flies expressing monoubiquitination-defective Asx mutant exhibit developmental defects. Finally, the protein levels of ASXL2, BAP1 and UBE2E enzymes are highly correlated in mesothelioma tumors suggesting the importance of this signaling axis for tumor suppression. We propose that monoubiquitination orchestrates a molecular symbiosis relationship between ASXLs and BAP1.
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Affiliation(s)
- Salima Daou
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Haithem Barbour
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Oumaima Ahmed
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Louis Masclef
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Caroline Baril
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Nadine Sen Nkwe
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Daméhan Tchelougou
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Maxime Uriarte
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Laboratory of Proteomics and Bioanalytical Mass Spectrometry, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Derek Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Nazar Mashtalir
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Mika Tanji
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Jean-Yves Masson
- CHU de Quebec Research Center (Oncology Axis), Laval University Cancer Research Center, 9 McMahon, Quebec, PQ, G1R 2J6, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Laboratory of Proteomics and Bioanalytical Mass Spectrometry, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Haining Yang
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Michele Carbone
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, University of Montréal, Montréal, QC, H3T 1J4, Canada. .,Département de pathologie et biologie cellulaire, University of Montréal, Montréal, QC, H3C 3J7, Canada.
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada.
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Hunter RW, Hughey CC, Lantier L, Sundelin EI, Peggie M, Zeqiraj E, Sicheri F, Jessen N, Wasserman DH, Sakamoto K. Metformin reduces liver glucose production by inhibition of fructose-1-6-bisphosphatase. Nat Med 2018; 24:1395-1406. [PMID: 30150719 PMCID: PMC6207338 DOI: 10.1038/s41591-018-0159-7] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [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: 02/08/2016] [Accepted: 07/24/2018] [Indexed: 01/03/2023]
Abstract
Metformin is a first-line drug for the treatment of individuals with type 2 diabetes, yet its precise mechanism of action remains unclear. Metformin exerts its antihyperglycemic action primarily through lowering hepatic glucose production (HGP). This suppression is thought to be mediated through inhibition of mitochondrial respiratory complex I, and thus elevation of 5'-adenosine monophosphate (AMP) levels and the activation of AMP-activated protein kinase (AMPK), though this proposition has been challenged given results in mice lacking hepatic AMPK. Here we report that the AMP-inhibited enzyme fructose-1,6-bisphosphatase-1 (FBP1), a rate-controlling enzyme in gluconeogenesis, functions as a major contributor to the therapeutic action of metformin. We identified a point mutation in FBP1 that renders it insensitive to AMP while sparing regulation by fructose-2,6-bisphosphate (F-2,6-P2), and knock-in (KI) of this mutant in mice significantly reduces their response to metformin treatment. We observe this during a metformin tolerance test and in a metformin-euglycemic clamp that we have developed. The antihyperglycemic effect of metformin in high-fat diet-fed diabetic FBP1-KI mice was also significantly blunted compared to wild-type controls. Collectively, we show a new mechanism of action for metformin and provide further evidence that molecular targeting of FBP1 can have antihyperglycemic effects.
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Affiliation(s)
- Roger W Hunter
- Nestlé Institute of Health Sciences SA, Lausanne, Switzerland
- School of Physiology, Pharmacology & Neuroscience, University of Bristol, Bristol, UK
| | - Curtis C Hughey
- Department of Molecular Physiology and Biophysics and the Vanderbilt Mouse Metabolic Phenotyping Center, Vanderbilt University, Nashville, TN, USA
| | - Louise Lantier
- Department of Molecular Physiology and Biophysics and the Vanderbilt Mouse Metabolic Phenotyping Center, Vanderbilt University, Nashville, TN, USA
| | - Elias I Sundelin
- Departments of Clinical Medicine and Biomedicine, Aarhus University, Aarhus, Denmark
| | - Mark Peggie
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Elton Zeqiraj
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Niels Jessen
- Departments of Clinical Medicine and Biomedicine, Aarhus University, Aarhus, Denmark
| | - David H Wasserman
- Department of Molecular Physiology and Biophysics and the Vanderbilt Mouse Metabolic Phenotyping Center, Vanderbilt University, Nashville, TN, USA
| | - Kei Sakamoto
- Nestlé Institute of Health Sciences SA, Lausanne, Switzerland.
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35
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Gill MK, Christova T, Zhang YY, Gregorieff A, Zhang L, Narimatsu M, Song S, Xiong S, Couzens AL, Tong J, Krieger JR, Moran MF, Zlotta AR, van der Kwast TH, Gingras AC, Sicheri F, Wrana JL, Attisano L. A feed forward loop enforces YAP/TAZ signaling during tumorigenesis. Nat Commun 2018; 9:3510. [PMID: 30158528 PMCID: PMC6115388 DOI: 10.1038/s41467-018-05939-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [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: 11/07/2017] [Accepted: 07/30/2018] [Indexed: 12/13/2022] Open
Abstract
In most solid tumors, the Hippo pathway is inactivated through poorly understood mechanisms that result in the activation of the transcriptional regulators, YAP and TAZ. Here, we identify NUAK2 as a YAP/TAZ activator that directly inhibits LATS-mediated phosphorylation of YAP/TAZ and show that NUAK2 induction by YAP/TAZ and AP-1 is required for robust YAP/TAZ signaling. Pharmacological inhibition or loss of NUAK2 reduces the growth of cultured cancer cells and mammary tumors in mice. Moreover, in human patient samples, we show that NUAK2 expression is elevated in aggressive, high-grade bladder cancer and strongly correlates with a YAP/TAZ gene signature. These findings identify a positive feed forward loop in the Hippo pathway that establishes a key role for NUAK2 in enforcing the tumor-promoting activities of YAP/TAZ. Our results thus introduce a new opportunity for cancer therapeutics by delineating NUAK2 as a potential target for re-engaging the Hippo pathway. The Hippo pathway is frequently dysregulated in cancer. Here, the authors identify NUAK2 as negative regulator of the Hippo pathway from a siRNA kinome screen and show that NUAK2 promotes YAP/TAZ nuclear localisation while NUAK2 is a transcriptional target of YAP/TAZ, thus providing a feed forward loop to promote tumorigenesis.
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Affiliation(s)
- Mandeep K Gill
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Tania Christova
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ying Y Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Alex Gregorieff
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.,Department of Pathology, McGill University and Research Institute of the McGill University Health Center, Montreal, H4A 3J1, QC, Canada
| | - Liang Zhang
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 999077, Hong Kong, China.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong, 518057, China
| | - Masahiro Narimatsu
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Siyuan Song
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Shawn Xiong
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Amber L Couzens
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Jiefei Tong
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Jonathan R Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Michael F Moran
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Program in Cell Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Alexandre R Zlotta
- Department of Surgery, Division of Urology, University of Toronto, Mount Sinai Hospital and University Health Network, Toronto, M5G 1X5, ON, Canada
| | - Theodorus H van der Kwast
- Department of Pathology, Toronto General Hospital, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Frank Sicheri
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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36
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Koszela J, Pham NT, Evans D, Mann S, Perez-Pi I, Shave S, Ceccarelli DFJ, Sicheri F, Tyers M, Auer M. Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay. BMC Biol 2018; 16:88. [PMID: 30097011 PMCID: PMC6086040 DOI: 10.1186/s12915-018-0554-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 03/12/2018] [Accepted: 07/24/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and their modulators remains a challenge. Here, we report a broadly applicable, multiplexed, miniaturized on-bead technique for real-time monitoring of various ubiquitination-related enzymatic activities. The assay, termed UPS-confocal fluorescence nanoscanning (UPS-CONA), employs a substrate of interest immobilized on a micro-bead and a fluorescently labeled ubiquitin which, upon enzymatic conjugation to the substrate, is quantitatively detected on the bead periphery by confocal imaging. RESULTS UPS-CONA is suitable for studying individual enzymatic activities, including various E1, E2, and HECT-type E3 enzymes, and for monitoring multi-step reactions within ubiquitination cascades in a single experimental compartment. We demonstrate the power of the UPS-CONA technique by simultaneously following ubiquitin transfer from Ube1 through Ube2L3 to E6AP. We applied this multi-step setup to investigate the selectivity of five ubiquitination inhibitors reportedly targeting different classes of ubiquitination enzymes. Using UPS-CONA, we have identified a new activity of a small molecule E2 inhibitor, BAY 11-7082, and of a HECT E3 inhibitor, heclin, towards the Ube1 enzyme. CONCLUSIONS As a sensitive, quantitative, flexible, and reagent-efficient method with a straightforward protocol, UPS-CONA constitutes a powerful tool for interrogation of ubiquitination-related enzymatic pathways and their chemical modulators, and is readily scalable for large experiments.
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Affiliation(s)
- Joanna Koszela
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Nhan T. Pham
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - David Evans
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Stefan Mann
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Irene Perez-Pi
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Steven Shave
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Derek F. J. Ceccarelli
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, Ontario M5G 1X5 Canada
| | - Frank Sicheri
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, Ontario M5G 1X5 Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7 Canada
| | - Manfred Auer
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
- Biomedical Sciences, Medical School, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
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37
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Xiong S, Lorenzen K, Couzens AL, Templeton CM, Rajendran D, Mao DYL, Juang YC, Chiovitti D, Kurinov I, Guettler S, Gingras AC, Sicheri F. Structural Basis for Auto-Inhibition of the NDR1 Kinase Domain by an Atypically Long Activation Segment. Structure 2018; 26:1101-1115.e6. [PMID: 29983373 PMCID: PMC6087429 DOI: 10.1016/j.str.2018.05.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/28/2018] [Accepted: 05/17/2018] [Indexed: 11/27/2022]
Abstract
The human NDR family kinases control diverse aspects of cell growth, and are regulated through phosphorylation and association with scaffolds such as MOB1. Here, we report the crystal structure of the human NDR1 kinase domain in its non-phosphorylated state, revealing a fully resolved atypically long activation segment that blocks substrate binding and stabilizes a non-productive position of helix αC. Consistent with an auto-inhibitory function, mutations within the activation segment of NDR1 dramatically enhance in vitro kinase activity. Interestingly, NDR1 catalytic activity is further potentiated by MOB1 binding, suggesting that regulation through modulation of the activation segment and by MOB1 binding are mechanistically distinct. Lastly, deleting the auto-inhibitory activation segment of NDR1 causes a marked increase in the association with upstream Hippo pathway components and the Furry scaffold. These findings provide a point of departure for future efforts to explore the cellular functions and the mechanism of NDR1.
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MESH Headings
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Binding Sites
- Cell Cycle Proteins
- Cell Line, Tumor
- Cloning, Molecular
- Crystallography, X-Ray
- Epithelial Cells/cytology
- Epithelial Cells/enzymology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Gene Expression Regulation
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HEK293 Cells
- Hepatocyte Growth Factor/chemistry
- Hepatocyte Growth Factor/genetics
- Hepatocyte Growth Factor/metabolism
- Humans
- Kinetics
- Microtubule-Associated Proteins/chemistry
- Microtubule-Associated Proteins/genetics
- Microtubule-Associated Proteins/metabolism
- Models, Molecular
- Mutation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Serine-Threonine Kinases/chemistry
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/chemistry
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Serine-Threonine Kinase 3
- Signal Transduction
- Substrate Specificity
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Affiliation(s)
- Shawn Xiong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kristina Lorenzen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Amber L Couzens
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Catherine M Templeton
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Dushyandi Rajendran
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Daniel Y L Mao
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Yu-Chi Juang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - David Chiovitti
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Igor Kurinov
- Cornell University, Department of Chemistry and Chemical Biology, NE-CAT, Advanced Photon Source, Bldg. 436E, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK.
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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38
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Gorelik M, Manczyk N, Pavlenco A, Kurinov I, Sidhu SS, Sicheri F. A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases. Structure 2018; 26:1226-1236.e3. [PMID: 30033217 DOI: 10.1016/j.str.2018.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 01/09/2018] [Revised: 04/23/2018] [Accepted: 06/08/2018] [Indexed: 12/29/2022]
Abstract
Skp1-Cul1-F-box (SCF) E3 ligases constitute the largest and best-characterized family of the multisubunit E3 ligases with important cellular functions and numerous disease links. The specificity of an SCF E3 ligase is established by one of the 69 human F-box proteins that are recruited to Cul1 through the Skp1 adaptor. We previously reported generation of ubiquitin variants (UbVs) targeting Fbw7 and Fbw11, which inhibit ligase activity by binding at the F-box-Skp1 interface to competitively displace Cul1. In the present study, we employed an optimized engineering strategy to generate specific binding UbVs against 17 additional Skp1-F-box complexes. We validated our design strategy and uncovered the structural basis of binding specificity by crystallographic analyses of representative UbVs bound to Skp1-Fbl10 and Skp1-Fbl11. Our study highlights the power of combining phage display with structure-based design to develop UbVs targeting specific protein surfaces.
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Affiliation(s)
- Maryna Gorelik
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Noah Manczyk
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alevtina Pavlenco
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, Argonne, IL 60439, USA
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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39
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Zhao N, Cao J, Xu L, Tang Q, Dobrolecki LE, Lv X, Talukdar M, Lu Y, Wang X, Hu DZ, Shi Q, Xiang Y, Wang Y, Liu X, Bu W, Jiang Y, Li M, Gong Y, Sun Z, Ying H, Yuan B, Lin X, Feng XH, Hartig SM, Li F, Shen H, Chen Y, Han L, Zeng Q, Patterson JB, Kaipparettu BA, Putluri N, Sicheri F, Rosen JM, Lewis MT, Chen X. Pharmacological targeting of MYC-regulated IRE1/XBP1 pathway suppresses MYC-driven breast cancer. J Clin Invest 2018; 128:1283-1299. [PMID: 29480818 DOI: 10.1172/jci95873] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/16/2018] [Indexed: 12/20/2022] Open
Abstract
The unfolded protein response (UPR) is a cellular homeostatic mechanism that is activated in many human cancers and plays pivotal roles in tumor progression and therapy resistance. However, the molecular mechanisms for UPR activation and regulation in cancer cells remain elusive. Here, we show that oncogenic MYC regulates the inositol-requiring enzyme 1 (IRE1)/X-box binding protein 1 (XBP1) branch of the UPR in breast cancer via multiple mechanisms. We found that MYC directly controls IRE1 transcription by binding to its promoter and enhancer. Furthermore, MYC forms a transcriptional complex with XBP1, a target of IRE1, and enhances its transcriptional activity. Importantly, we demonstrate that XBP1 is a synthetic lethal partner of MYC. Silencing of XBP1 selectively blocked the growth of MYC-hyperactivated cells. Pharmacological inhibition of IRE1 RNase activity with small molecule inhibitor 8866 selectively restrained the MYC-overexpressing tumor growth in vivo in a cohort of preclinical patient-derived xenograft models and genetically engineered mouse models. Strikingly, 8866 substantially enhanced the efficacy of docetaxel chemotherapy, resulting in rapid regression of MYC-overexpressing tumors. Collectively, these data establish the synthetic lethal interaction of the IRE1/XBP1 pathway with MYC hyperactivation and provide a potential therapy for MYC-driven human breast cancers.
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Affiliation(s)
- Na Zhao
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jin Cao
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Longyong Xu
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lacey E Dobrolecki
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Xiangdong Lv
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Manisha Talukdar
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yang Lu
- Department of Molecular and Cellular Biology.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Xiaoran Wang
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Dorothy Z Hu
- Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Qing Shi
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Yunfei Wang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xia Liu
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Wen Bu
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and
| | - Yi Jiang
- Division of Biochemical Genetics, Baylor Genetics, Houston, Texas, USA
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yingyun Gong
- Department of Molecular and Cellular Biology.,Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Zheng Sun
- Department of Molecular and Cellular Biology.,Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Haoqiang Ying
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bo Yuan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xia Lin
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Xin-Hua Feng
- Department of Molecular and Cellular Biology.,Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China.,Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | | | - Feng Li
- Department of Molecular and Cellular Biology
| | - Haifa Shen
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, Texas, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Qingping Zeng
- Fosun Orinove PharmaTech Inc., Suzhou, Jiangsu, China
| | | | | | | | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey M Rosen
- Department of Molecular and Cellular Biology.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Michael T Lewis
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology.,Lester and Sue Smith Breast Center, and.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
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40
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Lavoie H, Sahmi M, Maisonneuve P, Marullo SA, Thevakumaran N, Jin T, Kurinov I, Sicheri F, Therrien M. MEK drives BRAF activation through allosteric control of KSR proteins. Nature 2018; 554:549-553. [PMID: 29433126 DOI: 10.1038/nature25478] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 12/22/2017] [Indexed: 01/29/2023]
Abstract
RAF family kinases have prominent roles in cancer. Their activation is dependent on dimerization of their kinase domains, which has emerged as a hindrance for drug development. In mammals, RAF family kinases include three catalytically competent enzymes (ARAF, BRAF and CRAF) and two pseudokinases (KSR1 and KSR2) that have been described as scaffolds owing to their apparent ability to bridge RAF isoforms and their substrate, mitogen-activated protein kinase kinase (MEK). Kinase suppressor of Ras (KSR) pseudokinases were also shown to dimerize with kinase-competent RAFs to stimulate catalysis allosterically. Although GTP-bound RAS can modulate the dimerization of RAF isoforms by engaging their RAS-binding domains, KSR1 and KSR2 lack an RAS-binding domain and therefore the regulatory principles underlying their dimerization with other RAF family members remain unknown. Here we show that the selective heterodimerization of BRAF with KSR1 is specified by direct contacts between the amino-terminal regulatory regions of each protein, comprising in part a novel domain called BRS in BRAF and the coiled-coil-sterile α motif (CC-SAM) domain in KSR1. We also discovered that MEK binding to the kinase domain of KSR1 asymmetrically drives BRAF-KSR1 heterodimerization, resulting in the concomitant stimulation of BRAF catalytic activity towards free MEK molecules. These findings demonstrate that KSR-MEK complexes allosterically activate BRAF through the action of N-terminal regulatory region and kinase domain contacts and challenge the accepted role of KSR as a scaffold for MEK recruitment to RAF.
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Affiliation(s)
- Hugo Lavoie
- Institute for Research in Immunology and Cancer Laboratory of Intracellular Signaling Université de Montréal C.P. 6128, Succursale Centre-Ville Montréal, Québec H3C 3J7, Canada
| | - Malha Sahmi
- Institute for Research in Immunology and Cancer Laboratory of Intracellular Signaling Université de Montréal C.P. 6128, Succursale Centre-Ville Montréal, Québec H3C 3J7, Canada
| | - Pierre Maisonneuve
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Sara A Marullo
- Institute for Research in Immunology and Cancer Laboratory of Intracellular Signaling Université de Montréal C.P. 6128, Succursale Centre-Ville Montréal, Québec H3C 3J7, Canada
| | - Neroshan Thevakumaran
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Ting Jin
- Institute for Research in Immunology and Cancer Laboratory of Intracellular Signaling Université de Montréal C.P. 6128, Succursale Centre-Ville Montréal, Québec H3C 3J7, Canada
| | - Igor Kurinov
- NE-CAT APS, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Marc Therrien
- Institute for Research in Immunology and Cancer Laboratory of Intracellular Signaling Université de Montréal C.P. 6128, Succursale Centre-Ville Montréal, Québec H3C 3J7, Canada.,Département de pathologie et biologie cellulaire, Université de Montréal, Québec H3C 3J7, Canada
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41
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Assadieskandar A, Yu C, Maisonneuve P, Liu X, Chen YC, Prakash GKS, Kurinov I, Sicheri F, Zhang C. Effects of rigidity on the selectivity of protein kinase inhibitors. Eur J Med Chem 2018; 146:519-528. [PMID: 29407977 DOI: 10.1016/j.ejmech.2018.01.053] [Citation(s) in RCA: 10] [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: 11/03/2017] [Revised: 12/28/2017] [Accepted: 01/16/2018] [Indexed: 12/18/2022]
Abstract
Established strategies for discovering selective kinase inhibitors are target-centric as they often target certain structural or reactive features in the target kinase. In the absence of such prominent features, there is a lack of general methods for discovering selective inhibitors. Here we describe a new strategy that exploits conformational flexibility of kinases for achieving selective kinase inhibition. Through ring closure, we designed and synthesized a panel of isoquinoline-containing compounds as rigidified analogs of an amidophenyl-containing parent compound. These analogs potently inhibit kinases including Abl and BRAF but have diminished inhibition against some other kinases compared to the parent compound. Sequence analysis reveals that many of the kinases that are potently inhibited by the isoquonoline-containing compounds contain a long insertion within their catalytic domains. A crystal structure of one rigid compound bound to BRAF confirmed its binding mode. Our findings highlight the potential of a novel strategy of rigidification for improving the selectivity of kinase inhibitors.
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Affiliation(s)
- Amir Assadieskandar
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, University Park, Los Angeles, CA 90089, USA
| | - Caiqun Yu
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, University Park, Los Angeles, CA 90089, USA
| | - Pierre Maisonneuve
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Xu Liu
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, University Park, Los Angeles, CA 90089, USA
| | - Ying-Chu Chen
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, University Park, Los Angeles, CA 90089, USA
| | - G K Surya Prakash
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, University Park, Los Angeles, CA 90089, USA
| | - Igor Kurinov
- NE-CAT APS, Building 436E, Argonne National Lab, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Chao Zhang
- Loker Hydrocarbon Research Institute & Department of Chemistry, University of Southern California, University Park, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
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43
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Canny MD, Moatti N, Wan LCK, Fradet-Turcotte A, Krasner D, Mateos-Gomez PA, Zimmermann M, Orthwein A, Juang YC, Zhang W, Noordermeer SM, Seclen E, Wilson MD, Vorobyov A, Munro M, Ernst A, Ng TF, Cho T, Cannon PM, Sidhu SS, Sicheri F, Durocher D. Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency. Nat Biotechnol 2017; 36:95-102. [PMID: 29176614 PMCID: PMC5762392 DOI: 10.1038/nbt.4021] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [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: 03/28/2016] [Accepted: 10/20/2017] [Indexed: 02/06/2023]
Abstract
Programmable nucleases, such as Cas9, are used for precise genome editing by homology-dependent repair (HDR)1–3. However, HDR efficiency is constrained by competition from other double-strand break (DSB) repair pathways, including non-homologous end-joining (NHEJ)4. We report the discovery of a genetically encoded inhibitor of 53BP1 that increases the efficiency of HDR-dependent genome editing in human and mouse cells. 53BP1 is a key regulator of DSB repair pathway choice in eukaryotic cells4, 5 and functions to favor NHEJ over HDR by suppressing end resection, which is the rate-limiting step in the initiation of HDR. We screened an existing combinatorial library of engineered ubiquitin variants6 for inhibitors of 53BP1. Expression of one variant, named i53 (inhibitor of 53BP1), in human and mouse cells blocked accumulation of 53BP1 at sites of DNA damage and improved gene targeting and chromosomal gene conversion with either double-stranded DNA or single-stranded oligonucleotide donors by up to 5.6-fold. Inhibition of 53BP1 is a robust method to increase efficiency of HDR-based precise genome editing.
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Affiliation(s)
- Marella D Canny
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Nathalie Moatti
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Leo C K Wan
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Amélie Fradet-Turcotte
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Danielle Krasner
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Pedro A Mateos-Gomez
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Langone Medical Center, New York, New York, USA
| | - Michal Zimmermann
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Alexandre Orthwein
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yu-Chi Juang
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Wei Zhang
- The Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - Sylvie M Noordermeer
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Eduardo Seclen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Marcus D Wilson
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andrew Vorobyov
- The Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - Meagan Munro
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andreas Ernst
- The Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - Timothy F Ng
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Tiffany Cho
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Ontario, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | - Frank Sicheri
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Ontario, Canada
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Sicheri F. Structural principles of protein kinase regulation. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317096787] [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: 11/10/2022] Open
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Xiong S, Couzens AL, Kean MJ, Mao DY, Guettler S, Kurinov I, Gingras AC, Sicheri F. Regulation of Protein Interactions by Mps One Binder (MOB1) Phosphorylation. Mol Cell Proteomics 2017; 16:1111-1125. [PMID: 28373297 DOI: 10.1074/mcp.m117.068130] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/27/2017] [Indexed: 12/22/2022] Open
Abstract
MOB1 is a multifunctional protein best characterized for its integrative role in regulating Hippo and NDR pathway signaling in metazoans and the Mitotic Exit Network in yeast. Human MOB1 binds both the upstream kinases MST1 and MST2 and the downstream AGC group kinases LATS1, LATS2, NDR1, and NDR2. Binding of MOB1 to MST1 and MST2 is mediated by its phosphopeptide-binding infrastructure, the specificity of which matches the phosphorylation consensus of MST1 and MST2. On the other hand, binding of MOB1 to the LATS and NDR kinases is mediated by a distinct interaction surface on MOB1. By assembling both upstream and downstream kinases into a single complex, MOB1 facilitates the activation of the latter by the former through a trans-phosphorylation event. Binding of MOB1 to its upstream partners also renders MOB1 a substrate, which serves to differentially regulate its two protein interaction activities (at least in vitro). Our previous interaction proteomics analysis revealed that beyond associating with MST1 (and MST2), MOB1A and MOB1B can associate in a phosphorylation-dependent manner with at least two other signaling complexes, one containing the Rho guanine exchange factors (DOCK6-8) and the other containing the serine/threonine phosphatase PP6. Whether these complexes are recruited through the same mode of interaction as MST1 and MST2 remains unknown. Here, through a comprehensive set of biochemical, biophysical, mutational and structural studies, we quantitatively assess how phosphorylation of MOB1A regulates its interaction with both MST kinases and LATS/NDR family kinases in vitro Using interaction proteomics, we validate the significance of our in vitro studies and also discover that the phosphorylation-dependent recruitment of PP6 phosphatase and Rho guanine exchange factor protein complexes differ in key respects from that elucidated for MST1 and MST2. Together our studies confirm and extend previous work to delineate the intricate regulatory steps in key signaling pathways.
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Affiliation(s)
- Shawn Xiong
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5.,§Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - Amber L Couzens
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5
| | - Michelle J Kean
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5
| | - Daniel Y Mao
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5
| | - Sebastian Guettler
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5.,¶The Institute of Cancer Research, Divisions of Structural Biology and Cancer Biology, London, UK, SW7 3RP
| | - Igor Kurinov
- ‖NE-CAT APS, Building 436E, Argonne National Lab, 9700 S. Cass Avenue, Argonne, Illinois 60439
| | - Anne-Claude Gingras
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5; .,**Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - Frank Sicheri
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5; .,§Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8.,**Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
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46
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Couzens AL, Xiong S, Knight JDR, Mao DY, Guettler S, Picaud S, Kurinov I, Filippakopoulos P, Sicheri F, Gingras AC. MOB1 Mediated Phospho-recognition in the Core Mammalian Hippo Pathway. Mol Cell Proteomics 2017; 16:1098-1110. [PMID: 28373298 PMCID: PMC5461540 DOI: 10.1074/mcp.m116.065490] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 11/13/2016] [Revised: 04/03/2017] [Indexed: 01/13/2023] Open
Abstract
The Hippo tumor suppressor pathway regulates organ size and tissue homoeostasis in response to diverse signaling inputs. The core of the pathway consists of a short kinase cascade: MST1 and MST2 phosphorylate and activate LATS1 and LATS2, which in turn phosphorylate and inactivate key transcriptional coactivators, YAP1 and TAZ (gene WWTR1). The MOB1 adapter protein regulates both phosphorylation reactions firstly by concurrently binding to the upstream MST and downstream LATS kinases to enable the trans phosphorylation reaction, and secondly by allosterically activating the catalytic function of LATS1 and LATS2 to directly stimulate phosphorylation of YAP and TAZ. Studies of yeast Mob1 and human MOB1 revealed that the ability to recognize phosphopeptide sequences in their interactors, Nud1 and MST2 respectively, was critical to their roles in regulating the Mitotic Exit Network in yeast and the Hippo pathway in metazoans. However, the underlying rules of phosphopeptide recognition by human MOB1, the implications of binding specificity for Hippo pathway signaling, and the generality of phosphopeptide binding function to other human MOB family members remained elusive. Employing proteomics, peptide arrays and biochemical analyses, we systematically examine the phosphopeptide binding specificity of MOB1 and find it to be highly complementary to the substrate phosphorylation specificity of MST1 and MST2. We demonstrate that autophosphorylation of MST1 and MST2 on several threonine residues provides multiple MOB1 binding sites with varying binding affinities which in turn contribute to a redundancy of MST1-MOB1 protein interactions in cells. The crystal structures of MOB1A in complex with two favored phosphopeptide sites in MST1 allow for a full description of the MOB1A phosphopeptide-binding consensus. Lastly, we show that the phosphopeptide binding properties of MOB1A are conserved in all but one of the seven MOB family members in humans, thus providing a starting point for uncovering their elusive cellular functions.
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Affiliation(s)
- Amber L Couzens
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5
| | - Shawn Xiong
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5.,§Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - James D R Knight
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5
| | - Daniel Y Mao
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5
| | - Sebastian Guettler
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5.,¶New address: The Institute of Cancer Research, Divisions of Structural Biology and Cancer Biology, London, UK, SW7 3RP
| | - Sarah Picaud
- ‖Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Igor Kurinov
- **NE-CAT APS, Building 436E, Argonne National Lab, 9700 S. Cass Avenue, Argonne, Illinois 60439
| | - Panagis Filippakopoulos
- ‖Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,‡‡Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, U.K
| | - Frank Sicheri
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5, .,§Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada, M5S 1A8.,§§Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - Anne-Claude Gingras
- From the ‡Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada, M5G 1X5, .,§§Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
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47
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Manczyk N, Yates BP, Veggiani G, Ernst A, Sicheri F, Sidhu SS. Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha-helical ubiquitin interacting motif. Protein Sci 2017; 26:1060-1069. [PMID: 28276594 DOI: 10.1002/pro.3155] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 01/04/2017] [Accepted: 03/06/2017] [Indexed: 12/20/2022]
Abstract
Ubiquitin interacting motifs (UIMs) are short α-helices found in a number of eukaryotic proteins. UIMs interact weakly but specifically with ubiquitin conjugated to other proteins, and in so doing, mediate specific cellular signals. Here we used phage display to generate ubiquitin variants (UbVs) targeting the N-terminal UIM of the yeast Vps27 protein. Selections yielded UbV.v27.1, which recognized the cognate UIM with high specificity relative to other yeast UIMs and bound with an affinity more than two orders of magnitude higher than that of ubiquitin. Structural and mutational studies of the UbV.v27.1-UIM complex revealed the molecular details for the enhanced affinity and specificity of UbV.v27.1, and underscored the importance of changes at the binding interface as well as at positions that do not contact the UIM. Our study highlights the power of the phage display approach for selecting UbVs with unprecedented affinity and high selectivity for particular α-helical UIM domains within proteomes, and it establishes a general approach for the development of inhibitors targeting interactions of this type.
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Affiliation(s)
- Noah Manczyk
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Bradley P Yates
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Gianluca Veggiani
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, 60590, Germany
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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48
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Wan LCK, Maisonneuve P, Szilard RK, Lambert JP, Ng TF, Manczyk N, Huang H, Laister R, Caudy AA, Gingras AC, Durocher D, Sicheri F. Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7. Nucleic Acids Res 2016; 45:805-817. [PMID: 27903914 PMCID: PMC5314774 DOI: 10.1093/nar/gkw1181] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 08/19/2016] [Revised: 11/01/2016] [Accepted: 11/15/2016] [Indexed: 12/17/2022] Open
Abstract
The KEOPS/EKC complex is a tRNA modification complex involved in the biosynthesis of N6-threonylcarbamoyladenosine (t6A), a universally conserved tRNA modification found on ANN-codon recognizing tRNAs. In archaea and eukaryotes, KEOPS is composed of OSGEP/Kae1, PRPK/Bud32, TPRKB/Cgi121 and LAGE3/Pcc1. In fungi, KEOPS contains an additional subunit, Gon7, whose orthologs outside of fungi, if existent, remain unidentified. In addition to displaying defective t6A biosynthesis, Saccharomyces cerevisiae strains harboring KEOPS mutations are compromised for telomere homeostasis, growth and transcriptional co-activation. To identify a Gon7 ortholog in multicellular eukaryotes as well as to uncover KEOPS-interacting proteins that may link t6A biosynthesis to the diverse set of KEOPS mutant phenotypes, we conducted a proteomic analysis of human KEOPS. This work identified 152 protein interactors, one of which, C14ORF142, interacted strongly with all four KEOPS subunits, suggesting that it may be a core component of human KEOPS. Further characterization of C14ORF142 revealed that it shared a number of biophysical and biochemical features with fungal Gon7, suggesting that C14ORF142 is the human ortholog of Gon7. In addition, our proteomic analysis identified specific interactors for different KEOPS subcomplexes, hinting that individual KEOPS subunits may have additional functions outside of t6A biosynthesis.
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Affiliation(s)
- Leo C K Wan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Pierre Maisonneuve
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Rachel K Szilard
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Timothy F Ng
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Noah Manczyk
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1,Canada
| | - Hao Huang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzen, 518055, China
| | - Rob Laister
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzen, 518055, China
| | - Amy A Caudy
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.,Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, ON, M5S 3E1, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.,Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
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Spencer-Smith R, Koide A, Zhou Y, Eguchi RR, Sha F, Gajwani P, Santana D, Gupta A, Jacobs M, Herrero-Garcia E, Cobbert J, Lavoie H, Smith M, Rajakulendran T, Dowdell E, Okur MN, Dementieva I, Sicheri F, Therrien M, Hancock JF, Ikura M, Koide S, O'Bryan JP. Inhibition of RAS function through targeting an allosteric regulatory site. Nat Chem Biol 2016; 13:62-68. [PMID: 27820802 DOI: 10.1038/nchembio.2231] [Citation(s) in RCA: 204] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/22/2016] [Indexed: 11/09/2022]
Abstract
RAS GTPases are important mediators of oncogenesis in humans. However, pharmacological inhibition of RAS has proved challenging. Here we describe a functionally critical region, located outside the effector lobe of RAS, that can be targeted for inhibition. We developed NS1, a synthetic binding protein (monobody) that bound with high affinity to both GTP- and GDP-bound states of H-RAS and K-RAS but not N-RAS. NS1 potently inhibited growth factor signaling and oncogenic H-RAS- and K-RAS-mediated signaling and transformation but did not block oncogenic N-RAS, BRAF or MEK1. NS1 bound the α4-β6-α5 region of RAS, which disrupted RAS dimerization and nanoclustering and led to blocking of CRAF-BRAF heterodimerization and activation. These results establish the importance of the α4-β6-α5 interface in RAS-mediated signaling and define a previously unrecognized site in RAS for inhibiting RAS function.
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Affiliation(s)
- Russell Spencer-Smith
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA.,Jesse Brown VA Medical Center, Chicago, Illinois, USA
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA.,Department of Medicine, New York University Langone Medical Center, New York, New York, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, USA
| | - Raphael R Eguchi
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Fern Sha
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Priyanka Gajwani
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Dianicha Santana
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA
| | - Miranda Jacobs
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Erika Herrero-Garcia
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA.,Jesse Brown VA Medical Center, Chicago, Illinois, USA
| | - Jacqueline Cobbert
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Hugo Lavoie
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montreal, Quebec, Canada
| | - Matthew Smith
- Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Thanashan Rajakulendran
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Evan Dowdell
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Mustafa Nazir Okur
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Irina Dementieva
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Frank Sicheri
- Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montreal, Quebec, Canada
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, Houston, Texas, USA
| | - Mitsuhiko Ikura
- Department of Medical Biophysics, Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, New York, USA
| | - John P O'Bryan
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA.,University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois, USA.,Jesse Brown VA Medical Center, Chicago, Illinois, USA
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Wilson MD, Benlekbir S, Fradet-Turcotte A, Sherker A, Julien JP, McEwan A, Noordermeer SM, Sicheri F, Rubinstein JL, Durocher D. The structural basis of modified nucleosome recognition by 53BP1. Nature 2016; 536:100-3. [PMID: 27462807 DOI: 10.1038/nature18951] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/21/2016] [Indexed: 02/07/2023]
Abstract
DNA double-strand breaks (DSBs) elicit a histone modification cascade that controls DNA repair. This pathway involves the sequential ubiquitination of histones H1 and H2A by the E3 ubiquitin ligases RNF8 and RNF168, respectively. RNF168 ubiquitinates H2A on lysine 13 and lysine 15 (refs 7, 8) (yielding H2AK13ub and H2AK15ub, respectively), an event that triggers the recruitment of 53BP1 (also known as TP53BP1) to chromatin flanking DSBs. 53BP1 binds specifically to H2AK15ub-containing nucleosomes through a peptide segment termed the ubiquitination-dependent recruitment motif (UDR), which requires the simultaneous engagement of histone H4 lysine 20 dimethylation (H4K20me2) by its tandem Tudor domain. How 53BP1 interacts with these two histone marks in the nucleosomal context, how it recognizes ubiquitin, and how it discriminates between H2AK13ub and H2AK15ub is unknown. Here we present the electron cryomicroscopy (cryo-EM) structure of a dimerized human 53BP1 fragment bound to a H4K20me2-containing and H2AK15ub-containing nucleosome core particle (NCP-ubme) at 4.5 Å resolution. The structure reveals that H4K20me2 and H2AK15ub recognition involves intimate contacts with multiple nucleosomal elements including the acidic patch. Ubiquitin recognition by 53BP1 is unusual and involves the sandwiching of the UDR segment between ubiquitin and the NCP surface. The selectivity for H2AK15ub is imparted by two arginine fingers in the H2A amino-terminal tail, which straddle the nucleosomal DNA and serve to position ubiquitin over the NCP-bound UDR segment. The structure of the complex between NCP-ubme and 53BP1 reveals the basis of 53BP1 recruitment to DSB sites and illuminates how combinations of histone marks and nucleosomal elements cooperate to produce highly specific chromatin responses, such as those elicited following chromosome breaks.
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