1
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Guo HZ, Feng RX, Zhang YJ, Yu YH, Lu W, Liu JJ, Yang SX, Zhao C, Zhang ZL, Yu SH, Jin H, Qian SX, Li JY, Zhu J, Shi J. A CD36-dependent non-canonical lipid metabolism program promotes immune escape and resistance to hypomethylating agent therapy in AML. Cell Rep Med 2024; 5:101592. [PMID: 38843841 PMCID: PMC11228649 DOI: 10.1016/j.xcrm.2024.101592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/05/2024] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Environmental lipids are essential for fueling tumor energetics, but whether these exogenous lipids transported into cancer cells facilitate immune escape remains unclear. Here, we find that CD36, a transporter for exogenous lipids, promotes acute myeloid leukemia (AML) immune evasion. We show that, separately from its established role in lipid oxidation, CD36 on AML cells senses oxidized low-density lipoprotein (OxLDL) to prime the TLR4-LYN-MYD88-nuclear factor κB (NF-κB) pathway, and exogenous palmitate transfer via CD36 further potentiates this innate immune pathway by supporting ZDHHC6-mediated MYD88 palmitoylation. Subsequently, NF-κB drives the expression of immunosuppressive genes that inhibit anti-tumor T cell responses. Notably, high-fat-diet or hypomethylating agent decitabine treatment boosts the immunosuppressive potential of AML cells by hijacking CD36-dependent innate immune signaling, leading to a dampened therapeutic effect. This work is of translational interest because lipid restriction by US Food and Drug Administration (FDA)-approved lipid-lowering statin drugs improves the efficacy of decitabine therapy by weakening leukemic CD36-mediated immunosuppression.
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MESH Headings
- CD36 Antigens/metabolism
- CD36 Antigens/genetics
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Lipid Metabolism/drug effects
- Decitabine/pharmacology
- Decitabine/therapeutic use
- Lipoproteins, LDL/metabolism
- Animals
- NF-kappa B/metabolism
- Cell Line, Tumor
- Myeloid Differentiation Factor 88/metabolism
- Myeloid Differentiation Factor 88/genetics
- Mice
- Signal Transduction/drug effects
- Tumor Escape/drug effects
- Drug Resistance, Neoplasm/drug effects
- Toll-Like Receptor 4/metabolism
- Acyltransferases/genetics
- Immunity, Innate/drug effects
- Mice, Inbred C57BL
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Affiliation(s)
- He-Zhou Guo
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China; Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Rui-Xue Feng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Yan-Jie Zhang
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Ye-Hua Yu
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Wei Lu
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jia-Jia Liu
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shao-Xin Yang
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Chong Zhao
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Zhao-Li Zhang
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shan-He Yu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China
| | - Hui Jin
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Si-Xuan Qian
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Jian-Yong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China.
| | - Jiang Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao-Tong University, Shanghai, China.
| | - Jun Shi
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.
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2
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Munoz-Robles BG, DeForest CA. Irreversible light-activated SpyLigation mediates split-protein assembly in 4D. Nat Protoc 2024; 19:1015-1052. [PMID: 38253657 PMCID: PMC11288621 DOI: 10.1038/s41596-023-00938-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/23/2023] [Indexed: 01/24/2024]
Abstract
The conditional assembly of split-protein pairs to modulate biological activity is commonly achieved by fusing split-protein fragments to dimerizing components that bring inactive pairs into close proximity in response to an exogenous trigger. However, current methods lack full spatial and temporal control over reconstitution, require sustained activation and lack specificity. Here light-activated SpyLigation (LASL), based on the photoregulation of the covalent SpyTag (ST)/SpyCatcher (SC) peptide-protein reaction, assembles nonfunctional split fragment pairs rapidly and irreversibly in solution, in engineered biomaterials and intracellularly. LASL introduces an ortho-nitrobenzyl(oNB)-caged lysine into SC's reactive site to generate a photoactivatable SC (pSC). Split-protein pairs of interest fused to pSC and ST are conditionally assembled via near-ultraviolet or pulsed near-infrared irradiation, as the uncaged SC can react with ST to ligate appended fragments. We describe procedures for the efficient synthesis of the photocaged amino acid that is incorporated within pSC (<5 days) as well as the design and cloning of LASL plasmids (1-4 days) for recombinant protein expression in either Escherichia coli (5-6 days) or mammalian cells (4-6 days), which require some prior expertise in protein engineering. We provide a chemoenzymatic scheme for appending bioorthogonal reactive handles onto E. coli-purified pSC protein (<4 days) that permits LASL component incorporation and patterned protein activation within many common biomaterial platforms. Given that LASL is irreversible, the photolithographic patterning procedures are fast and do not require sustained light exposure. Overall, LASL can be used to interrogate and modulate cell signaling in various settings.
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Affiliation(s)
- Brizzia G Munoz-Robles
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Cole A DeForest
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA.
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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3
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Shkarina K, Broz P. Selective induction of programmed cell death using synthetic biology tools. Semin Cell Dev Biol 2024; 156:74-92. [PMID: 37598045 DOI: 10.1016/j.semcdb.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Regulated cell death (RCD) controls the removal of dispensable, infected or malignant cells, and is thus essential for development, homeostasis and immunity of multicellular organisms. Over the last years different forms of RCD have been described (among them apoptosis, necroptosis, pyroptosis and ferroptosis), and the cellular signaling pathways that control their induction and execution have been characterized at the molecular level. It has also become apparent that different forms of RCD differ in their capacity to elicit inflammation or an immune response, and that RCD pathways show a remarkable plasticity. Biochemical and genetic studies revealed that inhibition of a given pathway often results in the activation of back-up cell death mechanisms, highlighting close interconnectivity based on shared signaling components and the assembly of multivalent signaling platforms that can initiate different forms of RCD. Due to this interconnectivity and the pleiotropic effects of 'classical' cell death inducers, it is challenging to study RCD pathways in isolation. This has led to the development of tools based on synthetic biology that allow the targeted induction of RCD using chemogenetic or optogenetic methods. Here we discuss recent advances in the development of such toolset, highlighting their advantages and limitations, and their application for the study of RCD in cells and animals.
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Affiliation(s)
- Kateryna Shkarina
- Institute of Innate Immunity, University Hospital Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
| | - Petr Broz
- Department of Immunobiology, University of Lausanne, Switzerland.
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4
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Shi Y, Bashian EE, Hou Y, Wu P. Chemical immunology: Recent advances in tool development and applications. Cell Chem Biol 2024; 31:S2451-9456(24)00080-1. [PMID: 38508196 DOI: 10.1016/j.chembiol.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
Immunology was one of the first biological fields to embrace chemical approaches. The development of new chemical approaches and techniques has provided immunologists with an impressive arsenal of tools to address challenges once considered insurmountable. This review focuses on advances at the interface of chemistry and immunobiology over the past two decades that have not only opened new avenues in basic immunological research, but also revolutionized drug development for the treatment of cancer and autoimmune diseases. These include chemical approaches to understand and manipulate antigen presentation and the T cell priming process, to facilitate immune cell trafficking and regulate immune cell functions, and therapeutic applications of chemical approaches to disease control and treatment.
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Affiliation(s)
- Yujie Shi
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eleanor E Bashian
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yingqin Hou
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peng Wu
- Department of Molecular and Cellular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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5
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Riaud M, Maxwell J, Soria-Bretones I, Dankner M, Li M, Rose AAN. The role of CRAF in cancer progression: from molecular mechanisms to precision therapies. Nat Rev Cancer 2024; 24:105-122. [PMID: 38195917 DOI: 10.1038/s41568-023-00650-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
The RAF family of kinases includes key activators of the pro-tumourigenic mitogen-activated protein kinase pathway. Hyperactivation of RAF proteins, particularly BRAF and CRAF, drives tumour progression and drug resistance in many types of cancer. Although BRAF is the most studied RAF protein, partially owing to its high mutation incidence in melanoma, the role of CRAF in tumourigenesis and drug resistance is becoming increasingly clinically relevant. Here, we summarize the main known regulatory mechanisms and gene alterations that contribute to CRAF activity, highlighting the different oncogenic roles of CRAF, and categorize RAF1 (CRAF) mutations according to the effect on kinase activity. Additionally, we emphasize the effect that CRAF alterations may have on drug resistance and how precision therapies could effectively target CRAF-dependent tumours. Here, we discuss preclinical and clinical findings that may lead to improved treatments for all types of oncogenic RAF1 alterations in cancer.
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Affiliation(s)
- Melody Riaud
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jennifer Maxwell
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Isabel Soria-Bretones
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Matthew Dankner
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Meredith Li
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - April A N Rose
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada.
- Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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6
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Shui S, Buckley S, Scheller L, Correia BE. Rational design of small-molecule responsive protein switches. Protein Sci 2023; 32:e4774. [PMID: 37656809 PMCID: PMC10510469 DOI: 10.1002/pro.4774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Small-molecule responsive protein switches are powerful tools for controlling cellular processes. These switches are designed to respond rapidly and specifically to their inducer. They have been used in numerous applications, including the regulation of gene expression, post-translational protein modification, and signal transduction. Typically, small-molecule responsive protein switches consist of two proteins that interact with each other in the presence or absence of a small molecule. Recent advances in computational protein design already contributed to the development of protein switches with an expanded range of small-molecule inducers and increasingly sophisticated switch mechanisms. Further progress in the engineering of small-molecule responsive switches is fueled by cutting-edge computational design approaches, which will enable more complex and precise control over cellular processes and advance synthetic biology applications in biotechnology and medicine. Here, we discuss recent milestones and how technological advances are impacting the development of chemical switches.
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Affiliation(s)
- Sailan Shui
- Laboratory of Protein Design and Immunoengineering (LPDI)STI, EPFLLausanneSwitzerland
- Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
| | - Stephen Buckley
- Laboratory of Protein Design and Immunoengineering (LPDI)STI, EPFLLausanneSwitzerland
- Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
| | - Leo Scheller
- Laboratory of Protein Design and Immunoengineering (LPDI)STI, EPFLLausanneSwitzerland
- Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
| | - Bruno E. Correia
- Laboratory of Protein Design and Immunoengineering (LPDI)STI, EPFLLausanneSwitzerland
- Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
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7
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Rohrer L, Spohr C, Beha C, Griffin R, Braun S, Halbach S, Brummer T. Analysis of RAS and drug induced homo- and heterodimerization of RAF and KSR1 proteins in living cells using split Nanoluc luciferase. Cell Commun Signal 2023; 21:136. [PMID: 37316874 DOI: 10.1186/s12964-023-01146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The dimerization of RAF kinases represents a key event in their activation cycle and in RAS/ERK pathway activation. Genetic, biochemical and structural approaches provided key insights into this process defining RAF signaling output and the clinical efficacy of RAF inhibitors (RAFi). However, methods reporting the dynamics of RAF dimerization in living cells and in real time are still in their infancy. Recently, split luciferase systems have been developed for the detection of protein-protein-interactions (PPIs), incl. proof-of-concept studies demonstrating the heterodimerization of the BRAF and RAF1 isoforms. Due to their small size, the Nanoluc luciferase moieties LgBiT and SmBiT, which reconstitute a light emitting holoenzyme upon fusion partner promoted interaction, appear as well-suited to study RAF dimerization. Here, we provide an extensive analysis of the suitability of the Nanoluc system to study the homo- and heterodimerization of BRAF, RAF1 and the related KSR1 pseudokinase. We show that KRASG12V promotes the homo- and heterodimerization of BRAF, while considerable KSR1 homo- and KSR1/BRAF heterodimerization already occurs in the absence of this active GTPase and requires a salt bridge between the CC-SAM domain of KSR1 and the BRAF-specific region. We demonstrate that loss-of-function mutations impairing key steps of the RAF activation cycle can be used as calibrators to gauge the dynamics of heterodimerization. This approach identified the RAS-binding domains and the C-terminal 14-3-3 binding motifs as particularly critical for the reconstitution of RAF mediated LgBiT/SmBiT reconstitution, while the dimer interface was less important for dimerization but essential for downstream signaling. We show for the first time that BRAFV600E, the most common BRAF oncoprotein whose dimerization status is controversially portrayed in the literature, forms homodimers in living cells more efficiently than its wildtype counterpart. Of note, Nanoluc activity reconstituted by BRAFV600E homodimers is highly sensitive to the paradox-breaking RAFi PLX8394, indicating a dynamic and specific PPI. We report the effects of eleven ERK pathway inhibitors on RAF dimerization, incl. third-generation compounds that are less-defined in terms of their dimer promoting abilities. We identify Naporafenib as a potent and long-lasting dimerizer and show that the split Nanoluc approach discriminates between type I, I1/2 and II RAFi. Video Abstract.
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Affiliation(s)
- Lino Rohrer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Corinna Spohr
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Carina Beha
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Ricarda Griffin
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, Freiburg, 79104, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany.
- Center for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, 79104, Germany.
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8
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Ruskowitz ER, Munoz-Robles BG, Strange AC, Butcher CH, Kurniawan S, Filteau JR, DeForest CA. Spatiotemporal functional assembly of split protein pairs through a light-activated SpyLigation. Nat Chem 2023; 15:694-704. [PMID: 37069270 PMCID: PMC10164143 DOI: 10.1038/s41557-023-01152-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/26/2023] [Indexed: 04/19/2023]
Abstract
Proteins provide essential functional regulation of many bioprocesses across all scales of life; however, new techniques to specifically modulate protein activity within living systems and in engineered biomaterials are needed to better interrogate fundamental cell signalling and guide advanced decisions of biological fate. Here we establish a generalizable strategy to rapidly and irreversibly activate protein function with full spatiotemporal control. Through the development of a genetically encoded and light-activated SpyLigation (LASL), bioactive proteins can be stably reassembled from non-functional split fragment pairs following brief exposure (typically minutes) to cytocompatible light. Employing readily accessible photolithographic processing techniques to specify when, where and how much photoligation occurs, we demonstrate precise protein activation of UnaG, NanoLuc and Cre recombinase using LASL in solution, biomaterials and living mammalian cells, as well as optical control over protein subcellular localization. Looking forward, we expect that these photoclick-based optogenetic approaches will find tremendous utility in probing and directing complex cellular fates in both time and three-dimensional space.
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Affiliation(s)
- Emily R Ruskowitz
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | | | - Alder C Strange
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Carson H Butcher
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Sebastian Kurniawan
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jeremy R Filteau
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Cole A DeForest
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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9
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Tawaratsumida K, Redecke V, Wu R, Kuriakose J, Bouchard JJ, Mittag T, Lohman BK, Mishra A, High AA, Häcker H. A phospho-tyrosine-based signaling module using SPOP, CSK, and LYN controls TLR-induced IRF activity. SCIENCE ADVANCES 2022; 8:eabq0084. [PMID: 35857476 PMCID: PMC9269885 DOI: 10.1126/sciadv.abq0084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Toll-like receptors (TLRs) recognize pathogen- and host-derived factors and control immune responses via the adaptor protein MyD88 and members of the interferon regulatory transcription factor (IRF) family. IRFs orchestrate key effector functions, including cytokine release, cell differentiation, and, under certain circumstances, inflammation pathology. Here, we show that IRF activity is generically controlled by the Src kinase family member LYN, which phosphorylates all TLR-induced IRFs at a conserved tyrosine residue, resulting in K48-linked polyubiquitination and proteasomal degradation of IRFs. We further show that LYN activity is controlled by the upstream kinase C-terminal Src kinase (CSK), whose activity, in turn, is controlled by the adaptor protein SPOP, which serves as molecular bridge to recruit CSK into the TLR signaling complex and to activate CSK catalytic activity. Consistently, deletion of SPOP or CSK results in increased LYN activity, LYN-directed IRF degradation, and inhibition of IRF transcriptional activity. Together, the data reveal a key regulatory mechanism for IRF family members controlling TLR biology.
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Affiliation(s)
- Kazuki Tawaratsumida
- Laboratory of Innate Immunity and Signal Transduction, Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Vanessa Redecke
- Laboratory of Innate Immunity and Signal Transduction, Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Ruiqiong Wu
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jeeba Kuriakose
- Children’s GMP, LLC., St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jill J. Bouchard
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brian K. Lohman
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Anthony A. High
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hans Häcker
- Laboratory of Innate Immunity and Signal Transduction, Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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10
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Maresin 1 alleviates sevoflurane-induced neuroinflammation in neonatal rats via JAK2/STAT3/IL-6 pathways. Int Immunopharmacol 2022; 108:108912. [DOI: 10.1016/j.intimp.2022.108912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022]
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11
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Zhao J, Luo Z. Discovery of Raf Family Is a Milestone in Deciphering the Ras-Mediated Intracellular Signaling Pathway. Int J Mol Sci 2022; 23:ijms23095158. [PMID: 35563547 PMCID: PMC9101324 DOI: 10.3390/ijms23095158] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/27/2023] Open
Abstract
The Ras-Raf-MEK-ERK signaling pathway, the first well-established MAPK pathway, plays essential roles in cell proliferation, survival, differentiation and development. It is activated in over 40% of human cancers owing to mutations of Ras, membrane receptor tyrosine kinases and other oncogenes. The Raf family consists of three isoforms, A-Raf, B-Raf and C-Raf. Since the first discovery of a truncated mutant of C-Raf as a transforming oncogene carried by a murine retrovirus, forty years of extensive studies have provided a wealth of information on the mechanisms underlying the activation, regulation and biological functions of the Raf family. However, the mechanisms by which activation of A-Raf and C-Raf is accomplished are still not completely understood. In contrast, B-Raf can be easily activated by binding of Ras-GTP, followed by cis-autophosphorylation of the activation loop, which accounts for the fact that this isoform is frequently mutated in many cancers, especially melanoma. The identification of oncogenic B-Raf mutations has led to accelerated drug development that targets Raf signaling in cancer. However, the effort has not proved as effective as anticipated, inasmuch as the mechanism of Raf activation involves multiple steps, factors and phosphorylation of different sites, as well as complex interactions between Raf isoforms. In this review, we will focus on the physiological complexity of the regulation of Raf kinases and their connection to the ERK phosphorylation cascade and then discuss the role of Raf in tumorigenesis and the clinical application of Raf inhibitors in the treatment of cancer.
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Affiliation(s)
- Jingtong Zhao
- Queen Mary School, Nanchang University, Nanchang 330031, China;
| | - Zhijun Luo
- Queen Mary School, Nanchang University, Nanchang 330031, China;
- Provincial Key Laboratory of Tumor Pathogens and Molecular Pathology, Nanchang University, Nanchang 330031, China
- NCU-QMUL Joint Research Institute of Precision Medical Science, Nanchang 330031, China
- Correspondence:
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12
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Singh AK, Saharan K, Baral S, Luan S, Vasudevan D. Crystal packing reveals rapamycin-mediated homodimerization of an FK506-binding domain. Int J Biol Macromol 2022; 206:670-680. [PMID: 35218805 DOI: 10.1016/j.ijbiomac.2022.02.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/28/2022]
Abstract
Chemically induced dimerization (CID) is used to induce proximity and result in artificial complex formation between a pair of proteins involved in biological processes in cells to investigate and regulate these processes. The induced heterodimerization of FKBP fusion proteins by rapamycin and FK506 has been extensively exploited as a chemically induced dimerization system to regulate and understand highly dynamic cellular processes. Here, we report the crystal structure of the AtFKBP53 FKBD in complex with rapamycin. The crystal packing reveals an unusual feature whereby two rapamycin molecules appear to mediate homodimerization of the FKBD. The triene arm of rapamycin appears to play a significant role in forming this dimer. This forms the first structural report of rapamycin-mediated homodimerization of an FKBP. The structural information on the rapamycin-mediated FKBD dimerization may be employed to design and synthesize covalently linked dimeric rapamycin, which may subsequently serve as a chemically induced dimerization system for the regulation and characterization of cellular processes.
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Affiliation(s)
- Ajit Kumar Singh
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India
| | - Ketul Saharan
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India; Regional Centre for Biotechnology, Faridabad 121001, India
| | - Somanath Baral
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India; School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Dileep Vasudevan
- Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, India.
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13
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Dang DT. Molecular Approaches to Protein Dimerization: Opportunities for Supramolecular Chemistry. Front Chem 2022; 10:829312. [PMID: 35211456 PMCID: PMC8861298 DOI: 10.3389/fchem.2022.829312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Protein dimerization plays a key role in many biological processes. Most cellular events such as enzyme activation, transcriptional cofactor recruitment, signal transduction, and even pathogenic pathways are significantly regulated via protein-protein interactions. Understanding and controlling the molecular mechanisms that regulate protein dimerization is crucial for biomedical applications. The limitations of engineered protein dimerization provide an opportunity for molecular chemistry to induce dimerization of protein in biological events. In this review, molecular control over dimerization of protein and activation in this respect are discussed. The well known molecule glue-based approaches to induced protein dimerization provide powerful tools to modulate the functionality of dimerized proteins and are shortly highlighted. Subsequently metal ion, nucleic acid and host-guest chemistry are brought forward as novel approaches for orthogonal control over dimerization of protein. The specific focus of the review will be on host-guest systems as novel, robust and versatile supramolecular approaches to modulate the dimerization of proteins, using functional proteins as model systems.
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14
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JAK2/STAT3 inhibition attenuates intestinal ischemia-reperfusion injury via promoting autophagy: in vitro and in vivo study. Mol Biol Rep 2022; 49:2857-2867. [PMID: 35067814 DOI: 10.1007/s11033-021-07099-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/16/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Intestinal ischemia-reperfusion (I/R) causes severe injury to the intestine, leading to systemic inflammation and multiple organ failure. Autophagy is a stress-response mechanism that can protect against I/R injury by removing damaged organelles and toxic protein aggregates. Recent evidence has identified JAK-STAT signaling pathway as a new regulator of autophagy process, however, their regulatory relationship in intestinal I/R remains unknown. METHODS AND RESULTS We systematically analyzed intestinal transcriptome data and found that JAK-STAT pathway was largely activated in response to I/R with most significant upregulation observed for JAK2 and STAT3. ChIP-Seq and luciferase assays in an in vitro oxygen-glucose deprivation and reoxygenation model revealed that activated JAK2/STAT3 signaling directly inhibited the transcription of autophagy regulator Beclin-1, leading to the suppression of autophagy and the activation of intestinal cell death. These findings were further confirmed in an in vivo mouse model, in which, intestinal I/R injury was associated with the activation of JAK2/STAT3 pathway and the deactivation of Beclin-1-mediated autophagy, while inhibiting JAK2/STAT3 with AG490 reactivated autophagy and improved survival after intestinal I/R injury. CONCLUSIONS JAK2/STAT3 signaling suppresses autophagy process during intestinal I/R, while inhibiting JAK-STAT can be protective against intestinal I/R injury by activating autophagy. These findings expand our knowledge on intestinal I/R injury and provide therapeutic targets for clinical treatment.
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15
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Kawashima K, Hirota-Tsukimachi M, Toma T, Koga R, Iwamaru K, Kanemaru Y, Yanae M, Ahagon A, Nakamura Y, Anraku K, Tateishi H, Gohda J, Inoue JI, Otsuka M, Fujita M. Development of chimeric receptor activator of nuclear factor-kappa B with glutathione S-transferase in the extracellular domain: Artificial switch in a membrane receptor. Chem Biol Drug Des 2021; 99:573-584. [PMID: 34882966 DOI: 10.1111/cbdd.14002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/23/2021] [Accepted: 12/05/2021] [Indexed: 11/26/2022]
Abstract
Various chimeric receptors have been developed and used for biological experiments. In the present study, we constructed three types of chimeric receptor activator of nuclear factor-kappa B (RANK) with the glutathione S-transferase (GST) protein in the extracellular domain, and stimulated them using newly synthesized chemical trimerizers with three glutathiones. Although this stimulation did not activate these proteins, we unexpectedly found that the chimera named RANK-GST-SC, in which GST replaced a major part of the RANK extracellular domain, activated nuclear factor-kappa B (NF-κB) signaling approximately sixfold more strongly than wild-type RANK without the ligand. The dimerization of extracellular GST is considered to function as a switch outside the cell, and signal transduction then occurs. GST has been widely employed as a tag for protein purification; GST-fusion protein can be conveniently captured by glutathione-conjugated beads and easily purified from impurity. The present study is a pioneering example of the novel utility of GST and provides information for the development of new chemical biology systems.
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Affiliation(s)
- Kanako Kawashima
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Mayuko Hirota-Tsukimachi
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tsugumasa Toma
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ryoko Koga
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kana Iwamaru
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yosuke Kanemaru
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Misato Yanae
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ami Ahagon
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yurine Nakamura
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kensaku Anraku
- Department of Medical Technology, Kumamoto Health Science University, Kumamoto, Japan
| | - Hiroshi Tateishi
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jun-Ichiro Inoue
- Research Platform Office, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Science Farm Ltd., Kumamoto, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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16
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Sampson J, Richards MW, Choi J, Fry AM, Bayliss R. Phase-separated foci of EML4-ALK facilitate signalling and depend upon an active kinase conformation. EMBO Rep 2021; 22:e53693. [PMID: 34661367 PMCID: PMC8647013 DOI: 10.15252/embr.202153693] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 12/11/2022] Open
Abstract
Variants of the oncogenic EML4-ALK fusion protein contain a similar region of ALK encompassing the kinase domain, but different portions of EML4. Here, we show that EML4-ALK V1 and V3 proteins form cytoplasmic foci that contain components of the MAPK, PLCγ and PI3K signalling pathways. The ALK inhibitors ceritinib and lorlatinib dissolve these foci and EML4-ALK V3 but not V1 protein re-localises to microtubules, an effect recapitulated in a catalytically inactive EML4-ALK mutant. Mutations that promote a constitutively active ALK stabilise the cytoplasmic foci even in the presence of these inhibitors. In contrast, the inhibitor alectinib increases foci formation of both wild-type and catalytically inactive EML4-ALK V3 proteins, but not a Lys-Glu salt bridge mutant. We propose that EML4-ALK foci formation occurs as a result of transient association of stable EML4-ALK trimers mediated through an active conformation of the ALK kinase domain. Our results demonstrate the formation of EML4-ALK cytoplasmic foci that orchestrate oncogenic signalling and reveal that their assembly depends upon the conformational state of the catalytic domain and can be differentially modulated by structurally divergent ALK inhibitors.
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Affiliation(s)
- Josephina Sampson
- School of Molecular and Cellular BiologyAstbury Centre for Structural Molecular BiologyFaculty of Biological SciencesUniversity of LeedsLeedsUK
| | - Mark W Richards
- School of Molecular and Cellular BiologyAstbury Centre for Structural Molecular BiologyFaculty of Biological SciencesUniversity of LeedsLeedsUK
| | - Jene Choi
- Department of PathologyAsan Medical CenterUniversity of Ulsan College of MedicineSeoulKorea
| | - Andrew M Fry
- Department of Molecular and Cell BiologyUniversity of LeicesterLeicesterUK
| | - Richard Bayliss
- School of Molecular and Cellular BiologyAstbury Centre for Structural Molecular BiologyFaculty of Biological SciencesUniversity of LeedsLeedsUK
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17
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Wagner HJ, Mohsenin H, Weber W. Synthetic Biology-Empowered Hydrogels for Medical Diagnostics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 178:197-226. [PMID: 33582837 DOI: 10.1007/10_2020_158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Synthetic biology is strongly inspired by concepts of engineering science and aims at the design and generation of artificial biological systems in different fields of research such as diagnostics, analytics, biomedicine, or chemistry. To this aim, synthetic biology uses an engineering approach relying on a toolbox of molecular sensors and switches that endows cellular hosts with non-natural computing functions and circuits. Importantly, this concept is not only limited to cellular approaches. Synthetic biological building blocks have also conferred sensing and switching capability to otherwise inactive materials. This principle has attracted high interest for the development of biohybrid materials capable of sensing and responding to specific molecular stimuli, such as disease biomarkers, antibiotics, or heavy metals. Moreover, the interconnection of individual sense-and-respond materials to complex materials systems has enabled the processing of, for example, multiple inputs or the amplification of signals using feedback topologies. Such systems holding high potential for applications in the analytical and diagnostic sectors will be described in this chapter.
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Affiliation(s)
- Hanna J Wagner
- Faculty of Biology, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Hasti Mohsenin
- Faculty of Biology, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Wilfried Weber
- Faculty of Biology, Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany.
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18
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Yap J, Deepak RNVK, Tian Z, Ng WH, Goh KC, Foo A, Tee ZH, Mohanam MP, Sim YRM, Degirmenci U, Lam P, Chen Z, Fan H, Hu J. The stability of R-spine defines RAF inhibitor resistance: A comprehensive analysis of oncogenic BRAF mutants with in-frame insertion of αC-β4 loop. SCIENCE ADVANCES 2021; 7:7/24/eabg0390. [PMID: 34108213 PMCID: PMC8189578 DOI: 10.1126/sciadv.abg0390] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Although targeting BRAF mutants with RAF inhibitors has achieved promising outcomes in cancer therapy, drug resistance remains a remarkable challenge, and underlying molecular mechanisms are not fully understood. Here, we characterized a previously unknown group of oncogenic BRAF mutants with in-frame insertions (LLRins506 or VLRins506) of αC-β4 loop. Using structure modeling and molecular dynamics simulation, we found that these insertions formed a large hydrophobic network that stabilizes R-spine and thus triggers the catalytic activity of BRAF. Furthermore, these insertions disrupted BRAF dimer interface and impaired dimerization. Unlike BRAF(V600E), these BRAF mutants with low dimer affinity were strongly resistant to all RAF inhibitors in clinic or clinical trials, which arises from their stabilized R-spines. As predicted by molecular docking, the stabilized R-spines in other BRAF mutants also conferred drug resistance. Together, our data indicated that the stability of R-spine but not dimer affinity determines the RAF inhibitor resistance of oncogenic BRAF mutants.
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Affiliation(s)
- Jiajun Yap
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - R N V Krishna Deepak
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Zizi Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wan Hwa Ng
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Kah Chun Goh
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Alicia Foo
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Zi Heng Tee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Manju Payini Mohanam
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Yuen Rong M Sim
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Ufuk Degirmenci
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
| | - Paula Lam
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, MD9, Singapore 117593, Singapore
- Cellvec Pte. Ltd., 100 Pasir Panjang Road, #04-02, Singapore 118518, Singapore
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hao Fan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Jiancheng Hu
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescen, Singapore 169610, Singapore
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19
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Morgan CW, Dale IL, Thomas AP, Hunt J, Chin JW. Selective CRAF Inhibition Elicits Transactivation. J Am Chem Soc 2021; 143:4600-4606. [PMID: 33750116 PMCID: PMC8041278 DOI: 10.1021/jacs.0c11958] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Discovering molecules that regulate
closely related protein isoforms
is challenging, and in many cases the consequences of isoform-specific
pharmacological regulation remains unknown. RAF isoforms are commonly
mutated oncogenes that serve as effector kinases in MAP kinase signaling.
BRAF/CRAF heterodimers are believed to be the primary RAF signaling
species, and many RAF inhibitors lead to a “paradoxical activation”
of RAF kinase activity through transactivation of the CRAF protomer;
this leads to resistance mechanisms and secondary tumors. It has been
hypothesized that CRAF-selective inhibition might bypass paradoxical
activation, but no CRAF-selective inhibitor has been reported and
the consequences of pharmacologically inhibiting CRAF have remained
unknown. Here, we use bio-orthogonal ligand tethering (BOLT) to selectively
target inhibitors to CRAF. Our results suggest that selective CRAF
inhibition promotes paradoxical activation and exemplify how BOLT
may be used to triage potential targets for drug discovery before
any target-selective small molecules are known.
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Affiliation(s)
- Charles W Morgan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ian L Dale
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Andrew P Thomas
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - James Hunt
- Antibody Discovery & Protein Engineering, R&D, AstraZeneca, Cambridge CB21 6GH, United Kingdom
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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20
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Brayshaw LL, Martinez-Fleites C, Athanasopoulos T, Southgate T, Jespers L, Herring C. The role of small molecules in cell and gene therapy. RSC Med Chem 2021; 12:330-352. [PMID: 34046619 PMCID: PMC8130622 DOI: 10.1039/d0md00221f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/25/2020] [Indexed: 01/22/2023] Open
Abstract
Cell and gene therapies have achieved impressive results in the treatment of rare genetic diseases using gene corrected stem cells and haematological cancers using chimeric antigen receptor T cells. However, these two fields face significant challenges such as demonstrating long-term efficacy and safety, and achieving cost-effective, scalable manufacturing processes. The use of small molecules is a key approach to overcome these barriers and can benefit cell and gene therapies at multiple stages of their lifecycle. For example, small molecules can be used to optimise viral vector production during manufacturing or used in the clinic to enhance the resistance of T cell therapies to the immunosuppressive tumour microenvironment. Here, we review current uses of small molecules in cell and gene therapy and highlight opportunities for medicinal chemists to further consolidate the success of cell and gene therapies.
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Affiliation(s)
- Lewis L Brayshaw
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Carlos Martinez-Fleites
- Protein Degradation Group, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Takis Athanasopoulos
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Thomas Southgate
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Laurent Jespers
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Christopher Herring
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
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21
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Cook FA, Cook SJ. Inhibition of RAF dimers: it takes two to tango. Biochem Soc Trans 2021; 49:237-251. [PMID: 33367512 PMCID: PMC7924995 DOI: 10.1042/bst20200485] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
The RAS-regulated RAF-MEK1/2-ERK1/2 pathway promotes cell proliferation and survival and RAS and BRAF proteins are commonly mutated in cancer. This has fuelled the development of small molecule kinase inhibitors including ATP-competitive RAF inhibitors. Type I and type I½ ATP-competitive RAF inhibitors are effective in BRAFV600E/K-mutant cancer cells. However, in RAS-mutant cells these compounds instead promote RAS-dependent dimerisation and paradoxical activation of wild-type RAF proteins. RAF dimerisation is mediated by two key regions within each RAF protein; the RKTR motif of the αC-helix and the NtA-region of the dimer partner. Dimer formation requires the adoption of a closed, active kinase conformation which can be induced by RAS-dependent activation of RAF or by the binding of type I and I½ RAF inhibitors. Binding of type I or I½ RAF inhibitors to one dimer partner reduces the binding affinity of the other, thereby leaving a single dimer partner uninhibited and able to activate MEK. To overcome this paradox two classes of drug are currently under development; type II pan-RAF inhibitors that induce RAF dimer formation but bind both dimer partners thus allowing effective inhibition of both wild-type RAF dimer partners and monomeric active class I mutant RAF, and the recently developed "paradox breakers" which interrupt BRAF dimerisation through disruption of the αC-helix. Here we review the regulation of RAF proteins, including RAF dimers, and the progress towards effective targeting of the wild-type RAF proteins.
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Affiliation(s)
- Frazer A. Cook
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Simon J. Cook
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
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22
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Verbič A, Praznik A, Jerala R. A guide to the design of synthetic gene networks in mammalian cells. FEBS J 2020; 288:5265-5288. [PMID: 33289352 DOI: 10.1111/febs.15652] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
Synthetic biology aims to harness natural and synthetic biological parts and engineering them in new combinations and systems, producing novel therapies, diagnostics, bioproduction systems, and providing information on the mechanism of function of biological systems. Engineering cell function requires the rewiring or de novo construction of cell information processing networks. Using natural and synthetic signal processing elements, researchers have demonstrated a wide array of signal sensing, processing and propagation modules, using transcription, translation, or post-translational modification to program new function. The toolbox for synthetic network design is ever-advancing and has still ample room to grow. Here, we review the diversity of synthetic gene networks, types of building modules, techniques of regulation, and their applications.
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Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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23
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Kim DH, Kim KR, Hah SS. Syntheses of Two Cephem‐Containing Chemical Inducers of Dimerization to Develop a General Method of the Covalent Approach to Fused Proteins Using a Yeast Hybrid System. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.11931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Do Hyun Kim
- Department of Chemistry and Research Institute for Basic SciencesKyung Hee University Seoul 02447 South Korea
| | - Kyeong Rae Kim
- Department of Chemistry and Research Institute for Basic SciencesKyung Hee University Seoul 02447 South Korea
| | - Sang Soo Hah
- Department of Chemistry and Research Institute for Basic SciencesKyung Hee University Seoul 02447 South Korea
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24
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Gomez-Castillo L, Watanabe K, Jiang H, Kang S, Gu L. Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library. J Vis Exp 2020. [PMID: 32009651 DOI: 10.3791/60738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Protein dimerization events that occur only in the presence of a small-molecule ligand enable the development of small-molecule biosensors for the dissection and manipulation of biological pathways. Currently, only a limited number of chemically induced dimerization (CID) systems exist and engineering new ones with desired sensitivity and selectivity for specific small-molecule ligands remains a challenge in the field of protein engineering. We here describe a high throughput screening method, combinatorial binders-enabled selection of CID (COMBINES-CID), for the de novo engineering of CID systems applicable to a large variety of ligands. This method uses the two-step selection of a phage-displayed combinatorial nanobody library to obtain 1) "anchor binders" that first bind to a ligand of interest and then 2) "dimerization binders" that only bind to anchor binder-ligand complexes. To select anchor binders, a combinatorial library of over 109 complementarity-determining region (CDR)-randomized nanobodies is screened with a biotinylated ligand and hits are validated with the unlabeled ligand by bio-layer interferometry (BLI). To obtain dimerization binders, the nanobody library is screened with anchor binder-ligand complexes as targets for positive screening and the unbound anchor binders for negative screening. COMBINES-CID is broadly applicable to select CID binders with other immunoglobulin, non-immunoglobulin, or computationally designed scaffolds to create biosensors for in vitro and in vivo detection of drugs, metabolites, signaling molecules, etc.
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Affiliation(s)
- Luis Gomez-Castillo
- Department of Biochemistry and Institute for Protein Design, University of Washington
| | - Kurumi Watanabe
- Department of Biochemistry and Institute for Protein Design, University of Washington
| | - Huayi Jiang
- Department of Biochemistry and Institute for Protein Design, University of Washington
| | - Shoukai Kang
- Department of Biochemistry and Institute for Protein Design, University of Washington
| | - Liangcai Gu
- Department of Biochemistry and Institute for Protein Design, University of Washington;
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25
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Degirmenci U, Wang M, Hu J. Targeting Aberrant RAS/RAF/MEK/ERK Signaling for Cancer Therapy. Cells 2020; 9:E198. [PMID: 31941155 PMCID: PMC7017232 DOI: 10.3390/cells9010198] [Citation(s) in RCA: 296] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/29/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
The RAS/RAF/MEK/ERK (MAPK) signaling cascade is essential for cell inter- and intra-cellular communication, which regulates fundamental cell functions such as growth, survival, and differentiation. The MAPK pathway also integrates signals from complex intracellular networks in performing cellular functions. Despite the initial discovery of the core elements of the MAPK pathways nearly four decades ago, additional findings continue to make a thorough understanding of the molecular mechanisms involved in the regulation of this pathway challenging. Considerable effort has been focused on the regulation of RAF, especially after the discovery of drug resistance and paradoxical activation upon inhibitor binding to the kinase. RAF activity is regulated by phosphorylation and conformation-dependent regulation, including auto-inhibition and dimerization. In this review, we summarize the recent major findings in the study of the RAS/RAF/MEK/ERK signaling cascade, particularly with respect to the impact on clinical cancer therapy.
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Affiliation(s)
- Ufuk Degirmenci
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Mei Wang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
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26
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Röhm S, Krämer A, Knapp S. Function, Structure and Topology of Protein Kinases. PROTEINKINASE INHIBITORS 2020. [DOI: 10.1007/7355_2020_97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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27
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Kim YC, Lee SE, Kim SK, Jang HD, Hwang I, Jin S, Hong EB, Jang KS, Kim HS. Toll-like receptor mediated inflammation requires FASN-dependent MYD88 palmitoylation. Nat Chem Biol 2019; 15:907-916. [PMID: 31427815 DOI: 10.1038/s41589-019-0344-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/11/2019] [Indexed: 12/24/2022]
Abstract
Toll-like receptor (TLR)/myeloid differentiation primary response protein (MYD88) signaling aggravates sepsis by impairing neutrophil migration to infection sites. However, the role of intracellular fatty acids in TLR/MYD88 signaling is unclear. Here, inhibition of fatty acid synthase by C75 improved neutrophil chemotaxis and increased the survival of mice with sepsis in cecal ligation puncture and lipopolysaccharide-induced septic shock models. C75 specifically blocked TLR/MYD88 signaling in neutrophils. Treatment with GSK2194069 that targets a different domain of fatty acid synthase, did not block TLR signaling or MYD88 palmitoylation. De novo fatty acid synthesis and CD36-mediated exogenous fatty acid incorporation contributed to MYD88 palmitoylation. The binding of IRAK4 to the MYD88 intermediate domain and downstream signal activation required MYD88 palmitoylation at cysteine 113. MYD88 was palmitoylated by ZDHHC6, and ZDHHC6 knockdown decreased MYD88 palmitoylation and TLR/MYD88 activation upon lipopolysaccharide stimulus. Thus, intracellular saturated fatty acid-dependent palmitoylation of MYD88 by ZDHHC6 is a therapeutic target of sepsis.
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Affiliation(s)
- Young-Chan Kim
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Sang Eun Lee
- Cardiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Somi K Kim
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Hyun-Duk Jang
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Injoo Hwang
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Sooryeonhwa Jin
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Eun-Byeol Hong
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea.,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea
| | - Kyoung-Soon Jang
- Biomedical Omics Center, Korea Basic Science Institute, Cheongju, South Korea
| | - Hyo-Soo Kim
- Strategic Center of Cell & Bio Therapy, Seoul National University Hospital, Seoul, Korea. .,Korea Research-Driven Hospital, Seoul National University Hospital, Seoul, Korea. .,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea. .,World Class University Program, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul, Korea.
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28
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Kang S, Davidsen K, Gomez-Castillo L, Jiang H, Fu X, Li Z, Liang Y, Jahn M, Moussa M, DiMaio F, Gu L. COMBINES-CID: An Efficient Method for De Novo Engineering of Highly Specific Chemically Induced Protein Dimerization Systems. J Am Chem Soc 2019; 141:10948-10952. [PMID: 31260282 DOI: 10.1021/jacs.9b03522] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemically induced dimerization (CID) systems, in which two proteins dimerize only in the presence of a small molecule ligand, offer versatile tools for small molecule sensing and actuation. However, only a handful of CID systems exist and creating one with the desired sensitivity and specificity for any given ligand is an unsolved problem. Here, we developed a combinatorial binders-enabled selection of CID (COMBINES-CID) method broadly applicable to different ligands. We demonstrated a proof-of-principle by generating nanobody-based heterodimerization systems induced by cannabidiol with high ligand selectivity. We applied the CID system to a sensitive sandwich enzyme-linked immunosorbent assay-like assay of cannabidiol in body fluids with a detection limit of ∼0.25 ng/mL. COMBINES-CID provides an efficient, cost-effective solution for expanding the biosensor toolkit for small molecule detection.
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Affiliation(s)
- Shoukai Kang
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Kristian Davidsen
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Luis Gomez-Castillo
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Huayi Jiang
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Xiaonan Fu
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Zengpeng Li
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Yu Liang
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Molly Jahn
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Mahmoud Moussa
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
| | - Liangcai Gu
- Department of Biochemistry and Institute for Protein Design , University of Washington , Seattle , Washington 98195 , United States
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29
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Vanden Broeck A, McEwen AG, Chebaro Y, Potier N, Lamour V. Structural Basis for DNA Gyrase Interaction with Coumermycin A1. J Med Chem 2019; 62:4225-4231. [PMID: 30920824 DOI: 10.1021/acs.jmedchem.8b01928] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Coumermycin A1 is a natural aminocoumarin that inhibits bacterial DNA gyrase, a member of the GHKL proteins superfamily. We report here the first cocrystal structures of gyrase B bound to coumermycin A1, revealing that one coumermycin A1 molecule traps simultaneously two ATP-binding sites. The inhibited dimers from different species adopt distinct sequence-dependent conformations, alternative to the ATP-bound form. These structures provide a basis for the rational development of coumermycin A1 derivatives for antibiotherapy and biotechnology applications.
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Affiliation(s)
- Arnaud Vanden Broeck
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Alastair G McEwen
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Yassmine Chebaro
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Noëlle Potier
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes, UMR 7140 CNRS, University of Strasbourg, Strasbourg 67000 , France
| | - Valérie Lamour
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France.,Hôpitaux Universitaires de Strasbourg , Strasbourg 67000 , France
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30
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Hymowitz SG, Malek S. Targeting the MAPK Pathway in RAS Mutant Cancers. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031492. [PMID: 29440321 DOI: 10.1101/cshperspect.a031492] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite decades of extensive drug discovery efforts, there are currently no targeted therapies approved to treat KRAS mutant cancers. In this review, we highlight the challenges and opportunities in targeting KRAS mutant tumors through inhibition of mitogen-activated protein kinase (MAPK) signaling with conformation-specific kinase inhibitors. Through structural analysis and mechanistic studies with BRAF and mitogen-activated protein kinase (MEK) inhibitors, we describe how kinase-dependent and -independent functions of MAPK signaling components regulate KRAS-driven tumorigenesis and how these insights can be used to treat RAS mutant cancers with small molecule kinase inhibitors.
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Affiliation(s)
- Sarah G Hymowitz
- Department of Structural Biology, Genentech Inc., South San Francisco, California 94080
| | - Shiva Malek
- Department of Discovery Oncology, Genentech Inc., South San Francisco, California 94080
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31
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Yuan J, Ng WH, Lam PYP, Wang Y, Xia H, Yap J, Guan SP, Lee ASG, Wang M, Baccarini M, Hu J. The dimer-dependent catalytic activity of RAF family kinases is revealed through characterizing their oncogenic mutants. Oncogene 2018; 37:5719-5734. [PMID: 29930381 PMCID: PMC6202329 DOI: 10.1038/s41388-018-0365-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
Abstract
Although extensively studied for three decades, the molecular mechanisms that regulate the RAF/MEK/ERK kinase cascade remain ambiguous. Recent studies identified the dimerization of RAF as a key event in the activation of this cascade. Here, we show that in-frame deletions in the β3-αC loop activate ARAF as well as BRAF and other oncogenic kinases by enforcing homodimerization. By characterizing these RAF mutants, we find that ARAF has less allosteric and catalytic activity than the other two RAF isoforms, which arises from its non-canonical APE motif. Further, these RAF mutants exhibit a strong oncogenic potential, and a differential inhibitor resistance that correlates with their dimer affinity. Using these unique mutants, we demonstrate that active RAFs, including the BRAF(V600E) mutant, phosphorylate MEK in a dimer-dependent manner. This study characterizes a special category of oncogenic kinase mutations, and elucidates the molecular basis that underlies the differential ability of RAF isoforms to stimulate MEK-ERK pathway. Further, this study reveals a unique catalytic feature of RAF family kinases that can be exploited to control their activities for cancer therapies.
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Affiliation(s)
- Jimin Yuan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Wan Hwa Ng
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Paula Y P Lam
- Division of Cellular and Molecular Research, Singapore, Singapore
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Yu Wang
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Hongping Xia
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Jiajun Yap
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Shou Ping Guan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Ann S G Lee
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
- Office of Clinical & Academic Faculty Affairs, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Physiology, National University of Singapore, 2 Medical Drive, 117597, Singapore, Singapore
| | - Mei Wang
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Manuela Baccarini
- Max F. Perutz Laboratories, University of Vienna, Doktor-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, Singapore, Singapore.
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore.
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32
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Ippagunta SK, Pollock JA, Sharma N, Lin W, Chen T, Tawaratsumida K, High AA, Min J, Chen Y, Guy RK, Redecke V, Katzenellenbogen JA, Häcker H. Identification of Toll-like receptor signaling inhibitors based on selective activation of hierarchically acting signaling proteins. Sci Signal 2018; 11:11/543/eaaq1077. [PMID: 30108181 DOI: 10.1126/scisignal.aaq1077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Toll-like receptors (TLRs) recognize various pathogen- and host tissue-derived molecules and initiate inflammatory immune responses. Exaggerated or prolonged TLR activation, however, can lead to etiologically diverse diseases, such as bacterial sepsis, metabolic and autoimmune diseases, or stroke. Despite the apparent medical need, no small-molecule drugs against TLR pathways are clinically available. This may be because of the complex signaling mechanisms of TLRs, which are governed by a series of protein-protein interactions initiated by Toll/interleukin-1 receptor homology domains (TIR) found in TLRs and the cytoplasmic adaptor proteins TIRAP and MyD88. Oligomerization of TLRs with MyD88 or TIRAP leads to the recruitment of members of the IRAK family of kinases and the E3 ubiquitin ligase TRAF6. We developed a phenotypic drug screening system based on the inducible homodimerization of either TIRAP, MyD88, or TRAF6, that ranked hits according to their hierarchy of action. From a bioactive compound library, we identified methyl-piperidino-pyrazole (MPP) as a TLR-specific inhibitor. Structure-activity relationship analysis, quantitative proteomics, protein-protein interaction assays, and cellular thermal shift assays suggested that MPP targets the TIR domain of MyD88. Chemical evolution of the original MPP scaffold generated compounds with selectivity for distinct TLRs that interfered with specific TIR interactions. Administration of an MPP analog to mice protected them from TLR4-dependent inflammation. These results validate this phenotypic screening approach and suggest that the MPP scaffold could serve as a starting point for the development of anti-inflammatory drugs.
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Affiliation(s)
- Sirish K Ippagunta
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Julie A Pollock
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Naina Sharma
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kazuki Tawaratsumida
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Anthony A High
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yizhe Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Vanessa Redecke
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | | | - Hans Häcker
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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33
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Schneider T, Martinez-Martinez A, Cubillos-Rojas M, Bartrons R, Ventura F, Rosa JL. The E3 ubiquitin ligase HERC1 controls the ERK signaling pathway targeting C-RAF for degradation. Oncotarget 2018; 9:31531-31548. [PMID: 30140388 PMCID: PMC6101136 DOI: 10.18632/oncotarget.25847] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 07/12/2018] [Indexed: 12/14/2022] Open
Abstract
The RAF/MEK/ERK cascade is a conserved intracellular signaling pathway that controls fundamental cellular processes including growth, proliferation, differentiation, survival and migration. Aberrant regulation of this signaling pathway has long been associated with human cancers. A major point of regulation of this pathway occurs at the level of the serine/threonine protein kinase C-RAF. Here, we show how the E3 ubiquitin ligase HERC1 regulates ERK signaling. HERC1 knockdown induced cellular proliferation, which is associated with an increase in ERK phosphorylation and in C-RAF protein levels. We demonstrate that overexpression of wild-type C-RAF is sufficient to increase ERK phosphorylation. Experiments with pharmacological inhibitors of RAF activity, or with interference RNA, show that the regulation of ERK phosphorylation by HERC1 is RAF-dependent. Immunoprecipitation, pull-down and confocal fluorescence microscopy experiments demonstrate an interaction between HERC1 and C-RAF proteins. Mechanistically, HERC1 controls C-RAF stability by regulating its polyubiquitylation in a lysine 48-linked chain. In vitro ubiquitylation assays indicate that C-RAF is a substrate of the E3 ubiquitin ligase HERC1. Altogether, we show how HERC1 can regulate cell proliferation through the activation of ERK signaling by a mechanism that affects C-RAF’s stability.
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Affiliation(s)
- Taiane Schneider
- Departament de Ciències Fisiològiques, IDIBELL, Campus Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Arturo Martinez-Martinez
- Departament de Ciències Fisiològiques, IDIBELL, Campus Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Monica Cubillos-Rojas
- Departament de Ciències Fisiològiques, IDIBELL, Campus Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ramon Bartrons
- Departament de Ciències Fisiològiques, IDIBELL, Campus Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Francesc Ventura
- Departament de Ciències Fisiològiques, IDIBELL, Campus Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jose Luis Rosa
- Departament de Ciències Fisiològiques, IDIBELL, Campus Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
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34
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Yuan J, Ng WH, Yap J, Chia B, Huang X, Wang M, Hu J. The AMPK inhibitor overcomes the paradoxical effect of RAF inhibitors through blocking phospho-Ser-621 in the C terminus of CRAF. J Biol Chem 2018; 293:14276-14284. [PMID: 30030377 PMCID: PMC6139560 DOI: 10.1074/jbc.ra118.004597] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/17/2018] [Indexed: 11/15/2022] Open
Abstract
The dimerization-driven paradoxical activation of RAF proto-oncogene Ser/Thr kinase (RAF) is the predominant cause of drug resistance and toxicity in cancer therapies with RAF inhibitors. The scaffold protein 14-3-3, which binds to the RAF C terminus, is essential for RAF activation under physiological conditions, but the molecular basis is unclear. Here we investigated whether and how 14-3-3 regulates the dimerization-driven transactivation of the RAF isoform CRAF by RAF inhibitors and affects drug resistance and toxicity by virtue of the dominant role of CRAF in these processes. We demonstrated that 14-3-3 enhances the dimerization-driven transactivation of CRAF by stabilizing CRAF dimers. Further, we identified AMP-activated protein kinase (AMPK) and CRAF itself as two putative kinases that redundantly phosphorylate CRAF's C terminus and thereby control its association with 14-3-3. Next, we determined whether the combinatory inhibition of AMPK and CRAF could overcome the paradoxical effect of RAF inhibitors. We found that the AMPK inhibitor (AMPKi) not only blocked the RAF inhibitor–driven paradoxical activation of ERK signaling and cellular overgrowth in Ras-mutated cancer cells by blocking phosphorylation of Ser-621 in CRAF but also reduced the formation of drug-resistant clones of BRAFV600E-mutated cancer cells. Last, we investigated whether 14-3-3 binding to the C terminus of CRAF is required for CRAF catalytic activity and observed that it was dispensable in vivo. Altogether, our study unravels the molecular mechanism by which 14-3-3 regulates dimerization-driven RAF activation and identified AMPKi as a potential agent to counteract drug resistance and adverse effects of RAF inhibitors in cancer therapies.
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Affiliation(s)
- Jimin Yuan
- From the Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore and
| | - Wan Hwa Ng
- From the Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore and
| | - Jiajun Yap
- From the Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore and
| | - Brandon Chia
- From the Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore and
| | - Xuchao Huang
- From the Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore and
| | - Mei Wang
- the Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jiancheng Hu
- From the Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore and .,the Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
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35
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Hill ZB, Martinko AJ, Nguyen DP, Wells JA. Human antibody-based chemically induced dimerizers for cell therapeutic applications. Nat Chem Biol 2017; 14:112-117. [PMID: 29200207 PMCID: PMC6352901 DOI: 10.1038/nchembio.2529] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 10/20/2017] [Indexed: 01/27/2023]
Abstract
Chemically induced dimerizers (CIDs) have emerged as one of the most powerful tools to artificially regulate signaling pathways in cells; however, currently available CID systems lack the properties desired for use in regulating cellular therapies. Here, we report the development of human antibody-based chemically induced dimerizers (AbCIDs) from known small-molecule-protein complexes by selecting for synthetic antibodies that recognize the chemical epitope created by the bound small molecule. We demonstrate this concept by generating three antibodies that are highly selective for the BCL-xL/ABT-737 complex over BCL-xL alone. We show the potential of AbCIDs to be applied to regulating human cell therapies by using them to induce CRISPRa-mediated gene expression and to regulate CAR T-cell activation. We believe that the AbCIDs generated in this study will find application in regulating cell therapies, and that the general method of AbCID development may lead to the creation of many new and orthogonal CIDs.
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Affiliation(s)
- Zachary B Hill
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Alexander J Martinko
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Duy P Nguyen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
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36
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Hu L, Xu J, Xie X, Zhou Y, Tao P, Li H, Han X, Wang C, Liu J, Xu P, Neculai D, Xia Z. Oligomerization-primed coiled-coil domain interaction with Ubc13 confers processivity to TRAF6 ubiquitin ligase activity. Nat Commun 2017; 8:814. [PMID: 28993672 PMCID: PMC5634496 DOI: 10.1038/s41467-017-01290-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 09/06/2017] [Indexed: 11/30/2022] Open
Abstract
Ubiquitin ligase TRAF6, together with ubiquitin-conjugating enzyme Ubc13/Uev1, catalyzes processive assembly of unanchored K63-linked polyubiquitin chains for TAK1 activation in the IL-1R/TLR pathways. However, what domain and how it functions to enable TRAF6’s processivity are largely uncharacterized. Here, we find TRAF6 coiled-coil (CC) domain is crucial to enable its processivity. The CC domain mediates TRAF6 oligomerization to ensure efficient long polyubiquitin chain assembly. Mutating or deleting the CC domain impairs TRAF6 oligomerization and processive polyubiquitin chain assembly. Fusion of the CC domain to the E3 ubiquitin ligase CHIP/STUB1 renders the latter capable of NF-κB activation. Moreover, the CC domain, after oligomerization, interacts with Ubc13/Ub~Ubc13, which further contributes to TRAF6 processivity. Point mutations within the CC domain that weaken TRAF6 interaction with Ubc13/Ub~Ubc13 diminish TRAF6 processivity. Our results reveal that the CC oligomerization primes its interaction with Ubc13/Ub~Ubc13 to confer processivity to TRAF6 ubiquitin ligase activity. Ubiquitin ligase TRAF6 catalyzes assembly of free polyubiquitin chains for TAK1 activation in the IL-1R/TLR pathways, but the mechanism underlying its processivity is unclear. Here, the authors show that TRAF6 coiled-coil oligomerization domain primes its interaction with Ubc13/Ub~Ubc13 to confer processivity.
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Affiliation(s)
- Lin Hu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Jiafeng Xu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Xiaomei Xie
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Yiwen Zhou
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Panfeng Tao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Haidong Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Xu Han
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Chong Wang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Jian Liu
- Department of Surgical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Pinglong Xu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Dante Neculai
- College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Zongping Xia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310027, China.
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37
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Richtig G, Hoeller C, Kashofer K, Aigelsreiter A, Heinemann A, Kwong L, Pichler M, Richtig E. Beyond the BRAF
V
600E
hotspot: biology and clinical implications of rare BRAF
gene mutations in melanoma patients. Br J Dermatol 2017; 177:936-944. [DOI: 10.1111/bjd.15436] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 12/15/2022]
Affiliation(s)
- G. Richtig
- Institute of Experimental and Clinical Pharmacology; Medical University of Graz; Graz Austria
- Department of Dermatology; Medical University of Graz; Graz Austria
| | - C. Hoeller
- Department of Dermatology; Medical University of Vienna; Vienna Austria
| | - K. Kashofer
- Institute for Pathology; Medical University of Graz; Graz Austria
| | - A. Aigelsreiter
- Institute for Pathology; Medical University of Graz; Graz Austria
| | - A. Heinemann
- Institute of Experimental and Clinical Pharmacology; Medical University of Graz; Graz Austria
| | - L.N. Kwong
- Translational Molecular Pathology; The University of Texas MD Anderson Cancer Center; Houston TX U.S.A
| | - M. Pichler
- Division of Oncology; Medical University of Graz; Graz Austria
- Department of Experimental Therapeutics; The University of Texas MD Anderson Cancer Center; Houston TX U.S.A
| | - E. Richtig
- Department of Dermatology; Medical University of Graz; Graz Austria
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38
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Abstract
Metastatic melanoma is associated with poor outcome and is largely refractory to the historic standard of care. In recent years, the development of targeted small-molecule inhibitors and immunotherapy has revolutionised the care and improved the overall survival of these patients. Therapies targeting BRAF and MEK to block the mitogen-activated protein kinase (MAPK) pathway were the first to show unprecedented clinical responses. Following these encouraging results, antibodies targeting immune checkpoint inhibition molecules cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4), programmed cell death (PD)-1, and PD-ligand1(PD-L1) demonstrated sustained tumour regression in a significant subset of patients by enabling an anti-tumour immunologic response. Despite these landmark changes in practice, the majority of patients are either intrinsically resistant or rapidly acquire resistance to MAPK pathway inhibitors and immune checkpoint blockade treatment. The lack of response can be driven by mutations and non-mutational events in tumour cells, as well as by changes in the surrounding tumour microenvironment. Common resistance mechanisms bypass the dependence of tumour cells on initial MAPK pathway driver mutations during targeted therapy, and permit evasion of the host immune system to allow melanoma growth and survival following immunotherapy. This highlights the requirement for personalised treatment regimens that take into account patient-specific genetic and immunologic characteristics. Here we review the mechanisms by which melanomas display intrinsic resistance or acquire resistance to targeted therapy and immunotherapy.
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Affiliation(s)
- Matthew Winder
- Skin Cancer and Ageing, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
| | - Amaya Virós
- Skin Cancer and Ageing, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK. .,Salford Royal NHS Foundation Trust, Manchester, UK.
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39
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Chen M, Peters A, Huang T, Nan X. Ras Dimer Formation as a New Signaling Mechanism and Potential Cancer Therapeutic Target. Mini Rev Med Chem 2016; 16:391-403. [PMID: 26423697 PMCID: PMC5421135 DOI: 10.2174/1389557515666151001152212] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/31/2015] [Accepted: 09/18/2015] [Indexed: 12/12/2022]
Abstract
The K-, N-, and HRas small GTPases are key regulators of cell physiology and are frequently mutated in human cancers. Despite intensive research, previous efforts to target hyperactive Ras based on known mechanisms of Ras signaling have been met with little success. Several studies have provided compelling evidence for the existence and biological relevance of Ras dimers, establishing a new mechanism for regulating Ras activity in cells additionally to GTP-loading and membrane localization. Existing data also start to reveal how Ras proteins dimerize on the membrane. We propose a dimer model to describe Ras-mediated effector activation, which contrasts existing models of Ras signaling as a monomer or as a 5-8 membered multimer. We also discuss potential implications of this model in both basic and translational Ras biology.
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Affiliation(s)
| | | | | | - Xiaolin Nan
- Department of Biomedical Engineering, Knight Cancer Institute, and OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR.
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40
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Mitra S, Ghosh B, Gayen N, Roy J, Mandal AK. Bipartite Role of Heat Shock Protein 90 (Hsp90) Keeps CRAF Kinase Poised for Activation. J Biol Chem 2016; 291:24579-24593. [PMID: 27703006 DOI: 10.1074/jbc.m116.746420] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/21/2016] [Indexed: 01/27/2023] Open
Abstract
CRAF kinase maintains cell viability, growth, and proliferation by participating in the MAPK pathway. Unlike BRAF, CRAF requires continuous chaperoning by Hsp90 to retain MAPK signaling. However, the reason behind the continuous association of Hsp90 with CRAF is still elusive. In this study, we have identified the bipartite role of Hsp90 in chaperoning CRAF kinase. Hsp90 facilitates Ser-621 phosphorylation of CRAF and prevents the kinase from degradation. Co-chaperone Cdc37 assists in this phosphorylation event. However, after folding, the stability of the kinase becomes insensitive to Hsp90 inhibition, although the physical association between Hsp90 and CRAF remains intact. We observed that overexpression of Hsp90 stimulates MAPK signaling by activating CRAF. The interaction between Hsp90 and CRAF is substantially increased under an elevated level of cellular Hsp90 and in the presence of either active Ras (RasV12) or EGF. Surprisingly, enhanced binding of Hsp90 to CRAF occurs prior to the Ras-CRAF association and facilitates actin recruitment to CRAF for efficient Ras-CRAF interaction, which is independent of the ATPase activity of Hsp90. However, monomeric CRAF (CRAFR401H) shows abrogated interaction with both Hsp90 and actin, thereby affecting Hsp90-dependent CRAF activation. This finding suggests that stringent assemblage of Hsp90 keeps CRAF kinase equipped for participating in the MAPK pathway. Thus, the role of Hsp90 in CRAF maturation and activation acts as a limiting factor to maintain the function of a strong client like CRAF kinase.
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Affiliation(s)
- Shahana Mitra
- From the Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Baijayanti Ghosh
- From the Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Nilanjan Gayen
- From the Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Joydeep Roy
- From the Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Atin K Mandal
- From the Division of Molecular Medicine, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India.
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41
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Regan L, Hinrichsen MR, Oi C. Protein engineering strategies with potential applications for altering clinically relevant cellular pathways at the protein level. Expert Rev Proteomics 2016; 13:481-93. [PMID: 27031866 DOI: 10.1586/14789450.2016.1172966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
All diseases can be fundamentally viewed as the result of malfunctioning cellular pathways. Protein engineering offers the potential to develop new tools that will allow these dysfunctional pathways to be better understood, in addition to potentially providing new routes to restore proper function. Here we discuss different approaches that can be used to change the intracellular activity of a protein by intervening at the protein level: targeted protein sequestration, protein recruitment, protein degradation, and selective inhibition of binding interfaces. The potential of each of these tools to be developed into effective therapeutic treatments will also be discussed, along with any major barriers that currently block their translation into the clinic.
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Affiliation(s)
- Lynne Regan
- a Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA.,b Department of Chemistry , Yale University , New Haven , CT , USA.,c Integrated Graduate Program in Physical and Engineering Biology , Yale University , New Haven , CT , USA
| | - Michael R Hinrichsen
- a Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA
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42
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Hernandez MA, Patel B, Hey F, Giblett S, Davis H, Pritchard C. Regulation of BRAF protein stability by a negative feedback loop involving the MEK-ERK pathway but not the FBXW7 tumour suppressor. Cell Signal 2016; 28:561-71. [PMID: 26898828 PMCID: PMC6399479 DOI: 10.1016/j.cellsig.2016.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/08/2016] [Accepted: 02/15/2016] [Indexed: 01/06/2023]
Abstract
The V600EBRAF oncogenic mutation is detected in a wide range of human cancers and induces hyperactivation of the downstream MEK–ERK signalling cascade. Although output of the BRAF–MEK–ERK pathway is regulated by feed-forward RAF activity, feedback control also plays an important role. One such feedback pathway has been identified in Caenorhabditis elegans and involves ERK-mediated phosphorylation of BRAF within a CDC4 phosphodegron (CPD), targeting BRAF for degradation via CDC4 (also known as FBXW7), a component of the SKP1/CUL1/F-box (SCF) E3 ubiquitin ligase complex. Here we investigate this pathway in mammalian cells. Short-term expression of autochthonous V600EBRAF in mouse embryonic fibroblasts (MEFs) leads to down-regulation of BRAF protein levels in a proteasome-dependent manner and V600EBRAF has a reduced half-life compared to WTBRAF in HEK293T cells. These effects were reversed by treatment with the MEK inhibitor PD184352. We have identified the equivalent CPD at residues 400–405 in human BRAF and have found that mutation of ERK phosphorylation sites at residues T401 and S405 in V600EBRAF increases the half-life of the protein. While BRAF and FBXW7 co-immunoprecipitated, the overexpression of FBXW7 did not influence the half-life of either WTBRAF or V600EBRAF. Furthermore, disruption of the substrate-binding site of mouse FBXW7 using the R482Q mutation did not affect the interaction with BRAF and the expression levels of WTBRAF and V600EBRAF were not altered in MEFs derived from mice with the homozygous knockin R482QFBXW7 mutation. Overall these data confirm the existence of a negative feedback pathway by which BRAF protein stability is regulated by ERK. However, unlike the situation in C. elegans, FBXW7 does not play a unique role in mediating subsequent BRAF degradation. Expression of oncogenic V600EBRAF down-regulates BRAF expression at the protein level. V600EBRAF has a shorter half-life than WTBRAF. BRAF protein stability is subjected to feedback control by the MEK/ERK pathway. This feedback pathway is associated with the oncogene-induced senescence phenotype. ERK phosphorylation sites at T401 and S405 within a conserved CDC4 (FBXW7) phosphodegron of BRAF are involved in the feedback control pathway. The FBXW7 substrate recognition component of the SKP1/CUL1/F-box (SCF) complex binds to BRAF but is not uniquely involved in the regulation of its protein turnover.
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Affiliation(s)
- Maria Aguilar Hernandez
- Department of Molecular Cell Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Bipin Patel
- Department of Molecular Cell Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Fiona Hey
- Department of Molecular Cell Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Susan Giblett
- Department of Molecular Cell Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Hayley Davis
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Catrin Pritchard
- Department of Molecular Cell Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; Department of Cancer Studies, University of Leicester, University Road, Leicester LE1 7RH, UK.
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43
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Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Nora Rauch
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Ruth Pilkington
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Katja Rybakova
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Lan K. Nguyen
- Systems Biology Ireland; University College Dublin, Belfield; Dublin 4 Ireland
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute; Monash University; Melbourne Victoria 3800 Australia
| | - Boris N. Kholodenko
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptative Systems Laboratory; University College Dublin, Belfield; Dublin 4 Ireland
| | - Walter Kolch
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
- School of Medicine & Medical Sciences; University College Dublin, Belfield; Dublin 4 Ireland
| | - Edina Rosta
- Department of Chemistry; King's College London; London SE1 1DB UK
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44
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Perdios L, Bunney TD, Warren SC, Dunsby C, French PMW, Tate EW, Katan M. Time-resolved FRET reports FGFR1 dimerization and formation of a complex with its effector PLCγ1. Adv Biol Regul 2016; 60:6-13. [PMID: 26482290 PMCID: PMC4739061 DOI: 10.1016/j.jbior.2015.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/22/2015] [Indexed: 11/05/2022]
Abstract
In vitro and in vivo imaging of protein tyrosine kinase activity requires minimally invasive, molecularly precise optical probes to provide spatiotemporal mechanistic information of dimerization and complex formation with downstream effectors. We present here a construct with genetically encoded, site-specifically incorporated, bioorthogonal reporter that can be selectively labelled with exogenous fluorogenic probes to monitor the structure and function of fibroblast growth factor receptor (FGFR). GyrB.FGFR1KD.TC contains a coumermycin-induced artificial dimerizer (GyrB), FGFR1 kinase domain (KD) and a tetracysteine (TC) motif that enables fluorescent labelling with biarsenical dyes FlAsH-EDT2 and ReAsH-EDT2. We generated bimolecular system for time-resolved FRET (TR-FRET) studies, which pairs FlAsH-tagged GyrB.FGFR1KD.TC and N-terminal Src homology 2 (nSH2) domain of phospholipase Cγ (PLCγ), a downstream effector of FGFR1, fused to mTurquoise fluorescent protein (mTFP). We demonstrated phosphorylation-dependent TR-FRET readout of complex formation between mTFP.nSH2 and GyrB.FGFR1KD.TC. By further application of TR-FRET, we also demonstrated formation of the GyrB.FGFR1KD.TC homodimer by coumermycin-induced dimerization. Herein, we present a spectroscopic FRET approach to facilitate and propagate studies that would provide structural and functional insights for FGFR and other tyrosine kinases.
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Affiliation(s)
- Louis Perdios
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK; Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Tom D Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Sean C Warren
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Christopher Dunsby
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Paul M W French
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK.
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45
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Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angew Chem Int Ed Engl 2015; 55:983-6. [PMID: 26644280 PMCID: PMC4736688 DOI: 10.1002/anie.201509272] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Indexed: 12/19/2022]
Abstract
RAF kinases are key players in the MAPK signaling pathway and are important targets for personalized cancer therapy. RAF dimerization is part of the physiological activation mechanism, together with phosphorylation, and is known to convey resistance to RAF inhibitors. Herein, molecular dynamics simulations are used to show that phosphorylation of a key N-terminal acidic (NtA) motif facilitates RAF dimerization by introducing several interprotomer salt bridges between the αC-helix and charged residues upstream of the NtA motif. Additionally, we show that the R-spine of RAF interacts with a conserved Trp residue in the vicinity of the NtA motif, connecting the active sites of two protomers and thereby modulating the cooperative interactions in the RAF dimer. Our findings provide a first structure-based mechanism for the auto-transactivation of RAF and could be generally applicable to other kinases, opening new pathways for overcoming dimerization-related drug resistance.
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Affiliation(s)
- Pablo G Jambrina
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Nora Rauch
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Ruth Pilkington
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Katja Rybakova
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Lan K Nguyen
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, 4, Ireland.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, 3800, Australia
| | - Boris N Kholodenko
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptative Systems Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Walter Kolch
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland. .,School of Medicine & Medical Sciences, University College Dublin, Belfield, Dublin, 4, Ireland.
| | - Edina Rosta
- Department of Chemistry, King's College London, London, SE1 1DB, UK.
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46
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Peng SB, Henry JR, Kaufman MD, Lu WP, Smith BD, Vogeti S, Rutkoski TJ, Wise S, Chun L, Zhang Y, Van Horn RD, Yin T, Zhang X, Yadav V, Chen SH, Gong X, Ma X, Webster Y, Buchanan S, Mochalkin I, Huber L, Kays L, Donoho GP, Walgren J, McCann D, Patel P, Conti I, Plowman GD, Starling JJ, Flynn DL. Inhibition of RAF Isoforms and Active Dimers by LY3009120 Leads to Anti-tumor Activities in RAS or BRAF Mutant Cancers. Cancer Cell 2015; 28:384-98. [PMID: 26343583 DOI: 10.1016/j.ccell.2015.08.002] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/29/2015] [Accepted: 08/03/2015] [Indexed: 12/19/2022]
Abstract
LY3009120 is a pan-RAF and RAF dimer inhibitor that inhibits all RAF isoforms and occupies both protomers in RAF dimers. Biochemical and cellular analyses revealed that LY3009120 inhibits ARAF, BRAF, and CRAF isoforms with similar affinity, while vemurafenib or dabrafenib have little or modest CRAF activity compared to their BRAF activities. LY3009120 induces BRAF-CRAF dimerization but inhibits the phosphorylation of downstream MEK and ERK, suggesting that it effectively inhibits the kinase activity of BRAF-CRAF heterodimers. Further analyses demonstrated that LY3009120 also inhibits various forms of RAF dimers including BRAF or CRAF homodimers. Due to these unique properties, LY3009120 demonstrates minimal paradoxical activation, inhibits MEK1/2 phosphorylation, and exhibits anti-tumor activities across multiple models carrying KRAS, NRAS, or BRAF mutation.
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Affiliation(s)
| | | | | | - Wei-Ping Lu
- Deciphera Pharmaceuticals, LLC, Lawrence, KS 66044, USA
| | - Bryan D Smith
- Deciphera Pharmaceuticals, LLC, Lawrence, KS 66044, USA
| | - Subha Vogeti
- Deciphera Pharmaceuticals, LLC, Lawrence, KS 66044, USA
| | | | - Scott Wise
- Deciphera Pharmaceuticals, LLC, Lawrence, KS 66044, USA
| | - Lawrence Chun
- Emerald Biostructures, Bainbridge Island, WA 98110, USA
| | - Youyan Zhang
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | - Tinggui Yin
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Xiaoyi Zhang
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Vipin Yadav
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | - Xueqian Gong
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Xiwen Ma
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Yue Webster
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | | | | | - Lisa Kays
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | | | - Denis McCann
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Phenil Patel
- Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Ilaria Conti
- Eli Lilly and Company, Indianapolis, IN 46285, USA
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47
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Gollasch B, Basmanav FB, Nanda A, Fritz G, Mahmoudi H, Thiele H, Wehner M, Wolf S, Altmüller J, Nürnberg P, Frank J, Betz RC. Identification of a novel mutation inRIPK4in a kindred with phenotypic features of Bartsocas-Papas and CHAND syndromes. Am J Med Genet A 2015; 167A:2555-62. [DOI: 10.1002/ajmg.a.37233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 06/15/2015] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Arti Nanda
- Genetic Skin Diseases Clinic; As'ad Al-Hamad Dermatology Center; Al-Sabah Hospital Kuwait
| | - Günter Fritz
- Department of Neuropathology; Neurozentrum; University of Freiburg; Freiburg Germany
| | | | - Holger Thiele
- Cologne Center for Genomics (CCG); University of Cologne; Cologne Germany
| | - Maria Wehner
- Institute of Human Genetics; University of Bonn; Bonn Germany
| | - Sabrina Wolf
- Institute of Human Genetics; University of Bonn; Bonn Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG); University of Cologne; Cologne Germany
- Institute of Human Genetics; University of Cologne; Cologne Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG); University of Cologne; Cologne Germany
- Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
- Center for Molecular Medicine Cologne (CMMC); University of Cologne; Cologne Germany
| | - Jorge Frank
- Division of Dermatogenetics and Skin Cancer Center; Department of Dermatology; University of Düsseldorf; Düsseldorf Germany
| | - Regina C. Betz
- Institute of Human Genetics; University of Bonn; Bonn Germany
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48
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Abstract
RAF family kinases were among the first oncoproteins to be described more than 30 years ago. They primarily act as signalling relays downstream of RAS, and their close ties to cancer have fuelled a large number of studies. However, we still lack a systems-level understanding of their regulation and mode of action. The recent discovery that the catalytic activity of RAF depends on an allosteric mechanism driven by kinase domain dimerization is providing a vital new piece of information towards a comprehensive model of RAF function. The fact that current RAF inhibitors unexpectedly induce ERK signalling by stimulating RAF dimerization also calls for a deeper structural characterization of this family of kinases.
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49
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Chemical biology strategies for posttranslational control of protein function. ACTA ACUST UNITED AC 2015; 21:1238-52. [PMID: 25237866 DOI: 10.1016/j.chembiol.2014.08.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/08/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023]
Abstract
A common strategy to understand a biological system is to selectively perturb it and observe its response. Although technologies now exist to manipulate cellular systems at the genetic and transcript level, the direct manipulation of functions at the protein level can offer significant advantages in precision, speed, and reversibility. Combining the specificity of genetic manipulation and the spatiotemporal resolution of light- and small molecule-based approaches now allows exquisite control over biological systems to subtly perturb a system of interest in vitro and in vivo. Conditional perturbation mechanisms may be broadly characterized by change in intracellular localization, intramolecular activation, or degradation of a protein-of-interest. Here we review recent advances in technologies for conditional regulation of protein function and suggest further areas of potential development.
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Abstract
We have come a long way in the 55 years since Edmond Fischer and the late Edwin Krebs discovered that the activity of glycogen phosphorylase is regulated by reversible protein phosphorylation. Many of the fundamental molecular mechanisms that operate in biological signaling have since been characterized and the vast web of interconnected pathways that make up the cellular signaling network has been mapped in considerable detail. Nonetheless, it is important to consider how fast this field is still moving and the issues at the current boundaries of our understanding. One must also appreciate what experimental strategies have allowed us to attain our present level of knowledge. We summarize here some key issues (both conceptual and methodological), raise unresolved questions, discuss potential pitfalls, and highlight areas in which our understanding is still rudimentary. We hope these wide-ranging ruminations will be useful to investigators who carry studies of signal transduction forward during the rest of the 21st century.
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