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Bialves TS, Bastos LL, Parra JAA, Moysés MN, Marques E, de Castro Pimenta AM, Quintela FM, Mariano DCB, Carvalho FC, de Melo-Minardi RC, Boyle RT. Interaction of DisBa01 peptide from Bothrops alternatus venom with BRAF melanoma receptors: Modeling and molecular docking. Int J Biol Macromol 2024; 274:133283. [PMID: 38909731 DOI: 10.1016/j.ijbiomac.2024.133283] [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: 01/09/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 06/25/2024]
Abstract
Metastatic melanoma is highly aggressive and challenging, often leading to a grim prognosis. Its progression is swift, especially when mutations like BRAFV600E continuously activate pathways vital for cell growth and survival. Although several treatments target this mutation, resistance typically emerges over time. In recent decades, research has underscored the potential of snake venoms and peptides as bioactive substances for innovative drugs, including anti-coagulants, anti-microbial, and anti-cancer agents. Leveraging this knowledge, we propose employing a bioinformatics simulation approach to: a) Predict how well a peptide (DisBa01) from Bothrops alternatus snake venom binds to the melanoma receptor BRAFV600E via Molecular Docking. b) Identify the specific peptide binding sites on receptors and analyze their proximity to active receptor sites. c) Evaluate the behavior of resulting complexes through molecular dynamics simulations. d) Assess whether this peptide qualifies as a candidate for anti-melanoma therapy. Our findings reveal that DisBa01 enhances stability in the BRAFV600E melanoma receptor structure by binding to its RGD motif, an interaction absent in the BRAF WT model. Consequently, both docking and molecular dynamics simulations suggest that DisBa01 shows promise as a BRAFV600E inhibitor.
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Affiliation(s)
- Tatiane Senna Bialves
- Graduate Program in Physiological Sciences (PPGCF), Federal University of Rio Grande - FURG, Av. Italy, s/n - km 8 - Carreiros, Rio Grande, Rio Grande do Sul, Brazil.
| | - Luana Luiza Bastos
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - John Alexanders Amaya Parra
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maurício Nogueira Moysés
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edleusa Marques
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Adriano Monteiro de Castro Pimenta
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernando Marques Quintela
- Instituto Nacional de Pesquisas do Pantanal- Museu Paraense Emílio Goeldi, Av. Magalhães Barata, 376, Belém, Pará, Brazil
| | - Diego César Batista Mariano
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Frederico Chaves Carvalho
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Raquel C de Melo-Minardi
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Robert Tew Boyle
- Graduate Program in Physiological Sciences (PPGCF), Federal University of Rio Grande - FURG, Av. Italy, s/n - km 8 - Carreiros, Rio Grande, Rio Grande do Sul, Brazil
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2
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Tanaka R, Mrachek K, Arocho-Quinones E, Carlberg VM, Smith C, Kurzrock R, Deshmukh T. Dabrafenib for Pilocytic Astrocytoma With BRAF V599ins. JCO Precis Oncol 2024; 8:e2400055. [PMID: 38781546 DOI: 10.1200/po.24.00055] [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: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/09/2024] [Indexed: 05/25/2024] Open
Abstract
This report highlights the first pediatric case of pilocytic astrocytoma with BRAF V599ins mutation, successfully treated with dabrafenib.
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Affiliation(s)
- Ryuma Tanaka
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Kelly Mrachek
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI
| | | | | | - Candice Smith
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Razelle Kurzrock
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
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3
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Lauinger M, Christen D, Klar RFU, Roubaty C, Heilig CE, Stumpe M, Knox JJ, Radulovich N, Tamblyn L, Xie IY, Horak P, Forschner A, Bitzer M, Wittel UA, Boerries M, Ball CR, Heining C, Glimm H, Fröhlich M, Hübschmann D, Gallinger S, Fritsch R, Fröhling S, O'Kane GM, Dengjel J, Brummer T. BRAF Δβ3-αC in-frame deletion mutants differ in their dimerization propensity, HSP90 dependence, and druggability. SCIENCE ADVANCES 2023; 9:eade7486. [PMID: 37656784 DOI: 10.1126/sciadv.ade7486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
In-frame BRAF exon 12 deletions are increasingly identified in various tumor types. The resultant BRAFΔβ3-αC oncoproteins usually lack five amino acids in the β3-αC helix linker and sometimes contain de novo insertions. The dimerization status of BRAFΔβ3-αC oncoproteins, their precise pathomechanism, and their direct druggability by RAF inhibitors (RAFi) has been under debate. Here, we functionally characterize BRAFΔLNVTAP>F and two novel mutants, BRAFdelinsFS and BRAFΔLNVT>F, and compare them with other BRAFΔβ3-αC oncoproteins. We show that BRAFΔβ3-αC oncoproteins not only form stable homodimers and large multiprotein complexes but also require dimerization. Nevertheless, details matter as aromatic amino acids at the deletion junction of some BRAFΔβ3-αC oncoproteins, e.g., BRAFΔLNVTAP>F, increase their stability and dimerization propensity while conferring resistance to monomer-favoring RAFi such as dabrafenib or HSP 90/CDC37 inhibition. In contrast, dimer-favoring inhibitors such as naporafenib inhibit all BRAFΔβ3-αC mutants in cell lines and patient-derived organoids, suggesting that tumors driven by such oncoproteins are vulnerable to these compounds.
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Affiliation(s)
- Manuel Lauinger
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Daniel Christen
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rhena F U Klar
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carole Roubaty
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christoph E Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laura Tamblyn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Irene Y Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrea Forschner
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
| | - Michael Bitzer
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
- Center for Personalized Medicine Tübingen, Eberhard Karls University, Tübingen, Germany
- Department of Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Uwe A Wittel
- Department of General and Visceral Surgery, University of Freiburg Medical Center, Faculty of Medicine, 79106 Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Technische Universität Dresden, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Christoph Heining
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ralph Fritsch
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Department of Medical Oncology and Haematology, University Hospital of Zurich, Zurich, Switzerland
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Tilman Brummer
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany
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4
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Chessel A, De Crozé N, Molina MD, Taberner L, Dru P, Martin L, Lepage T. RAS-independent ERK activation by constitutively active KSR3 in non-chordate metazoa. Nat Commun 2023; 14:3970. [PMID: 37407549 DOI: 10.1038/s41467-023-39606-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 06/21/2023] [Indexed: 07/07/2023] Open
Abstract
During early development of the sea urchin embryo, activation of ERK signalling in mesodermal precursors is not triggered by extracellular RTK ligands but by a cell-autonomous, RAS-independent mechanism that was not understood. We discovered that in these cells, ERK signalling is activated through the transcriptional activation of a gene encoding a protein related to Kinase Suppressor of Ras, that we named KSR3. KSR3 belongs to a family of catalytically inactive allosteric activators of RAF. Phylogenetic analysis revealed that genes encoding kinase defective KSR3 proteins are present in most non-chordate metazoa but have been lost in flies and nematodes. We show that the structure of KSR3 factors resembles that of several oncogenic human RAF mutants and that KSR3 from echinoderms, cnidarians and hemichordates activate ERK signalling independently of RAS when overexpressed in cultured cells. Finally, we used the sequence of KSR3 factors to identify activating mutations of human B-RAF. These findings reveal key functions for this family of factors as activators of RAF in RAS-independent ERK signalling in invertebrates. They have implications on the evolution of the ERK signalling pathway and suggest a mechanism for its co-option in the course of evolution.
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Affiliation(s)
- Aline Chessel
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Noémie De Crozé
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Maria Dolores Molina
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
| | - Laura Taberner
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Philippe Dru
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Luc Martin
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France
| | - Thierry Lepage
- Institut de Biologie Valrose CNRS, Université Côte d'Azur, Nice, France.
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5
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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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6
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Yamasaki H, Uematsu Y, Okano K, Ichikawa M, Tei M, Hirabayashi M, Uchida K, Ono K, Hirao H. Establishment and characterization of urothelial carcinoma cell lines with and without BRAF mutation (V595E) in dogs. In Vitro Cell Dev Biol Anim 2022; 58:898-911. [PMID: 36477686 PMCID: PMC9780145 DOI: 10.1007/s11626-022-00736-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022]
Abstract
Each 5 urothelial carcinoma (UC) cell lines with and without the v-Raf murine sarcoma virus oncogene homolog B (BRAF) gene mutation (V595E) were established and examined V595E-related tumorigenic characteristics in dogs. No typical morphological features were observed in cloned cells with and without V595E. The cell proliferation of both cloned cells showed logarithmic growth curve and those doubling time were 24.9 ± 4.1 h in V595E ( +) and 29.3 ± 11.3 h in V595E ( -). On the growth curve of xenotransplanted tumor in severe combined immunodeficiency mice, 3 out of 5 V595E ( +) and 2 out of 5 V595E ( -) cloned cells revealed gradually and remarkably increasing curve, indicating clearly tumorigenicity. The xenotransplanted tumors with V595E ( +) showed typical features of UC, such as solid proliferation of pleomorphic tumor cells, formation of papillary structure, and glandular structure. Additionally, various vascular formation was observed, probably indicating an advanced growth phase of UC. In mitogen-activated protein kinase (MAPK) signaling pathway, cytoplasmic phosphorylated-BRAF (pBRAF) and cytoplasmic and nuclear phosphorylated-ERK1/2 (pERK1/2) were detected in all 4 tumors with V595E ( +), whereas only cytoplasmic and nuclear pERK1/2 was detected in tumors with V595E ( -). Since V595E can directly activate MAPK signaling pathway, coincidence of V595E with pBRAF (phosphor Thr598/Ser601) indicates acquired resistance to BRAF inhibitors. These established UC cell lines, especially V595E ( +) cell lines, are useful tool for understanding pathophysiological states and controlling therapeutic manners of UC in dogs.
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Affiliation(s)
- Hirofumi Yamasaki
- Japan Animal Referral Medical Center, 2-5-8 Kuji, Takatsu-Ku, Kawasaki-Shi, Kanagawa, 213-0032, Japan
| | - Yosuke Uematsu
- Canine-Lab, 3-5-2 Ueno, Taito-Ku, Tokyo, 110-0005, Japan
| | - Kumiko Okano
- Japan Animal Referral Medical Center, 2-5-8 Kuji, Takatsu-Ku, Kawasaki-Shi, Kanagawa, 213-0032, Japan
| | - Mika Ichikawa
- Japan Animal Referral Medical Center, 2-5-8 Kuji, Takatsu-Ku, Kawasaki-Shi, Kanagawa, 213-0032, Japan
| | - Meina Tei
- Japan Animal Referral Medical Center, 2-5-8 Kuji, Takatsu-Ku, Kawasaki-Shi, Kanagawa, 213-0032, Japan
| | - Miyuki Hirabayashi
- Department of Veterinary Pathology, Faculty of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Kazuyuki Uchida
- Department of Veterinary Pathology, Faculty of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Kenichiro Ono
- Japan Animal Referral Medical Center, 2-5-8 Kuji, Takatsu-Ku, Kawasaki-Shi, Kanagawa, 213-0032, Japan.
| | - Hidehiro Hirao
- Japan Animal Referral Medical Center, 2-5-8 Kuji, Takatsu-Ku, Kawasaki-Shi, Kanagawa, 213-0032, Japan
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7
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Yamasaki H, Uematsu Y, Hayashi Y, Yamashita M, Tei M, Uchida K, Ono K, Hirao H. Coincidence of v-raf murine sarcoma viral oncogene homolog B mutation (V595E) with phosphorylated v-raf murine sarcoma viral oncogene homolog B in urothelial carcinoma in dogs. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2022; 86:286-293. [PMID: 36211215 PMCID: PMC9536355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/20/2022] [Indexed: 04/03/2023]
Abstract
Expression of phosphorylated v-raf murine sarcoma viral oncogene homolog B (pBRAF) and phosphorylated extracellular signal-regulated kinase1/2 (pERK1/2) were investigated in urothelial carcinoma (UC) in dogs with or without the BRAF gene mutation (V595E). Among the 10 cases of UC with V595E (-), cytoplasmic immunoreactivity against pBRAF of neoplastic cells was reported in 8, with 7 displaying moderate reactivity and 1 displaying intense reactivity. Nuclear immunoreactivity against pBRAF was detected in 5 cases; however, these reactivities were non-specific, due to pBRAF being limited in the cytoplasm. In addition, positive cytoplasmic immunoreactivity against pERK1/2 of neoplastic cells was detected in 7 cases and nuclear immunoreactivity against ERK1/2 was detected in 6 cases. Among the 13 cases of UC with V595E (+), cytoplasmic immunoreactivity against pBRAF of neoplastic cells was detected in all 13 cases and nuclear immunoreactivity against pBRAF was detected in 10 cases; however, the nuclear immunoreactivity was non-specific. Cytoplasmic immunoreactivity against pERK1/2 of neoplastic cells was detected in all 13 cases and nuclear immunoreactivity against pERK1/2 was also detected in all cases. As nuclear pERK1/2 indicates a progressive signaling process in the mitogen-activated protein kinase pathway, V595E (+) UC might be in its growing stage. Probable phosphorylated sites of pBRAF at Thr598/Ser601, detected in this study, are major and essential sites of the upstream rat sarcoma viral oncogene homolog (RAS) signaling pathway. In human cancers, the BRAF mutation never coincides with oncogenic RAS. To our knowledge, this is the first report on the simultaneous occurrence of the BRAF mutation (V595E) and pBRAF expression (at Thr598/Ser601) in dogs with UC with V595E (+).
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Affiliation(s)
- Hirofumi Yamasaki
- Japan Animal Referral Medical Center, Kawasaki, Japan (Yamasaki, Hayashi, Yamashita, Tei, Ono, Hirao); Canine-Lab, Tokyo, Japan (Uematsu); Department of Veterinary Pathology, The University of Tokyo (Uchida)
| | - Yosuke Uematsu
- Japan Animal Referral Medical Center, Kawasaki, Japan (Yamasaki, Hayashi, Yamashita, Tei, Ono, Hirao); Canine-Lab, Tokyo, Japan (Uematsu); Department of Veterinary Pathology, The University of Tokyo (Uchida)
| | - Yuhei Hayashi
- Japan Animal Referral Medical Center, Kawasaki, Japan (Yamasaki, Hayashi, Yamashita, Tei, Ono, Hirao); Canine-Lab, Tokyo, Japan (Uematsu); Department of Veterinary Pathology, The University of Tokyo (Uchida)
| | - Masao Yamashita
- Japan Animal Referral Medical Center, Kawasaki, Japan (Yamasaki, Hayashi, Yamashita, Tei, Ono, Hirao); Canine-Lab, Tokyo, Japan (Uematsu); Department of Veterinary Pathology, The University of Tokyo (Uchida)
| | - Meina Tei
- Japan Animal Referral Medical Center, Kawasaki, Japan (Yamasaki, Hayashi, Yamashita, Tei, Ono, Hirao); Canine-Lab, Tokyo, Japan (Uematsu); Department of Veterinary Pathology, The University of Tokyo (Uchida)
| | - Kazuyuki Uchida
- Japan Animal Referral Medical Center, Kawasaki, Japan (Yamasaki, Hayashi, Yamashita, Tei, Ono, Hirao); Canine-Lab, Tokyo, Japan (Uematsu); Department of Veterinary Pathology, The University of Tokyo (Uchida)
| | - Kenichiro Ono
- Japan Animal Referral Medical Center, Kawasaki, Japan (Yamasaki, Hayashi, Yamashita, Tei, Ono, Hirao); Canine-Lab, Tokyo, Japan (Uematsu); Department of Veterinary Pathology, The University of Tokyo (Uchida)
| | - Hidehiro Hirao
- Japan Animal Referral Medical Center, Kawasaki, Japan (Yamasaki, Hayashi, Yamashita, Tei, Ono, Hirao); Canine-Lab, Tokyo, Japan (Uematsu); Department of Veterinary Pathology, The University of Tokyo (Uchida)
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8
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Zerfaoui M, Tsumagari K, Toraih E, Errami Y, Ruiz E, Elaasar MSM, Krzysztof M, Sholl AB, Magdeldin S, Soudy M, Abd Elmageed ZY, Boulares AH, Kandil E. Nuclear interaction of Arp2/3 complex and BRAF V600E promotes aggressive behavior and vemurafenib resistance of thyroid cancer. Am J Cancer Res 2022; 12:3014-3033. [PMID: 35968344 PMCID: PMC9360225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/12/2022] [Indexed: 04/22/2023] Open
Abstract
The presence of mutant BRAF V600E correlates with the risk of recurrence in papillary thyroid cancer (PTC) patients. However, not all PTC patients with BRAF V600E are associated with poor prognosis. Thus, understanding the mechanisms by which certain PTC patients with nuclear BRAF V600E become aggressive and develop resistance to a selective BRAF inhibitor, PLX-4032, is urgently needed. The effect of nuclear localization of BRAFV600E using in vitro studies, xenograft mouse-model and human tissues was evaluated. PTC cells harboring a nuclear localization signal (NLS) of BRAFV600E were established and examined in nude mice implanted with TPC1-NLS-BRAFV600E cells followed by PLX-4032 treatment. Immunohistochemical (IHC) analysis was performed on 100 PTC specimens previously confirmed that they have BRAFV600E mutations. Our results demonstrate that 21 of 100 (21%) PTC tissues stained with specific BRAFV600E antibody had nuclear staining with more aggressive features compared to their cytosolic counterparts. In vitro studies show that BRAFV600E is transported between the nucleus and the cytosol through CRM1 and importin (α/β) system. Sequestration of BRAFV600E in the cytosol sensitized resistant cells to PLX-4032, whereas nuclear BRAFV600E was associated with aggressive phenotypes and developed drug resistance. Proteomic analysis revealed Arp2/3 complex members, actin-related protein 2 (ACTR2 aliases ARP2) and actin-related protein 3 (ACTR3 aliases ARP3), as the most enriched nuclear BRAFV600E partners. ACTR3 was highly correlated to lymph node stage and extrathyroidal extension and was validated with different functional assays. Our findings provide new insights into the clinical utility of the nuclear BRAFV600E as a prognostic marker for PTC aggressiveness and determine the efficacy of selective BRAFV600E inhibitor treatment which opens new avenues for future treatment options.
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Affiliation(s)
- Mourad Zerfaoui
- Department of Surgery, Tulane University School of MedicineUSA
| | - Koji Tsumagari
- Department of Surgery, Tulane University School of MedicineUSA
| | - Eman Toraih
- Department of Surgery, Tulane University School of MedicineUSA
| | - Youssef Errami
- Department of Surgery, Tulane University School of MedicineUSA
| | - Emmanuelle Ruiz
- Department of Surgery, Tulane University School of MedicineUSA
| | | | - Moroz Krzysztof
- Department of Pathology, Tulane University School of MedicineUSA
| | - Andrew B Sholl
- Department of Otolaryngology, Tulane University School of MedicineUSA
| | - Sameh Magdeldin
- Proteomics Research Program Unit, Basic Research Department, Children Cancer Hospital CairoEgypt
- Department of Physiology, Faculty of Veterinary Medicine, Suez Canal UniversityIsmailia 41522, Egypt
| | - Mohamed Soudy
- Proteomics Research Program Unit, Basic Research Department, Children Cancer Hospital CairoEgypt
| | - Zakaria Y Abd Elmageed
- Department of Surgery, Tulane University School of MedicineUSA
- Department of Pharmacology, Edward Via College of Osteopathic Medicine, University of LouisianaMonroe, USA
| | - A Hamid Boulares
- Department of Pharmacology, LSU Health Sciences CenterNew Orleans, LA, USA
| | - Emad Kandil
- Department of Surgery, Tulane University School of MedicineUSA
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9
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Bjorklund DM, Morgan RML, Oberoi J, Day KLIM, Galliou PA, Prodromou C. Recognition of BRAF by CDC37 and Re-Evaluation of the Activation Mechanism for the Class 2 BRAF-L597R Mutant. Biomolecules 2022; 12:biom12070905. [PMID: 35883461 PMCID: PMC9313131 DOI: 10.3390/biom12070905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022] Open
Abstract
The kinome specific co-chaperone, CDC37 (cell division cycle 37), is responsible for delivering BRAF (B-Rapidly Accelerated Fibrosarcoma) to the Hsp90 (heat shock protein 90) complex, where it is then translocated to the RAS (protooncogene product p21) complex at the plasma membrane for RAS mediated dimerization and subsequent activation. We identify a bipartite interaction between CDC37 and BRAF and delimitate the essential structural elements of CDC37 involved in BRAF recognition. We find an extended and conserved CDC37 motif, 20HPNID---SL--W31, responsible for recognizing the C-lobe of BRAF kinase domain, while the c-terminal domain of CDC37 is responsible for the second of the bipartite interaction with BRAF. We show that dimerization of BRAF, independent of nucleotide binding, can act as a potent signal that prevents CDC37 recognition and discuss the implications of mutations in BRAF and the consequences on signaling in a clinical setting, particularly for class 2 BRAF mutations.
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Affiliation(s)
- Dennis M. Bjorklund
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK;
| | - R. Marc L. Morgan
- Department of Life Sciences, Faculty of Natural Sciences, South Kensington Campus, Imperial College London, London SW7 2AZ, UK;
| | - Jasmeen Oberoi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK;
| | | | - Panagiota A. Galliou
- Laboratory of Biological Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Chrisostomos Prodromou
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK;
- Correspondence:
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10
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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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11
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Maloney RC, Zhang M, Liu Y, Jang H, Nussinov R. The mechanism of activation of MEK1 by B-Raf and KSR1. Cell Mol Life Sci 2022; 79:281. [PMID: 35508574 PMCID: PMC9068654 DOI: 10.1007/s00018-022-04296-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 12/01/2022]
Abstract
MEK1 interactions with B-Raf and KSR1 are key steps in Ras/Raf/MEK/ERK signaling. Despite this, vital mechanistic details of how these execute signal transduction are still enigmatic. Among these is why, despite B-Raf and KSR1 kinase domains similarity, the B-Raf/MEK1 and KSR1/MEK1 complexes have distinct contributions to MEK1 activation, and broadly, what is KSR1's role. Our molecular dynamics simulations clarify these still unresolved ambiguities. Our results reveal that the proline-rich (P-rich) loop of MEK1 plays a decisive role in MEK1 activation loop (A-loop) phosphorylation. In the inactive B-Raf/MEK1 heterodimer, the collapsed A-loop of B-Raf interacts with the P-rich loop and A-loop of MEK1, minimizing MEK1 A-loop fluctuation and preventing it from phosphorylation. In the active B-Raf/MEK1 heterodimer, the P-rich loop moves in concert with the A-loop of B-Raf as it extends. This reduces the number of residues interacting with MEK1 A-loop, allowing increased A-loop fluctuation, and bringing Ser222 closer to ATP for phosphorylation. B-Raf αG-helix Arg662 promotes MEK1 activation by orienting Ser218 towards ATP. In KSR1/MEK1, the KSR1 αG-helix has Ala826 in place of B-Raf Arg662. This difference results in much fewer interactions between KSR1 αG-helix and MEK1 A-loop, thus a more flexible A-loop. We postulate that if KSR1 were to adopt an active configuration with an extended A-loop as seen in other protein kinases, then the MEK1 P-rich loop would extend in a similar manner, as seen in the active B-Raf/MEK1 heterodimer. This would result in highly flexible MEK1 A-loop, and KSR1 functioning as an active, B-Raf-like, kinase.
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Affiliation(s)
- Ryan C Maloney
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.
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12
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Dai X, Zhang X, Yin Q, Hu J, Guo J, Gao Y, Snell AH, Inuzuka H, Wan L, Wei W. Acetylation-dependent regulation of BRAF oncogenic function. Cell Rep 2022; 38:110250. [PMID: 35045286 PMCID: PMC8813213 DOI: 10.1016/j.celrep.2021.110250] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/02/2021] [Accepted: 12/21/2021] [Indexed: 12/21/2022] Open
Abstract
Aberrant BRAF activation, including the BRAFV600E mutation, is frequently observed in human cancers. However, it remains largely elusive whether other types of post-translational modification(s) in addition to phosphorylation and ubiquitination-dependent regulation also modulate BRAF kinase activity. Here, we report that the acetyltransferase p300 activates the BRAF kinase by promoting BRAF K601 acetylation, a process that is antagonized by the deacetylase SIRT1. Notably, K601 acetylation facilitates BRAF dimerization with RAF proteins and KSR1. Furthermore, K601 acetylation promotes melanoma cell proliferation and contributes to BRAFV600E inhibitor resistance in BRAFV600E harboring melanoma cells. As such, melanoma patient-derived K601E oncogenic mutation mimics K601 acetylation to augment BRAF kinase activity. Our findings, therefore, uncover a layer of BRAF regulation and suggest p300 hyperactivation or SIRT1 deficiency as potential biomarkers to determine ERK activation in melanomas. In tumor cells, hyperactivation of the BRAF protein kinase propels uncontrolled cell proliferation. BRAF hyperactivation is also achieved through several post-translational mechanisms. Dai et al. present an acetylation-dependent regulation of BRAF kinase function in melanoma cells, which serves to enhance BRAF oncogenic function and contributes to BRAF inhibitor resistance.
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Affiliation(s)
- Xiangpeng Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130061, PR China; National-local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130061, PR China.
| | - Xiaoling Zhang
- Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130061, PR China; National-local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130061, PR China
| | - Qing Yin
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Jia Hu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan 430030, PR China
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yang Gao
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Aidan H Snell
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lixin Wan
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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13
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Al Shahrani M, Abohassan M, Y Alshahrani M, Hakami AR, Rajagopalan P. High-throughput virtual screening and preclinical analysis identifies CB-1, a novel potent dual B-Raf/c-Raf inhibitor, effective against wild and mutant variants of B-Raf expression in colorectal carcinoma. J Comput Aided Mol Des 2021; 35:1165-1176. [PMID: 34727304 DOI: 10.1007/s10822-021-00426-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 01/07/2023]
Abstract
Paradoxical Raf activation via Raf dimerization is a major drawback of wild/mutant B-Raf inhibitors. Herein, we report that CB-1 a novel, potent B-Raf/c-Raf dual inhibitor, effective against colon cancer cells, irrespective of their genetic status. High-throughput virtual screening of the ChemBridge library against wild B-Raf (B-RafWT), mutant B-Raf (B-RafV600E), and c-Raf was performed using an automated protocol with the AutoDock-VINA. Caco-2 and HT-29 cells were used. Of the 23,365 compounds screened computationally, CB-1 showed the highest binding energy towards B-RafWT with a ΔGbinding score of - 13.0 kcal/mol. The compound was also predicted to be effective against B-RafV600E and c-Raf molecules with ΔGbinding energies of - 10.6 and - 10.1 kcal/mol, respectively. The compound inhibited B-RafWT, B-RafV600E and c-Raf kinases with IC50 values of 27.13, 51.70, and 40.23 nM, respectively. The GI50 value of CB-1 was 247.9 nM in B-RafWT-expressing Caco-2 cells and 352.4 nM in B-RafV600E-expressing HT-29 cells. Dose-dependent increases in total apoptosis and G1 cell cycle phase arrest was observed in CB-1-treated colon cancer cells. The compound decreased B-Raf expression in both wild and mutant colon cancer cells. CB-1, a novel, potent dual B-Raf/c-Raf inhibitor was effective against colon cancer cells bearing wild-type and mutant variants of B-Raf expression.
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Affiliation(s)
- Mesfer Al Shahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Abohassan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Abdulrahim R Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Prasanna Rajagopalan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia.
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia.
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14
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Jung H, Bae K, Lee JY, Kim JH, Han HJ, Yoon HY, Yoon KA. Establishment of Canine Transitional Cell Carcinoma Cell Lines Harboring BRAF V595E Mutation as a Therapeutic Target. Int J Mol Sci 2021; 22:ijms22179151. [PMID: 34502061 PMCID: PMC8430554 DOI: 10.3390/ijms22179151] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/22/2022] Open
Abstract
Transitional cell carcinoma (TCC) is the most common malignant tumor of the canine urinary tract and tends to have a poor prognosis due to its invasive potential. Recent studies have reported that up to 80% of canine urothelial carcinoma has the BRAF V595E mutation, which is homologous to the human V600E mutation. Activating the BRAF mutation is an actionable target for developing effective therapeutic agents inhibiting the BRAF/mitogen-activated protein kinase (MAPK) pathway in canine cancer as well as human cancer. We established novel canine TCC cell lines from two tumor tissues and one metastatic lymph node of canine TCC patients harboring the BRAF V595E mutation. Tumor tissues highly expressed the BRAF mutant and phosphorylated extracellular signal-related kinases (ERK)1/2 proteins. The derived cell lines demonstrated activated MAPK pathways. We also evaluated the cell lines for sensitivity to BRAF inhibitors. Sorafenib, a multiple kinase inhibitor targeting RAF/vascular endothelial growth factor receptor (VEGFR), successfully inhibited the BRAF/MAPK pathway and induced apoptosis. The established canine TCC cell lines responded with greater sensitivity to sorafenib than to vemurafenib, which is known as a specific BRAF inhibitor in human cancer. Our results demonstrated that canine TCC cells showed different responses compared to human cancer with the BRAF V600E mutation. These cell lines would be valuable research materials to develop therapeutic strategies for canine TCC patients.
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Affiliation(s)
- Hyojik Jung
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea; (H.J.); (K.B.); (J.Y.L.)
| | - Kieun Bae
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea; (H.J.); (K.B.); (J.Y.L.)
| | - Ja Young Lee
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea; (H.J.); (K.B.); (J.Y.L.)
| | - Jung-Hyun Kim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Hyun-Jung Han
- Department of Veterinary Emergency and Critical Care, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Hun-Young Yoon
- Department of Veterinary Surgery, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Kyong-Ah Yoon
- Department of Veterinary Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea; (H.J.); (K.B.); (J.Y.L.)
- Correspondence: ; Tel.: +82-2-450-3789; Fax: +82-2-450-3037
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15
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Zhang M, Jang H, Li Z, Sacks DB, Nussinov R. B-Raf autoinhibition in the presence and absence of 14-3-3. Structure 2021; 29:768-777.e2. [PMID: 33711246 PMCID: PMC9907365 DOI: 10.1016/j.str.2021.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/04/2021] [Accepted: 02/19/2021] [Indexed: 01/06/2023]
Abstract
Raf-activating mutations are frequent in cancer. In the basal state, B-Raf is autoinhibited by its upstream Ras-binding domain (RBD) and cysteine-rich domain (RBD-CRD) interacting with its kinase domain (KD) and the 14-3-3 dimer. Our comprehensive molecular dynamics simulations explore two autoinhibition scenarios in the presence and absence of the 14-3-3 dimer. When present, the 14-3-3 interaction with B-Raf stabilizes the RBD-CRD-KD interaction, interfering with the KD dimerization. Raf's pSer365 removal fails to induce large disruption. RBD-CRD release promotes KD fluctuations and reorientation for dimerization, consistent with experimental data. In the absence of 14-3-3, our sampled B-Raf conformations suggest that RBD-CRD can block the KD dimerization surface. Our results suggest a B-Raf activation mechanism, whereby one KD monomer is donated by 14-3-3-free B-Raf KD and the other by 14-3-3-bound KD. This mechanism can lead to homo- and heterodimers. These autoinhibition scenarios can transform autoinhibited B-Raf monomers into active B-Raf dimers.
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Affiliation(s)
- Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunoMetabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunoMetabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Zhigang Li
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - David B Sacks
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunoMetabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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16
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Xiao H, Lin S, Jiang D, Lin Y, Liu L, Zhang Q, He J, Chen Y. Association of Extracellular Signal-Regulated Kinase Genes With Myopia: A Longitudinal Study of Chinese Children. Front Genet 2021; 12:654869. [PMID: 34122509 PMCID: PMC8191505 DOI: 10.3389/fgene.2021.654869] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Objective The present study was designed to investigate whether the extracellular signal-regulated kinase (ERK) signaling pathway, a downstream component of dopamine signaling, is involved in myopia among Chinese children. Methods During a 3.5-year follow-up, 488 primary school students were enrolled in this study. Non-cycloplegic spherical equivalent refraction (SE) and other ocular parameters were assessed. Four variants of four genes in the ERK signaling pathway were selected: RASGRF1 rs6495367, PTPN5 rs1550870, PTPRR rs11178469, and PDGFRA rs6554163. SNPscan was used to genotype single-nucleotide polymorphisms (SNPs). PLINK software was used to assess the associations of the genetic variants with the occurrence or development of myopia, SE, and other ocular parameters. We created a protein-protein interaction (PPI) network and microRNA (miRNA)-gene network using String and Cytoscape and conducted enrichment analyses on the genes in these networks. Results In total, 426 children (baseline age: 7.28 ± 0.26 years; 236 (55.4%) boys and 190 girls) wereenrolled. After adjusting for confounding factors with 10,000 permutations, children with the CT or TT genotype of PTPN5 rs1550870 were more susceptible to myopia than those with the CC genotype (adjusted p = 0.011). Additionally, PTPN5 rs1550870 was correlated with significant myopic shift and increasing axial length (AL) and lens thickness (LT) but had a negative effect on central corneal thickness (CCT). RASGRF1 rs6495367 was negatively associated with myopic shift (additive: adjusted p = 0.034; dominant: adjusted p = 0.020), myopic SE and AL. PDGFRA rs6554163 TA or AA was negatively associated with increasing LT (adjusted p = 0.033). Evaluation of the effects of SNP-SNP combinations on incident myopia revealed a statistically significant one-locus model: PTPN5 rs1550870 [cross-validation consistency (CVC) = 10/10, adjusted p = 0.0107]. The genes in the PPI and miRNA-gene interaction networks were subjected to enrichment analyses, which suggested that these genes are involved mainly in eye development and dopaminergic synapse-related processes. Conclusion We identified genetic variants of crucial ERK signaling pathway genes that were significantly correlated with myopia and ocular parameter alterations in Chinese children. A combination of gene and miRNA functional analyses with enrichment analyses highlights the regulatory effects associated with ocular development and dopamine biological functions. This study offers novel clues to understand the role of dopamine in the molecular mechanisms of myopia.
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Affiliation(s)
- Haishao Xiao
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Shudan Lin
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Dandan Jiang
- The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yaoyao Lin
- The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Linjie Liu
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Qiqi Zhang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Juan He
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Yanyan Chen
- The Eye Hospital, Wenzhou Medical University, Wenzhou, China
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17
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Roskoski R. Hydrophobic and polar interactions of FDA-approved small molecule protein kinase inhibitors with their target enzymes. Pharmacol Res 2021; 169:105660. [PMID: 33971270 DOI: 10.1016/j.phrs.2021.105660] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
Dysregulation and mutations of protein kinases play causal roles in many diseases including cancer. The KLIFS (kinase-ligand interaction fingerprint and structure) catalog includes 85 ligand binding-site residues occurring in both the small and large protein kinase lobes. Except for allosteric inhibitors, all FDA-approved drug-target enzyme complexes display hydrophobic interactions involving catalytic spine residue-6 (KLIFS-77), catalytic spine residue-7 (KLIFS-11), and catalytic spine residue-8 (KLIFS-15) within the small lobe and residues within the hinge-linker region (KLIFS-46-52). Except for allosteric antagonists, the approved drugs form hydrogen bonds with the third hinge residue (KLIFS-48) of their target. Most of the approved drugs, including the allosteric inhibitors, interact with the small lobe gatekeeper residue (KLIFS-45). The type IIA inhibitors have the most hydrophobic interactions with their target enzymes. These include interactions with KLIFS-27/31/35/61/66 residues of the back pocket within both the small and large lobes. There is also interaction with KLIFS-68 (regulatory spine residue-1), the conserved histidine of the catalytic loop that is found in the back pocket of type II antagonists, but within the front pocket of the other types of inhibitors. Owing to the participation of protein kinase signaling cascades in a wide variety of physiological and pathological processes, one can foresee the increasing use of targeted inhibitors both as primary and secondary treatments for many illnesses. Further studies of protein kinase signal transduction pathways promise to yield new and actionable information that will serve as a basis for fundamental and applied biomedical breakthroughs.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC 28742-8814, United States.
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18
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Huang KL, Scott AD, Zhou DC, Wang LB, Weerasinghe A, Elmas A, Liu R, Wu Y, Wendl MC, Wyczalkowski MA, Baral J, Sengupta S, Lai CW, Ruggles K, Payne SH, Raphael B, Fenyö D, Chen K, Mills G, Ding L. Spatially interacting phosphorylation sites and mutations in cancer. Nat Commun 2021; 12:2313. [PMID: 33875650 PMCID: PMC8055881 DOI: 10.1038/s41467-021-22481-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 02/17/2021] [Indexed: 11/18/2022] Open
Abstract
Advances in mass-spectrometry have generated increasingly large-scale proteomics datasets containing tens of thousands of phosphorylation sites (phosphosites) that require prioritization. We develop a bioinformatics tool called HotPho and systematically discover 3D co-clustering of phosphosites and cancer mutations on protein structures. HotPho identifies 474 such hybrid clusters containing 1255 co-clustering phosphosites, including RET p.S904/Y928, the conserved HRAS/KRAS p.Y96, and IDH1 p.Y139/IDH2 p.Y179 that are adjacent to recurrent mutations on protein structures not found by linear proximity approaches. Hybrid clusters, enriched in histone and kinase domains, frequently include expression-associated mutations experimentally shown as activating and conferring genetic dependency. Approximately 300 co-clustering phosphosites are verified in patient samples of 5 cancer types or previously implicated in cancer, including CTNNB1 p.S29/Y30, EGFR p.S720, MAPK1 p.S142, and PTPN12 p.S275. In summary, systematic 3D clustering analysis highlights nearly 3,000 likely functional mutations and over 1000 cancer phosphosites for downstream investigation and evaluation of potential clinical relevance.
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Affiliation(s)
- Kuan-Lin Huang
- Department of Genetics and Genomics, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Adam D Scott
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Cui Zhou
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Liang-Bo Wang
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Amila Weerasinghe
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Abdulkadir Elmas
- Department of Genetics and Genomics, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruiyang Liu
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Yige Wu
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael C Wendl
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Jessika Baral
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Sohini Sengupta
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Kelly Ruggles
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Benjamin Raphael
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, USA
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA
| | - Ken Chen
- Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
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19
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Adderley JD, John von Freyend S, Jackson SA, Bird MJ, Burns AL, Anar B, Metcalf T, Semblat JP, Billker O, Wilson DW, Doerig C. Analysis of erythrocyte signalling pathways during Plasmodium falciparum infection identifies targets for host-directed antimalarial intervention. Nat Commun 2020; 11:4015. [PMID: 32782246 PMCID: PMC7419518 DOI: 10.1038/s41467-020-17829-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/16/2020] [Indexed: 02/08/2023] Open
Abstract
Intracellular pathogens mobilize host signaling pathways of their host cell to promote their own survival. Evidence is emerging that signal transduction elements are activated in a-nucleated erythrocytes in response to infection with malaria parasites, but the extent of this phenomenon remains unknown. Here, we fill this knowledge gap through a comprehensive and dynamic assessment of host erythrocyte signaling during infection with Plasmodium falciparum. We used arrays of 878 antibodies directed against human signaling proteins to interrogate the activation status of host erythrocyte phospho-signaling pathways at three blood stages of parasite asexual development. This analysis reveals a dynamic modulation of many host signalling proteins across parasite development. Here we focus on the hepatocyte growth factor receptor (c-MET) and the MAP kinase pathway component B-Raf, providing a proof of concept that human signaling kinases identified as activated by malaria infection represent attractive targets for antimalarial intervention. Plasmodium infection activates signaling pathways in a-nucleated erythrocytes. Here, Adderley et al. use a comprehensive antibody microarray to show that infection extensively modulates host cell signalling and that the host receptor tyrosine kinase c-MET supports Plasmodium falciparum proliferation.
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Affiliation(s)
- Jack D Adderley
- Centre for Chronic Inflammatory and Infectious and Diseases, Biomedical Sciences Cluster, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, 3083, Australia
| | - Simona John von Freyend
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Sarah A Jackson
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Megan J Bird
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Amy L Burns
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Burcu Anar
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Tom Metcalf
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jean-Philippe Semblat
- Institut National de la Transfusion Sanguine, Inserm UMR S1134, 75015, Paris, France
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.,Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.,Burnet Institute, Melbourne, VIC, 3004, Australia
| | - Christian Doerig
- Centre for Chronic Inflammatory and Infectious and Diseases, Biomedical Sciences Cluster, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, 3083, Australia.
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20
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Ras assemblies and signaling at the membrane. Curr Opin Struct Biol 2020; 62:140-148. [DOI: 10.1016/j.sbi.2020.01.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
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21
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Liu H, Nazmun N, Hassan S, Liu X, Yang J. BRAF mutation and its inhibitors in sarcoma treatment. Cancer Med 2020; 9:4881-4896. [PMID: 32476297 PMCID: PMC7367634 DOI: 10.1002/cam4.3103] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/26/2020] [Accepted: 04/16/2020] [Indexed: 12/11/2022] Open
Abstract
The mitogen‐activated protein kinase (MAPK) signaling pathway plays a significant role in mediating cellular physiological activities, such as proliferation, differentiation, apoptosis, and senescence. This signaling pathway is composed of several major proto‐oncogenes of RAS/RAF/MEK/ERK, among which the BRAF proto‐oncogene, as one of the three members of the RAF family, has a higher mutation rate than ARAF and CRAF and has attracted extensive attention. Regarding the BRAF mutation, approximately 95% of BRAF mutations belong to the BRAF V600E mutation, which can enhance the expression of the MAPK signaling pathway and is thus related to the occurrence and development of various malignant tumors and has been successfully identified as a therapeutic target. Moreover, drug resistance to BRAF inhibitor treatment also appears to be an important issue. Considering the successful use of BRAF inhibitors in melanoma, we provide a brief overview of the BRAF mutations, including their basic structures and activation mechanisms, and the new classification method for BRAF mutations. Most importantly, we summarize the results of BRAF inhibitor treatment in different sarcomas. To overcome drug resistance to BRAF inhibitor treatment, we also outline the different mechanisms of drug resistance to BRAF inhibitor treatment and introduce the combination strategy of BRAF inhibitors with other targeted therapies.
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Affiliation(s)
- Haotian Liu
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute & Hospital, Tianjin, P.R. China
| | - Nahar Nazmun
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute & Hospital, Tianjin, P.R. China.,National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, P.R. China.,International Medical School, Tianjin Medical University, Tianjin, P.R. China
| | - Shafat Hassan
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute & Hospital, Tianjin, P.R. China.,National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, P.R. China.,International Medical School, Tianjin Medical University, Tianjin, P.R. China
| | - Xinyue Liu
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute & Hospital, Tianjin, P.R. China.,National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, P.R. China
| | - Jilong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute & Hospital, Tianjin, P.R. China.,National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & Hospital, Tianjin, P.R. China
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22
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Brummer T, McInnes C. RAF kinase dimerization: implications for drug discovery and clinical outcomes. Oncogene 2020; 39:4155-4169. [PMID: 32269299 DOI: 10.1038/s41388-020-1263-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 12/19/2022]
Abstract
The RAF kinases activated by RAS GTPases regulate cell growth and division by signal transduction through the ERK cascade and mutations leading to constitutive activity are key drivers of human tumors, as are upstream activators including RAS and receptor tyrosine kinases. The development of first-generation RAF inhibitors, including vemurafenib (VEM) and dabrafenib led to initial excitement due to high response rates and profound regression of malignant melanomas carrying BRAFV600E mutations. The excitement about these unprecedented response rates, however, was tempered by tumor unresponsiveness through both intrinsic and acquired drug-resistance mechanisms. In recent years much insight into the complexity of the RAS-RAF axis has been obtained and inactivation and signal transduction mechanisms indicate that RAF dimerization is a critical step in multiple cellular contexts and plays a key role in resistance. Both homo- and hetero-dimerization of BRAF and CRAF can modulate therapeutic response and disease progression in patients treated with ATP-competitive inhibitors and are therefore highly clinically significant. Ten years after the definition of the RAF dimer interface (DIF) by crystallography, this review focuses on the implications of RAF kinase dimerization in signal transduction and for drug development, both from a classical ATP-competitive standpoint and from the perspective of new therapeutic strategies including inhibiting dimer formation. A structural perspective of the DIF, how dimerization impacts inhibitor activation and the structure-based design of next-generation RAF kinase inhibitors with unique mechanisms of action is presented. We also discuss potential fields of application for DIF inhibitors, ranging from non-V600E oncoproteins and BRAF fusions to tumors driven by aberrant receptor tyrosine kinase or RAS signaling.
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Affiliation(s)
- Tilman Brummer
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Strasse 17, 79104, Freiburg im Breisgau, Germany.,German Cancer Consortium DKTK Partner Site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Centre Freiburg, University of Freiburg, Freiburg im Breisgau, Germany
| | - Campbell McInnes
- Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA.
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23
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Jang H, Zhang M, Nussinov R. The quaternary assembly of KRas4B with Raf-1 at the membrane. Comput Struct Biotechnol J 2020; 18:737-748. [PMID: 32257057 PMCID: PMC7125320 DOI: 10.1016/j.csbj.2020.03.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 02/07/2023] Open
Abstract
Proximally located in the membrane, oncogenic Ras dimers (or nanoclusters) can recruit and promote Raf dimerization and MAPK (Raf/MEK/ERK) signaling. Among Ras isoforms, KRas4B is the most frequently mutated. Recent data on the binary KRas4B–Raf-1 complex suggested that Raf-1 CRD not only executes membrane anchorage, but also supports the high-affinity interaction of Raf-1 RBD with KRas4B catalytic domain. For a detailed mechanistic picture of Raf activation at the membrane, we employ explicit MD simulations of the quaternary KRas4B–Raf-1 complex. The complex contains two active GTP-bound KRas4B proteins forming a dimer through the allosteric lobe interface and two tandem RBD-CRD segments of Raf-1 interacting with the effector lobes at both ends of the KRas4B dimer. We show that Raf-1 RBD-CRD supports stable KRas4B dimer at preferred interface and orientation at the membrane, thereby cooperatively enhancing the affinity of the KRas4B–Raf-1 interaction. We propose that a Ras dimer at the membrane can increase the population of proximal Raf kinase domains, promoting kinase domain dimerization in the cytoplasm. Collectively, the dynamic Ras–Raf assembly promotes Raf activation not by allostery; instead, Ras activates Raf by shifting its ensemble toward kinase domain-accessible states through enhanced affinity at the membrane.
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Affiliation(s)
- Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mingzhen Zhang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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24
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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: 295] [Impact Index Per Article: 73.8] [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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25
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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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26
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Sun Q, Wang W. Structures of BRAF-MEK1-14-3-3 sheds light on drug discovery. Signal Transduct Target Ther 2019; 4:59. [PMID: 31871776 PMCID: PMC6908589 DOI: 10.1038/s41392-019-0096-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 02/05/2023] Open
Affiliation(s)
- Qiu Sun
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041 China
| | - Wenjing Wang
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041 China
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27
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Nussinov R, Tsai CJ, Jang H. Does Ras Activate Raf and PI3K Allosterically? Front Oncol 2019; 9:1231. [PMID: 31799192 PMCID: PMC6874141 DOI: 10.3389/fonc.2019.01231] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
The mechanism through which oncogenic Ras activates its effectors is vastly important to resolve. If allostery is at play, then targeting allosteric pathways could help in quelling activation of MAPK (Raf/MEK/ERK) and PI3K (PI3K/Akt/mTOR) cell proliferation pathways. On the face of it, allosteric activation is reasonable: Ras binding perturbs the conformational ensembles of its effectors. Here, however, we suggest that at least for Raf, PI3K, and NORE1A (RASSF5), that is unlikely. Raf's long disordered linker dampens effective allosteric activation. Instead, we suggest that the high-affinity Ras–Raf binding relieves Raf's autoinhibition, shifting Raf's ensemble from the inactive to the nanocluster-mediated dimerized active state, as Ras also does for NORE1A. PI3K is recruited and allosterically activated by RTK (e.g., EGFR) at the membrane. Ras restrains PI3K's distribution and active site orientation. It stabilizes and facilitates PIP2 binding at the active site and increases the PI3K residence time at the membrane. Thus, RTKs allosterically activate PI3Kα; however, merging their action with Ras accomplishes full activation. Here we review their activation mechanisms in this light and draw attention to implications for their pharmacology.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
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28
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Dynamic Protein Allosteric Regulation and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:25-43. [DOI: 10.1007/978-981-13-8719-7_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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29
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Cope N, Novak B, Candelora C, Wong K, Cavallo M, Gunderwala A, Liu Z, Li Y, Wang Z. Biochemical Characterization of Full-Length Oncogenic BRAF V600E together with Molecular Dynamics Simulations Provide Insight into the Activation and Inhibition Mechanisms of RAF Kinases. Chembiochem 2019; 20:2850-2861. [PMID: 31152574 DOI: 10.1002/cbic.201900266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Indexed: 12/12/2022]
Abstract
The most prevalent BRAF mutation, V600E, occurs frequently in melanoma and other cancers. Although extensive progress has been made toward understanding the biology of RAF kinases, little in vitro characterization of full-length BRAFV600E is available. Herein, we show the successful purification of active, full-length BRAFV600E from mammalian cells for in vitro experiments. Our biochemical characterization of intact BRAFV600E together with molecular dynamics (MD) simulations of the BRAF kinase domain and cell-based assays demonstrate that BRAFV600E has several unique features that contribute to its tumorigenesis. Firstly, steady-state kinetic analyses reveal that purified BRAFV600E is more active than fully activated wild-type BRAF; this is consistent with the notion that elevated signaling output is necessary for transformation. Secondly, BRAFV600E has a higher potential to form oligomers, despite the fact that the V600E substitution confers constitutive kinase activation independent of an intact side-to-side dimer interface. Thirdly, BRAFV600E bypasses inhibitory P-loop phosphorylation to enforce the necessary elevated signaling output for tumorigenesis. Together, these results provide new insight into the biochemical properties of BRAFV600E , complementing the understanding of BRAF regulation under normal and disease conditions.
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Affiliation(s)
- Nicholas Cope
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Borna Novak
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Christine Candelora
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Kenneth Wong
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Maria Cavallo
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Amber Gunderwala
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Zhiwei Liu
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Zhihong Wang
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
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30
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Park E, Rawson S, Li K, Kim BW, Ficarro SB, Pino GGD, Sharif H, Marto JA, Jeon H, Eck MJ. Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes. Nature 2019; 575:545-550. [PMID: 31581174 PMCID: PMC7014971 DOI: 10.1038/s41586-019-1660-y] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022]
Abstract
RAF family kinases are RAS-activated switches that initiate signaling through the MAP kinase cascade to control cellular proliferation, differentiation and survival1–3. RAF activity is tightly regulated, and inappropriate activation is a frequent cause of cancer4–6. At present, the structural basis for RAF regulation is poorly understood. Here we describe autoinhibited and active state structures of full-length BRAF in complexes with MEK1 and a 14-3-3 dimer, determined using cryo electron microscopy (cryo-EM). A 4.1Å resolution cryo-EM reconstruction reveals an inactive BRAF/MEK1 complex restrained in a cradle formed by the 14-3-3 dimer, which binds the phosphorylated S365 and S729 sites that flank the BRAF kinase domain. The BRAF cysteine-rich domain (CRD) occupies a central position that stabilizes this assembly, but the adjacent RAS-binding domain (RBD) is poorly ordered and peripheral. The 14-3-3 cradle maintains autoinhibition by sequestering the membrane-binding CRD and blocking dimerization of the BRAF kinase domain. In the active state, these inhibitory interactions are released and a single 14-3-3 dimer rearranges to bridge the C-terminal pS729 binding sites of two BRAFs, driving formation of an active, back-to-back BRAF dimer. Our structural snapshots provide a foundation for understanding normal RAF regulation and its mutational disruption in cancer and developmental syndromes.
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Affiliation(s)
- Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kunhua Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Byeong-Won Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gonzalo Gonzalez-Del Pino
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Humayun Sharif
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hyesung Jeon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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Malhotra S, Alsulami AF, Heiyun Y, Ochoa BM, Jubb H, Forbes S, Blundell TL. Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: A preliminary computational analysis of the COSMIC Cancer Gene Census. PLoS One 2019; 14:e0219935. [PMID: 31323058 PMCID: PMC6641202 DOI: 10.1371/journal.pone.0219935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
Genomics and genome screening are proving central to the study of cancer. However, a good appreciation of the protein structures coded by cancer genes is also invaluable, especially for the understanding of functions, for assessing ligandability of potential targets, and for designing new drugs. To complement the wealth of information on the genetics of cancer in COSMIC, the most comprehensive database for cancer somatic mutations available, structural information obtained experimentally has been brought together recently in COSMIC-3D. Even where structural information is available for a gene in the Cancer Gene Census, a list of genes in COSMIC with substantial evidence supporting their impacts in cancer, this information is quite often for a single domain in a larger protein or for a single protomer in a multiprotein assembly. Here, we show that over 60% of the genes included in the Cancer Gene Census are predicted to possess multiple domains. Many are also multicomponent and membrane-associated molecular assemblies, with mutations recorded in COSMIC affecting such assemblies. However, only 469 of the gene products have a structure represented in the PDB, and of these only 87 structures have 90-100% coverage over the sequence and 69 have less than 10% coverage. As a first step to bridging gaps in our knowledge in the many cases where individual protein structures and domains are lacking, we discuss our attempts of protein structure modelling using our pipeline and investigating the effects of mutations using two of our in-house methods (SDM2 and mCSM) and identifying potential driver mutations. This allows us to begin to understand the effects of mutations not only on protein stability but also on protein-protein, protein-ligand and protein-nucleic acid interactions. In addition, we consider ways to combine the structural information with the wealth of mutation data available in COSMIC. We discuss the impacts of COSMIC missense mutations on protein structure in order to identify and assess the molecular consequences of cancer-driving mutations.
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Affiliation(s)
- Sony Malhotra
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ali F. Alsulami
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Yang Heiyun
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Harry Jubb
- Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Simon Forbes
- Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Thamizhoviya G, Vanisree AJ. Enriched environment modulates behavior, myelination and augments molecules governing the plasticity in the forebrain region of rats exposed to chronic immobilization stress. Metab Brain Dis 2019; 34:875-887. [PMID: 30604029 DOI: 10.1007/s11011-018-0370-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/11/2018] [Indexed: 01/10/2023]
Abstract
Recently, several reports on chronic stress have shown that prolonged exposure to stress contributes to psychological and neurological complications. However, the impact of stress-induced alterations in myelination remains to be unexplored. Therefore, in the current study, the rats were subjected to immobilization stress (IS) followed by enriched environment (EE) and the behavioral, neurochemical changes pertaining to neuronal survival pathway, in addition, to the ultrastructural changes in myelin in forebrain (FB) region of rats were analyzed. Immobilization stress-exposed rats (4 h/day IS, for 28 days) exhibited increased anhedonia, anxiety, immobility, and reduced social interaction, which could be reflected in increased levels of corticosterone. In contrast, exposure to EE (4 h IS+2 h EE/day, for 28 days) was found to minimize anhedonic state, supress the depressive-like features, enhance social interaction and also reduce the levels of corticosterone. The ultrastructural changes in the FB region of the brain revealed that IS group showed enhanced g-ratio indicating decreased myelin thickness, while EE group exhibited reduced g-ratio manifesting increased myelination. Further, the study revealed that IS exposed group showed decreased levels of NGF, TrkA, PI3K, AKT, ERK, CREB, and MBP in FB regions whereas EE group could preserve normal protein and mRNA levels of these neuronal survival molecules. The results from this study suggest that EE exerts a positive impact by improving myelination in rats exposed to chronic immobilization stress.
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Ho NTT, Kutzner A, Heese K. A Novel Divergent Gene Transcription Paradigm-the Decisive, Brain-Specific, Neural |-Srgap2-Fam72a-| Master Gene Paradigm. Mol Neurobiol 2019; 56:5891-5899. [PMID: 30685845 DOI: 10.1007/s12035-019-1486-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/10/2019] [Indexed: 01/22/2023]
Abstract
Brain development and repair largely depend on neural stem cells (NSCs). Here, we suggest that two genes, i.e., Srgap2 (SLIT-ROBO Rho GTPase-activating protein 2) and Fam72a (family with sequence similarity to 72, member A), constitute a single, NSC-specific, |-Srgap2-Fam72a-| master gene pair co-existing in reciprocal functional dependency. This gene pair has a dual, commonly used, intergenic region (IGR) promotor, which is a prerequisite in controlling human brain plasticity. We applied fluorescence cellular microscopy and fluorescence-activated cell sorting (FACS) to assess rat |-Srgap2-Fam72a-| master gene IGR promotor activity upon stimulation with two contrary growth factors: nerve growth factor (Ngf, a differentiation growth factor) and epidermal growth factor (Egf, a mitotic growth factor). We found that Ngf and Egf acted on the same IGR gene promotor element of the |-Srgap2-Fam72a-| master gene to mediate cell differentiation and proliferation, respectively. Ngf mediated Srgap2 expression and neuronal survival and differentiation while Egf activated Fam72a transcription and cell proliferation. Our data provide new insights into the specific regulation of the |-Srgap2-Fam72a-| master gene with its dual IGR promotor that controls two reverse-oriented functional-dependent genes located on opposite DNA strands. This structure represents a novel paradigm for controlling transcription of divergent genes in regulating NSC gene expression. This paradigm may allow for novel therapeutic approaches to restore or improve higher cognitive functions and cure cancers.
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Affiliation(s)
- Nguyen Thi Thanh Ho
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
| | - Arne Kutzner
- Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea.
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34
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B-Raf deficiency impairs tumor initiation and progression in a murine breast cancer model. Oncogene 2019; 38:1324-1339. [DOI: 10.1038/s41388-018-0663-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 11/22/2018] [Accepted: 12/11/2018] [Indexed: 02/07/2023]
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35
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Terrell EM, Morrison DK. Ras-Mediated Activation of the Raf Family Kinases. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033746. [PMID: 29358316 DOI: 10.1101/cshperspect.a033746] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The extracellular signal-regulated kinase (ERK) cascade comprised of the Raf, MEK, and ERK protein kinases constitutes a key effector cascade used by the Ras GTPases to relay signals regulating cell growth, survival, proliferation, and differentiation. Of the ERK cascade components, the regulation of the Raf kinases is by far the most complex, involving changes in subcellular localization, protein and lipid interactions, as well as alterations in the Raf phosphorylation state. The Raf kinases interact directly with active, membrane-localized Ras, and this interaction is often the first step in the Raf activation process, which ultimately results in ERK activation and the downstream phosphorylation of cellular targets that will specify a particular biological response. Here, we will examine our current understanding of how Ras promotes Raf activation, focusing on the molecular mechanisms that contribute to the Raf activation/inactivation cycle.
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Affiliation(s)
- Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, Maryland 21702
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, Maryland 21702
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36
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Tsai CJ, Nussinov R. Allosteric activation of RAF in the MAPK signaling pathway. Curr Opin Struct Biol 2018; 53:100-106. [DOI: 10.1016/j.sbi.2018.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 07/11/2018] [Accepted: 07/18/2018] [Indexed: 01/07/2023]
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37
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Zhou C, Li J, Wang Y, Xue S, Zhang Y. Association of BRAF gene and TSHR with cervical lymph node metastasis of papillary thyroid microcarcinoma. Oncol Lett 2018; 17:183-194. [PMID: 30655754 PMCID: PMC6313223 DOI: 10.3892/ol.2018.9572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 09/13/2018] [Indexed: 01/09/2023] Open
Abstract
Differences in BRAF gene mutation frequency and thyroid-stimulating hormone receptor (TSHR) protein expression in thyroid tissues were detected to investigate their association with local tissue invasion and cervical lymph node metastasis potential of papillary thyroid microcarcinoma (PTMC). The BRAF gene mutation frequency and TSHR expression in PTMC patients were detected via qPCR and immunohistochemical method, and the association between them was discussed combined with the clinical and pathological parameters. Kruskal-Wallis test was used for the univariate correlation analyses and comparison of mutation rate and expression rate, and Chi-square test was used for the association of central lymph node metastasis with BRAF gene and TSHR. The BRAFV600E mutation only existed in patients with thyroid cancer. Τhe larger the number of metastatic central lymph nodes was, the higher the proportion of BRAFV600E mutation would be. Τhe BRAFV600E mutation was related to the primary lesion size, capsular infiltration and lymph node metastasis of PTMC (P<0.05). The expression of TSHR in PTMC tissues was < those in thyroid benign lesions and para-carcinoma normal tissues, which was positively associated with the central lymph node metastasis (P<0.05). Τhe low expression of TSHR was related to the primary lesion size, capsular infiltration and metastatic lymph nodes of PTMC (P<0.05). The BRAFV600E and TSHR may be involved in the occurrence and lymphatic metastasis of PTMC. The BRAFV600E mutation has no association with the TSHR protein expression (P=0.256), but the coincidence coefficient indicates that their diagnostic significance in PTMC is not similar, so BRAFV600E mutation and TSHR protein expression can be used jointly in the prediction of invasion and lymph node metastasis of PTMC, which may be more meaningful for clinical guidance.
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Affiliation(s)
- Changxin Zhou
- Department of Thyroid and Breast Surgery, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Jinbo Li
- Department of General Surgery, Gaotang County People's Hospital, Liaocheng, Shandong 252800, P.R. China
| | - Yu Wang
- Department of Thoracic Surgery, Liaocheng Tumor Hospital, Liaocheng, Shandong 252800, P.R. China
| | - Shoukun Xue
- Department of Thyroid and Breast Surgery, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Yang Zhang
- Department of Thyroid and Breast Surgery, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
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Autoinhibition in Ras effectors Raf, PI3Kα, and RASSF5: a comprehensive review underscoring the challenges in pharmacological intervention. Biophys Rev 2018; 10:1263-1282. [PMID: 30269291 PMCID: PMC6233353 DOI: 10.1007/s12551-018-0461-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 02/06/2023] Open
Abstract
Autoinhibition is an effective mechanism that guards proteins against spurious activation. Despite its ubiquity, the distinct organizations of the autoinhibited states and their release mechanisms differ. Signaling is most responsive to the cell environment only if a small shift in the equilibrium is required to switch the system from an inactive (occluded) to an active (exposed) state. Ras signaling follows this paradigm. This underscores the challenge in pharmacological intervention to exploit and enhance autoinhibited states. Here, we review autoinhibition and release mechanisms at the membrane focusing on three representative Ras effectors, Raf protein kinase, PI3Kα lipid kinase, and NORE1A (RASSF5) tumor suppressor, and point to the ramifications to drug discovery. We further touch on Ras upstream and downstream signaling, Ras activation, and the Ras superfamily in this light, altogether providing a broad outlook of the principles and complexities of autoinhibition.
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39
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Liu T, Wang Z, Guo P, Ding N. Electrostatic mechanism of V600E mutation-induced B-Raf constitutive activation in colorectal cancer: molecular implications for the selectivity difference between type-I and type-II inhibitors. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 48:73-82. [DOI: 10.1007/s00249-018-1334-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/10/2018] [Accepted: 09/06/2018] [Indexed: 02/04/2023]
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40
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Targeting oncogenic Raf protein-serine/threonine kinases in human cancers. Pharmacol Res 2018; 135:239-258. [DOI: 10.1016/j.phrs.2018.08.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
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41
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Awad RM, De Vlaeminck Y, Maebe J, Goyvaerts C, Breckpot K. Turn Back the TIMe: Targeting Tumor Infiltrating Myeloid Cells to Revert Cancer Progression. Front Immunol 2018; 9:1977. [PMID: 30233579 PMCID: PMC6127274 DOI: 10.3389/fimmu.2018.01977] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022] Open
Abstract
Tumor cells frequently produce soluble factors that favor myelopoiesis and recruitment of myeloid cells to the tumor microenvironment (TME). Consequently, the TME of many cancer types is characterized by high infiltration of monocytes, macrophages, dendritic cells and granulocytes. Experimental and clinical studies show that most myeloid cells are kept in an immature state in the TME. These studies further show that tumor-derived factors mold these myeloid cells into cells that support cancer initiation and progression, amongst others by enabling immune evasion, tumor cell survival, proliferation, migration and metastasis. The key role of myeloid cells in cancer is further evidenced by the fact that they negatively impact on virtually all types of cancer therapy. Therefore, tumor-associated myeloid cells have been designated as the culprits in cancer. We review myeloid cells in the TME with a focus on the mechanisms they exploit to support cancer cells. In addition, we provide an overview of approaches that are under investigation to deplete myeloid cells or redirect their function, as these hold promise to overcome resistance to current cancer therapies.
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42
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Cope N, Candelora C, Wong K, Kumar S, Nan H, Grasso M, Novak B, Li Y, Marmorstein R, Wang Z. Mechanism of BRAF Activation through Biochemical Characterization of the Recombinant Full-Length Protein. Chembiochem 2018; 19:1988-1997. [PMID: 29992710 DOI: 10.1002/cbic.201800359] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Indexed: 12/17/2022]
Abstract
BRAF kinase plays an important role in mitogen-activated protein kinase (MAPK) signaling and harbors activating mutations in about half of melanomas and in a smaller percentage in many other cancers. Despite its importance, few in vitro studies have been performed to characterize the biochemical properties of full-length BRAF. Herein, a strategy to generate an active, intact form of BRAF protein suitable for in vitro enzyme kinetics is described. It is shown that purified, intact BRAF protein autophosphorylates the kinase activation loop and this can be enhanced by binding the MEK protein substrate through an allosteric mechanism. These studies provide in vitro evidence that BRAF selectively binds to active RAS and that the BRAF/CRAF heterodimer is the most active form, relative to their respective homodimers. Full-length BRAF analysis with small-molecule BRAF inhibitors shows that two drugs, dabrafenib and vemurafenib, can modestly enhance kinase activity of BRAF at low concentration. Taken together, this characterization of intact BRAF contributes to a framework for understanding its role in cell signaling.
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Affiliation(s)
- Nicholas Cope
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Christine Candelora
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Kenneth Wong
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Sujeet Kumar
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Haihan Nan
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Michael Grasso
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Borna Novak
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
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43
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Evolution of oncogenic signatures of mutation hotspots in tyrosine kinases supports the atavistic hypothesis of cancer. Sci Rep 2018; 8:8256. [PMID: 29844492 PMCID: PMC5974376 DOI: 10.1038/s41598-018-26653-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/03/2018] [Indexed: 12/14/2022] Open
Abstract
Cancer has been shown as an evolutionary process emerging hallmarks that are reminiscent of unicellular organisms. Since cancer is mostly driven by somatic mutations, especially by oncogenic hotspot mutations, we proposed a molecular atavism of cancer caused by gain-of-function mutations in oncogenes. As tyrosine kinase (TK) family contains the largest subgroup of oncogenes with hotspot mutations, we traced the most predominant mutation hotspots of TK oncogenes across phylogeny with the domain information and adjacent sequences integrated as onco-signatures. We detected 9 out of 17 TK oncogenes with onco-homologs possessing an onco-signature, which could be divided into two classes by whether their onco-homologs existed in mammals or not. In Class I we identified mammalian onco-homologs assuming oncogenic functions with onco-signatures always intact in cancer, such as HCK and LYN. In Class II with no bona fide mammalian onco-homologs, Pyk2, a protist onco-homolog with an onco-signature of BRAF was found assuming oncogenic-like functions. Onco-signatures in both classes root deep in the primitive system. Together, these evidences supported our proposal that cancer can be driven by reverse evolution of oncogenes through gain-of-function mutations. And also for the first time, we provided the specific targets for experimental verification of the atavistic hypothesis of cancer.
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44
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Eisenhardt AE, Sprenger A, Röring M, Herr R, Weinberg F, Köhler M, Braun S, Orth J, Diedrich B, Lanner U, Tscherwinski N, Schuster S, Dumaz N, Schmidt E, Baumeister R, Schlosser A, Dengjel J, Brummer T. Phospho-proteomic analyses of B-Raf protein complexes reveal new regulatory principles. Oncotarget 2018; 7:26628-52. [PMID: 27034005 PMCID: PMC5042004 DOI: 10.18632/oncotarget.8427] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 03/07/2016] [Indexed: 12/19/2022] Open
Abstract
B-Raf represents a critical physiological regulator of the Ras/RAF/MEK/ERK-pathway and a pharmacological target of growing clinical relevance, in particular in oncology. To understand how B-Raf itself is regulated, we combined mass spectrometry with genetic approaches to map its interactome in MCF-10A cells as well as in B-Raf deficient murine embryonic fibroblasts (MEFs) and B-Raf/Raf-1 double deficient DT40 lymphoma cells complemented with wildtype or mutant B-Raf expression vectors. Using a multi-protease digestion approach, we identified a novel ubiquitination site and provide a detailed B-Raf phospho-map. Importantly, we identify two evolutionary conserved phosphorylation clusters around T401 and S419 in the B-Raf hinge region. SILAC labelling and genetic/biochemical follow-up revealed that these clusters are phosphorylated in the contexts of oncogenic Ras, sorafenib induced Raf dimerization and in the background of the V600E mutation. We further show that the vemurafenib sensitive phosphorylation of the T401 cluster occurs in trans within a Raf dimer. Substitution of the Ser/Thr-residues of this cluster by alanine residues enhances the transforming potential of B-Raf, indicating that these phosphorylation sites suppress its signaling output. Moreover, several B-Raf phosphorylation sites, including T401 and S419, are somatically mutated in tumors, further illustrating the importance of phosphorylation for the regulation of this kinase.
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Affiliation(s)
- Anja E Eisenhardt
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Adrian Sprenger
- Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Institute for Experimental and Clinical Pharmacology and Toxicology, ALU, Freiburg, Germany.,INSERM U976 and Universitéi Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Michael Röring
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Ricarda Herr
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Florian Weinberg
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Martin Köhler
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Joachim Orth
- Institute for Experimental and Clinical Pharmacology and Toxicology, ALU, Freiburg, Germany
| | - Britta Diedrich
- Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Department of Dermatology, University Medical Centre, ALU, Freiburg, Germany
| | - Ulrike Lanner
- Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Natalja Tscherwinski
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Simon Schuster
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Nicolas Dumaz
- INSERM U976 and Universitéi Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Enrico Schmidt
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Ralf Baumeister
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, ALU, Freiburg, Germany
| | - Andreas Schlosser
- Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Jörn Dengjel
- Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Department of Dermatology, University Medical Centre, ALU, Freiburg, Germany.,Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, ALU, Freiburg, Germany.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany.,Institute of Biology III, Faculty of Biology, ALU, Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany
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45
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Previtali V, Trujillo C, Boisson JC, Khartabil H, Hénon E, Rozas I. Development of the first model of a phosphorylated, ATP/Mg 2+-containing B-Raf monomer by molecular dynamics simulations: a tool for structure-based design. Phys Chem Chem Phys 2017; 19:31177-31185. [PMID: 29139502 DOI: 10.1039/c7cp05038k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A model of phosphorylated and ATP-containing B-Raf protein kinase is needed as a tool for the structure-based design of new allosteric inhibitors, since no crystal structure of such a system has been resolved. Here, we present the development of such a model as well as a thorough analysis of its structural features. This model was prepared using a systematic molecular dynamics approach considering the presence or absence of both the phosphate group at the Thr599 site and the ATP molecule. Then, different structural features (i.e. DFG motif, Mg2+ binding loop, activation loop, phosphorylation site and αC-helix region) were analysed for each trajectory to validate the aimed 2pBRAF_ATP model. Moreover, the structure and activating interactions of this 2pBRAF_ATP model were found to be in agreement with previously reported information. Finally, the model was further validated by means of a molecular docking study with our previously developed lead compound I confirming that this ATP-containing, phosphorylated protein model is suitable for further structure-based design studies.
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Affiliation(s)
- Viola Previtali
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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46
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Phosphorylation of the C-Raf N Region Promotes Raf Dimerization. Mol Cell Biol 2017; 37:MCB.00132-17. [PMID: 28694330 DOI: 10.1128/mcb.00132-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 12/11/2022] Open
Abstract
The activation of Raf kinases by the small GTPase Ras requires two major sets of phosphorylations. One set lies within the activation loop, and the other lies within the N-terminal acidic region (N region). In the most abundant isoform of Raf, C-Raf, N-region phosphorylations occur on serine 338 (S338) and tyrosine 341 (Y341) and are thought to provide allosteric activation of the Raf dimer. We show that the phosphorylations of these N-region sites does not require C-Raf dimerization, but rather, they precede dimerization. One of these phosphorylations (phospho-Y341) is required for C-Raf dimerization, and this action can be replicated by phosphomimetic mutants both in vivo and in vitro The role of the phosphorylation of Y341 in promoting Raf dimerization is distinct from its well-known function in facilitating S338 phosphorylation. In Ras mutant pancreatic cancer cell lines, the phosphorylation and dimerization of C-Raf are basally elevated. Dimerization is thought to contribute to their elevated growth rate through their activation of the mitogen-activated protein (MAP) kinase (extracellular signal-regulated kinase [ERK]) signaling cascade. Blocking the tyrosine phosphorylation of C-Raf with Src family inhibitors blocks growth, basal dimerization, and ERK activation in these cells. We suggest that the kinases mediating C-Raf Y341 phosphorylation are potential candidate drug targets in selected Ras-dependent cancers.
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47
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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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48
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Lim CS, Kang X, Mirabella V, Zhang H, Bu Q, Araki Y, Hoang ET, Wang S, Shen Y, Choi S, Kaang BK, Chang Q, Pang ZP, Huganir RL, Zhu JJ. BRaf signaling principles unveiled by large-scale human mutation analysis with a rapid lentivirus-based gene replacement method. Genes Dev 2017; 31:537-552. [PMID: 28404629 PMCID: PMC5393050 DOI: 10.1101/gad.294413.116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/13/2017] [Indexed: 12/18/2022]
Abstract
Rapid advances in genetics are linking mutations on genes to diseases at an exponential rate, yet characterizing the gene-mutation-cell-behavior relationships essential for precision medicine remains a daunting task. More than 350 mutations on small GTPase BRaf are associated with various tumors, and ∼40 mutations are associated with the neurodevelopmental disorder cardio-facio-cutaneous syndrome (CFC). We developed a fast cost-effective lentivirus-based rapid gene replacement method to interrogate the physiopathology of BRaf and ∼50 disease-linked BRaf mutants, including all CFC-linked mutants. Analysis of simultaneous multiple patch-clamp recordings from 6068 pairs of rat neurons with validation in additional mouse and human neurons and multiple learning tests from 1486 rats identified BRaf as the key missing signaling effector in the common synaptic NMDA-R-CaMKII-SynGap-Ras-BRaf-MEK-ERK transduction cascade. Moreover, the analysis creates the original big data unveiling three general features of BRaf signaling. This study establishes the first efficient procedure that permits large-scale functional analysis of human disease-linked mutations essential for precision medicine.
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Affiliation(s)
- Chae-Seok Lim
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.,Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Xi Kang
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Vincent Mirabella
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.,Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | - Huaye Zhang
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.,Department of Microbiology, Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Qian Bu
- Waisman Center, University of Wisconsin School of Medicine, Madison, Wisconsin 53705, USA.,Department of Medical Genetics, University of Wisconsin School of Medicine, Madison, Wisconsin 53705, USA
| | - Yoichi Araki
- Department of Neuroscience, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Elizabeth T Hoang
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.,Undergraduate Class of 2014, Department of Psychology, University of Virginia College of Arts and Sciences, Charlottesville, Virginia 22908, USA
| | - Shiqiang Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ying Shen
- Department of Neurobiology, Key Laboratory of Medical Neurobiology of Ministry of Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Sukwoo Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Bong-Kiun Kaang
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Qiang Chang
- Waisman Center, University of Wisconsin School of Medicine, Madison, Wisconsin 53705, USA.,Department of Medical Genetics, University of Wisconsin School of Medicine, Madison, Wisconsin 53705, USA
| | - Zhiping P Pang
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.,Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | - Richard L Huganir
- Department of Neuroscience, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - J Julius Zhu
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.,Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
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49
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Wan L, Chen M, Cao J, Dai X, Yin Q, Zhang J, Song SJ, Lu Y, Liu J, Inuzuka H, Katon JM, Berry K, Fung J, Ng C, Liu P, Song MS, Xue L, Bronson RT, Kirschner MW, Cui R, Pandolfi PP, Wei W. The APC/C E3 Ligase Complex Activator FZR1 Restricts BRAF Oncogenic Function. Cancer Discov 2017; 7:424-441. [PMID: 28174173 DOI: 10.1158/2159-8290.cd-16-0647] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 12/14/2022]
Abstract
BRAF drives tumorigenesis by coordinating the activation of the RAS/RAF/MEK/ERK oncogenic signaling cascade. However, upstream pathways governing BRAF kinase activity and protein stability remain undefined. Here, we report that in primary cells with active APCFZR1, APCFZR1 earmarks BRAF for ubiquitination-mediated proteolysis, whereas in cancer cells with APC-free FZR1, FZR1 suppresses BRAF through disrupting BRAF dimerization. Moreover, we identified FZR1 as a direct target of ERK and CYCLIN D1/CDK4 kinases. Phosphorylation of FZR1 inhibits APCFZR1, leading to elevation of a cohort of oncogenic APCFZR1 substrates to facilitate melanomagenesis. Importantly, CDK4 and/or BRAF/MEK inhibitors restore APCFZR1 E3 ligase activity, which might be critical for their clinical effects. Furthermore, FZR1 depletion cooperates with AKT hyperactivation to transform primary melanocytes, whereas genetic ablation of Fzr1 synergizes with Pten loss, leading to aberrant coactivation of BRAF/ERK and AKT signaling in mice. Our findings therefore reveal a reciprocal suppression mechanism between FZR1 and BRAF in controlling tumorigenesis.Significance: FZR1 inhibits BRAF oncogenic functions via both APC-dependent proteolysis and APC-independent disruption of BRAF dimers, whereas hyperactivated ERK and CDK4 reciprocally suppress APCFZR1 E3 ligase activity. Aberrancies in this newly defined signaling network might account for BRAF hyperactivation in human cancers, suggesting that targeting CYCLIN D1/CDK4, alone or in combination with BRAF/MEK inhibition, can be an effective anti-melanoma therapy. Cancer Discov; 7(4); 424-41. ©2017 AACR.See related commentary by Zhang and Bollag, p. 356This article is highlighted in the In This Issue feature, p. 339.
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Affiliation(s)
- Lixin Wan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts. .,Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ming Chen
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Juxiang Cao
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts.
| | - Xiangpeng Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Qing Yin
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Su-Jung Song
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Life Science, FIST, Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Jesse M Katon
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Kelsey Berry
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Jacqueline Fung
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Christopher Ng
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Pengda Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Min Sup Song
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lian Xue
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Roderick T Bronson
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Rutao Cui
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, Massachusetts.
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
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50
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Diedrich B, Rigbolt KT, Röring M, Herr R, Kaeser-Pebernard S, Gretzmeier C, Murphy RF, Brummer T, Dengjel J. Discrete cytosolic macromolecular BRAF complexes exhibit distinct activities and composition. EMBO J 2017; 36:646-663. [PMID: 28093501 DOI: 10.15252/embj.201694732] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 12/06/2016] [Accepted: 12/09/2016] [Indexed: 12/19/2022] Open
Abstract
As a central element within the RAS/ERK pathway, the serine/threonine kinase BRAF plays a key role in development and homeostasis and represents the most frequently mutated kinase in tumors. Consequently, it has emerged as an important therapeutic target in various malignancies. Nevertheless, the BRAF activation cycle still raises many mechanistic questions as illustrated by the paradoxical action and side effects of RAF inhibitors. By applying SEC-PCP-SILAC, we analyzed protein-protein interactions of hyperactive BRAFV600E and wild-type BRAF (BRAFWT). We identified two macromolecular, cytosolic BRAF complexes of distinct molecular composition and phosphorylation status. Hyperactive BRAFV600E resides in large complexes of higher molecular mass and activity, while BRAFWT is confined to smaller, slightly less active complexes. However, expression of oncogenic K-RasG12V, either by itself or in combination with RAF dimer promoting inhibitors, induces the incorporation of BRAFWT into large, active complexes, whereas pharmacological inhibition of BRAFV600E has the opposite effect. Thus, the quaternary structure of BRAF complexes is shaped by its activation status, the conformation of its kinase domain, and clinically relevant inhibitors.
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Affiliation(s)
- Britta Diedrich
- Department of Dermatology, Medical Center - University of Freiburg, Freiburg, Germany.,ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
| | - Kristoffer Tg Rigbolt
- Department of Dermatology, Medical Center - University of Freiburg, Freiburg, Germany.,ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
| | - Michael Röring
- Faculty of Medicine, Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Freiburg, Germany
| | - Ricarda Herr
- Faculty of Medicine, Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Freiburg, Germany
| | | | - Christine Gretzmeier
- Department of Dermatology, Medical Center - University of Freiburg, Freiburg, Germany.,ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Robert F Murphy
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany.,Computational Biology Department and Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tilman Brummer
- ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany .,Faculty of Medicine, Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, Germany.,Comprehensive Cancer Centre, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörn Dengjel
- Department of Dermatology, Medical Center - University of Freiburg, Freiburg, Germany .,ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany.,Department of Biology, University of Fribourg, Fribourg, Switzerland.,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany.,Centre for Biological Signalling Studies BIOSS, University of Freiburg, Freiburg, Germany
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