1
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Steffen CL, Manoharan GB, Pavic K, Yeste-Vázquez A, Knuuttila M, Arora N, Zhou Y, Härmä H, Gaigneaux A, Grossmann TN, Abankwa DK. Identification of an H-Ras nanocluster disrupting peptide. Commun Biol 2024; 7:837. [PMID: 38982284 PMCID: PMC11233548 DOI: 10.1038/s42003-024-06523-9] [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: 10/07/2023] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Hyperactive Ras signalling is found in most cancers. Ras proteins are only active in membrane nanoclusters, which are therefore potential drug targets. We previously showed that the nanocluster scaffold galectin-1 (Gal1) enhances H-Ras nanoclustering via direct interaction with the Ras binding domain (RBD) of Raf. Here, we establish that the B-Raf preference of Gal1 emerges from the divergence of the Raf RBDs at their proposed Gal1-binding interface. We then identify the L5UR peptide, which disrupts this interaction by binding with low micromolar affinity to the B- and C-Raf-RBDs. Its 23-mer core fragment is sufficient to interfere with H-Ras nanoclustering, modulate Ras-signalling and moderately reduce cell viability. These latter two phenotypic effects may also emerge from the ability of L5UR to broadly engage with several RBD- and RA-domain containing Ras interactors. The L5UR-peptide core fragment is a starting point for the development of more specific reagents against Ras-nanoclustering and -interactors.
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Affiliation(s)
- Candy Laura Steffen
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Karolina Pavic
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Matias Knuuttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health, Houston, TX, 77030, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health, Houston, TX, 77030, USA
| | - Harri Härmä
- Chemistry of Drug Development, Department of Chemistry, University of Turku, 20500, Turku, Finland
| | - Anthoula Gaigneaux
- Bioinformatics Core, Department of Life Sciences and Medicine, University of Luxembourg, 4367, Esch-sur-Alzette, Luxembourg
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Daniel Kwaku Abankwa
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
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2
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Hu M, Li H, Zhu K, Guo L, Zhao M, Zhan H, Devreotes PN, Qing Q. Electric field modulation of ERK dynamics shows dependency on waveform and timing. Sci Rep 2024; 14:3167. [PMID: 38326365 PMCID: PMC10850077 DOI: 10.1038/s41598-024-53018-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
Different exogenous electric fields (EF) can guide cell migration, disrupt proliferation, and program cell development. Studies have shown that many of these processes were initiated at the cell membrane, but the mechanism has been unclear, especially for conventionally non-excitable cells. In this study, we focus on the electrostatic aspects of EF coupling with the cell membrane by eliminating Faradaic processes using dielectric-coated microelectrodes. Our data unveil a distinctive biphasic response of the ERK signaling pathway of epithelial cells (MCF10A) to alternate current (AC) EF. The ERK signal exhibits both inhibition and activation phases, with the former triggered by a lower threshold of AC EF, featuring a swifter peaking time and briefer refractory periods than the later-occurring activation phase, induced at a higher threshold. Interestingly, the biphasic ERK responses are sensitive to the waveform and timing of EF stimulation pulses, depicting the characteristics of electrostatic and dissipative interactions. Blocker tests and correlated changes of active Ras on the cell membrane with ERK signals indicated that both EGFR and Ras were involved in the rich ERK dynamics induced by EF. We propose that the frequency-dependent dielectric relaxation process could be an important mechanism to couple EF energy to the cell membrane region and modulate membrane protein-initiated signaling pathways, which can be further explored to precisely control cell behavior and fate with high temporal and spatial resolution.
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Affiliation(s)
- Minxi Hu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Houpu Li
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Kan Zhu
- Department of Dermatology, University of California, Davis, CA, 95616, USA
| | - Liang Guo
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Min Zhao
- Department of Dermatology, University of California, Davis, CA, 95616, USA
- Department of Ophthalmology and Vision Science, University of California, Davis, CA, 95616, USA
| | - Huiwang Zhan
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Peter N Devreotes
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Quan Qing
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA.
- Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.
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3
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Henkels KM, Miller TE, Naji A, van der Hoeven R, Liang H, Zhou Y, Hammond GR, Hancock JF, Cho KJ. Myotubularin-related proteins regulate KRAS function by controlling plasma membrane levels of polyphosphoinositides and phosphatidylserine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576612. [PMID: 38328115 PMCID: PMC10849561 DOI: 10.1101/2024.01.22.576612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
KRAS is a small GTPase, ubiquitously expressed in mammalian cells, that functions as a molecular switch to regulate cell proliferation and differentiation. Oncogenic mutations that render KRAS constitutively active occur frequently in human cancers. KRAS must localize to the plasma membrane (PM) for biological activity. KRAS PM binding is mediated by interactions of the KRAS membrane anchor with phosphatidylserine (PtdSer), therefore, depleting PM PtdSer content abrogates KRAS PM binding and oncogenic function. From a genome-wide siRNA screen to search for genes that regulate KRAS PM localization, we identified a set of phosphatidylinositol (PI) 3-phosphatase family members: myotubularin-related (MTMR) proteins 2, 3, 4 and 7. Here we show that knockdown of MTMR 2/3/4/7 expression disrupts KRAS PM interactions. The molecular mechanism involves depletion of PM PI 4-phosphate (PI4P) levels, which in turn disrupts the subcellular localization and operation of oxysterol-binding protein related protein (ORP) 5, a PtdSer lipid transfer protein that maintains PM PtdSer content. Concomitantly, silencing MTMR 2/3/4/7 expression elevates PM levels of PI3P and reduces PM and total cellular levels of PtdSer. In summary we propose that the PI 3-phosphatase activity provided by MTMR proteins is required to generate PM PI for the synthesis of PM PI4P, which in turn, promotes the PM localization of PtdSer and KRAS.
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Affiliation(s)
- Karen M. Henkels
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, USA
| | - Taylor E. Miller
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, USA
| | - Ali Naji
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Ransome van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Gerald R.V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - John F. Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Kwang-jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, USA
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4
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Rehl KM, Selvakumar J, Pitsch RL, Hoang D, Arumugam K, Harshman SW, Gorfe AA, Cho KJ. A new ferrocene derivative blocks K-Ras localization and function by oxidative modification at His95. Life Sci Alliance 2023; 6:e202302094. [PMID: 37666666 PMCID: PMC10477449 DOI: 10.26508/lsa.202302094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/06/2023] Open
Abstract
Ras proteins are membrane-bound GTPases that regulate essential cellular processes at the plasma membrane (PM). Constitutively active mutations of K-Ras, one of the three Ras isoforms in mammalian cells, are frequently found in human cancers. Ferrocene derivatives, which elevate cellular reactive oxygen species (ROS), have shown to block the growth of non-small cell lung cancers harboring oncogenic mutant K-Ras. Here, we tested a novel ferrocene derivative on the growth of pancreatic ductal adenocarcinoma and non-small cell lung cancer. Our compound, which elevated cellular ROS levels, inhibited the growth of K-Ras-driven cancers, and abrogated the PM binding and signaling of K-Ras in an isoform-specific manner. These effects were reversed upon antioxidant supplementation, suggesting a ROS-mediated mechanism. We further identified that K-Ras His95 residue plays an important role in this process, and it is putatively oxidized by cellular ROS. Together, our study demonstrates that the redox system directly regulates K-Ras/PM binding and signaling via oxidative modification at the His95, and proposes a role of oncogenic mutant K-Ras in the recently described antioxidant-induced growth and metastasis of K-Ras-driven cancers.
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Affiliation(s)
- Kristen M Rehl
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| | - Jayaraman Selvakumar
- Department of Chemistry, College of Science and Mathematics, Wright State University, Dayton, OH, USA
| | - Rhonda L Pitsch
- https://ror.org/02e2egq70 Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
| | - Don Hoang
- Department of Chemistry, College of Science and Mathematics, Wright State University, Dayton, OH, USA
| | - Kuppuswamy Arumugam
- Department of Chemistry, College of Science and Mathematics, Wright State University, Dayton, OH, USA
| | - Sean W Harshman
- https://ror.org/02e2egq70 Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
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5
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Mendiratta G, Stites E. Theoretical analysis reveals a role for RAF conformational autoinhibition in paradoxical activation. eLife 2023; 12:e82739. [PMID: 37823369 PMCID: PMC10627510 DOI: 10.7554/elife.82739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/10/2023] [Indexed: 10/13/2023] Open
Abstract
RAF kinase inhibitors can, under certain conditions, increase RAF kinase signaling. This process, which is commonly referred to as 'paradoxical activation' (PA), is incompletely understood. We use mathematical and computational modeling to investigate PA and derive rigorous analytical expressions that illuminate the underlying mechanism of this complex phenomenon. We find that conformational autoinhibition modulation by a RAF inhibitor could be sufficient to create PA. We find that experimental RAF inhibitor drug dose-response data that characterize PA across different types of RAF inhibitors are best explained by a model that includes RAF inhibitor modulation of three properties: conformational autoinhibition, dimer affinity, and drug binding within the dimer (i.e., negative cooperativity). Overall, this work establishes conformational autoinhibition as a robust mechanism for RAF inhibitor-driven PA based solely on equilibrium dynamics of canonical interactions that comprise RAF signaling and inhibition.
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Affiliation(s)
- Gaurav Mendiratta
- Integrative Biology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Edward Stites
- Department of Laboratory Medicine, Yale UniversityNew HavenUnited States
- Yale Cancer Center, Yale School of MedicineNew HavenUnited States
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6
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Rehl KM, Selvakumar J, Hoang D, Arumugam K, Gorfe AA, Cho KJ. A new ferrocene derivative blocks KRAS localization and function by oxidative modification at His95. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534499. [PMID: 37034642 PMCID: PMC10081197 DOI: 10.1101/2023.03.28.534499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Ras proteins are membrane-bound GTPases that regulate essential cellular processes at the plasma membrane (PM). Constitutively active mutations of K-Ras, one of the three Ras isoforms in mammalian cells, are frequently found in human cancers. Ferrocene derivatives, which elevate cellular reactive oxygen species (ROS), have shown to block the growth of non-small cell lung cancers (NSCLCs) harboring oncogenic mutant K-Ras. Here, we developed and tested a novel ferrocene derivative on the growth of human pancreatic ductal adenocarcinoma (PDAC) and NSCLC. Our compound inhibited the growth of K-Ras-dependent PDAC and NSCLC and abrogated the PM binding and signaling of K-Ras, but not other Ras isoforms. These effects were reversed upon antioxidant supplementation, suggesting a ROS-mediated mechanism. We further identified K-Ras His95 residue in the G-domain as being involved in the ferrocene-induced K-Ras PM dissociation via oxidative modification. Together, our studies demonstrate that the redox system directly regulates K-Ras PM binding and signaling via oxidative modification at the His95, and proposes a role of oncogenic mutant K-Ras in the recently described antioxidant-induced metastasis in K-Ras-driven lung cancers.
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7
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Dynamic regulation of RAS and RAS signaling. Biochem J 2023; 480:1-23. [PMID: 36607281 PMCID: PMC9988006 DOI: 10.1042/bcj20220234] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023]
Abstract
RAS proteins regulate most aspects of cellular physiology. They are mutated in 30% of human cancers and 4% of developmental disorders termed Rasopathies. They cycle between active GTP-bound and inactive GDP-bound states. When active, they can interact with a wide range of effectors that control fundamental biochemical and biological processes. Emerging evidence suggests that RAS proteins are not simple on/off switches but sophisticated information processing devices that compute cell fate decisions by integrating external and internal cues. A critical component of this compute function is the dynamic regulation of RAS activation and downstream signaling that allows RAS to produce a rich and nuanced spectrum of biological outputs. We discuss recent findings how the dynamics of RAS and its downstream signaling is regulated. Starting from the structural and biochemical properties of wild-type and mutant RAS proteins and their activation cycle, we examine higher molecular assemblies, effector interactions and downstream signaling outputs, all under the aspect of dynamic regulation. We also consider how computational and mathematical modeling approaches contribute to analyze and understand the pleiotropic functions of RAS in health and disease.
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8
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Ozdemir ES, Koester AM, Nan X. Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Genes (Basel) 2022; 13:219. [PMID: 35205266 PMCID: PMC8872464 DOI: 10.3390/genes13020219] [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: 01/07/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Formation of Ras multimers, including dimers and nanoclusters, has emerged as an exciting, new front of research in the 'old' field of Ras biomedicine. With significant advances made in the past few years, we are beginning to understand the structure of Ras multimers and, albeit preliminary, mechanisms that regulate their formation in vitro and in cells. Here we aim to synthesize the knowledge accrued thus far on Ras multimers, particularly the presence of multiple globular (G-) domain interfaces, and discuss how membrane nanodomain composition and structure would influence Ras multimer formation. We end with some general thoughts on the potential implications of Ras multimers in basic and translational biology.
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Affiliation(s)
- E. Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
| | - Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
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9
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Mysore VP, Zhou ZW, Ambrogio C, Li L, Kapp JN, Lu C, Wang Q, Tucker MR, Okoro JJ, Nagy-Davidescu G, Bai X, Plückthun A, Jänne PA, Westover KD, Shan Y, Shaw DE. A structural model of a Ras-Raf signalosome. Nat Struct Mol Biol 2021; 28:847-857. [PMID: 34625747 PMCID: PMC8643099 DOI: 10.1038/s41594-021-00667-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/25/2021] [Indexed: 01/29/2023]
Abstract
The protein K-Ras functions as a molecular switch in signaling pathways regulating cell growth. In the human mitogen-activated protein kinase (MAPK) pathway, which is implicated in many cancers, multiple K-Ras proteins are thought to assemble at the cell membrane with Ras effector proteins from the Raf family. Here we propose an atomistic structural model for such an assembly. Our starting point was an asymmetric guanosine triphosphate-mediated K-Ras dimer model, which we generated using unbiased molecular dynamics simulations and verified with mutagenesis experiments. Adding further K-Ras monomers in a head-to-tail fashion led to a compact helical assembly, a model we validated using electron microscopy and cell-based experiments. This assembly stabilizes K-Ras in its active state and presents composite interfaces to facilitate Raf binding. Guided by existing experimental data, we then positioned C-Raf, the downstream kinase MEK1 and accessory proteins (Galectin-3 and 14-3-3σ) on and around the helical assembly. The resulting Ras-Raf signalosome model offers an explanation for a large body of data on MAPK signaling.
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Affiliation(s)
| | - Zhi-Wei Zhou
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chiara Ambrogio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Turin, Italy
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonas N Kapp
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Chunya Lu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qi Wang
- D. E. Shaw Research, New York, NY, USA
| | | | - Jeffrey J Okoro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Xiaochen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - David E Shaw
- D. E. Shaw Research, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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10
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RAS Dimers: The Novice Couple at the RAS-ERK Pathway Ball. Genes (Basel) 2021; 12:genes12101556. [PMID: 34680951 PMCID: PMC8535645 DOI: 10.3390/genes12101556] [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: 09/14/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023] Open
Abstract
Signals conveyed through the RAS-ERK pathway constitute a pivotal regulatory element in cancer-related cellular processes. Recently, RAS dimerization has been proposed as a key step in the relay of RAS signals, critically contributing to RAF activation. RAS clustering at plasma membrane microdomains and endomembranes facilitates RAS dimerization in response to stimulation, promoting RAF dimerization and subsequent activation. Remarkably, inhibiting RAS dimerization forestalls tumorigenesis in cellular and animal models. Thus, the pharmacological disruption of RAS dimers has emerged as an additional target for cancer researchers in the quest for a means to curtail aberrant RAS activity.
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11
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Parkkola H, Siddiqui FA, Oetken-Lindholm C, Abankwa D. FLIM-FRET Analysis of Ras Nanoclustering and Membrane-Anchorage. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:233-250. [PMID: 33977480 DOI: 10.1007/978-1-0716-1190-6_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
On the plasma membrane, Ras is organized into laterally segregated proteo-lipid complexes called nanoclusters. The extent of Ras nanoclustering correlates with its signaling output, positioning nanocluster as dynamic signaling gain modulators. Recent evidence suggests that stacked dimers of Ras and Raf are elemental units at least of one type of Ras nanocluster. However, it is still incompletely understood, in which physiological contexts nanoclustering is regulated and which constituents are parts of nanocluster. Nonetheless, disruption of nanoclustering faithfully diminishes Ras activity in cells, suggesting Ras nanocluster as potential drug targets.While there are several methods available to study Ras nanocluster , fluorescence or Förster resonance energy transfer (FRET ) between fluorescently labeled, nanoclustered Ras proteins is a relatively simple readout. FRET measurements using fluorescence lifetime imaging microscopy (FLIM ) have proven to be robust and sensitive to determine Ras nanoclustering changes. Loss of FRET that emerges due to nanoclustering reports on all processes upstream of Ras nanoclustering, i.e., also on proper trafficking or lipid modification of Ras. Here we report our standard FLIM-FRET protocol to measure nanoclustering-dependent FRET of Ras in mammalian cells. Importantly, nanoclustering-dependent FRET is one of the few methods that can detect differences between the Ras isoforms.
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Affiliation(s)
- Hanna Parkkola
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Farid Ahmad Siddiqui
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Daniel Abankwa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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12
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Henkels KM, Rehl KM, Cho KJ. Blocking K-Ras Interaction With the Plasma Membrane Is a Tractable Therapeutic Approach to Inhibit Oncogenic K-Ras Activity. Front Mol Biosci 2021; 8:673096. [PMID: 34222333 PMCID: PMC8244928 DOI: 10.3389/fmolb.2021.673096] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/20/2021] [Indexed: 12/12/2022] Open
Abstract
Ras proteins are membrane-bound small GTPases that promote cell proliferation, differentiation, and apoptosis. Consistent with this key regulatory role, activating mutations of Ras are present in ∼19% of new cancer cases in the United States per year. K-Ras is one of the three ubiquitously expressed isoforms in mammalian cells, and oncogenic mutations in this isoform account for ∼75% of Ras-driven cancers. Therefore, pharmacological agents that block oncogenic K-Ras activity would have great clinical utility. Most efforts to block oncogenic Ras activity have focused on Ras downstream effectors, but these inhibitors only show limited clinical benefits in Ras-driven cancers due to the highly divergent signals arising from Ras activation. Currently, four major approaches are being extensively studied to target K-Ras–driven cancers. One strategy is to block K-Ras binding to the plasma membrane (PM) since K-Ras requires the PM binding for its signal transduction. Here, we summarize recently identified molecular mechanisms that regulate K-Ras–PM interaction. Perturbing these mechanisms using pharmacological agents blocks K-Ras–PM binding and inhibits K-Ras signaling and growth of K-Ras–driven cancer cells. Together, these studies propose that blocking K-Ras–PM binding is a tractable strategy for developing anti–K-Ras therapies.
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Affiliation(s)
- Karen M Henkels
- Department of Biochemistry and Molecular Biology, School of Boonshoft School of Medicine, Wright State University, Dayton, OH, United States
| | - Kristen M Rehl
- Department of Biochemistry and Molecular Biology, School of Boonshoft School of Medicine, Wright State University, Dayton, OH, United States
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, School of Boonshoft School of Medicine, Wright State University, Dayton, OH, United States
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13
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Gorfe AA, Cho KJ. Approaches to inhibiting oncogenic K-Ras. Small GTPases 2021; 12:96-105. [PMID: 31438765 PMCID: PMC7849769 DOI: 10.1080/21541248.2019.1655883] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023] Open
Abstract
Activating somatic K-Ras mutations are associated with >15% all human tumors and up to 90% of specific tumor types such as pancreatic cancer. Successfully inhibiting abnormal K-Ras signaling would therefore be a game changer in cancer therapy. However, K-Ras has long been considered an undruggable target for various reasons. This view is now changing by the discovery of allosteric inhibitors that directly target K-Ras and inhibit its functions, and by the identification of new mechanisms to dislodge it from the plasma membrane and thereby abrogate its cellular activities. In this review, we will discuss recent progresses and challenges to inhibiting aberrant K-Ras functions by these two approaches. We will also provide a broad overview of other approaches such as inhibition of K-Ras effectors, and offer a brief perspective on the way forward.
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Affiliation(s)
- Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Programs of Biochemistry & Cell and Therapeutics & Pharmacology, MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
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14
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Kiel C, Matallanas D, Kolch W. The Ins and Outs of RAS Effector Complexes. Biomolecules 2021; 11:236. [PMID: 33562401 PMCID: PMC7915224 DOI: 10.3390/biom11020236] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
RAS oncogenes are among the most commonly mutated proteins in human cancers. They regulate a wide range of effector pathways that control cell proliferation, survival, differentiation, migration and metabolic status. Including aberrations in these pathways, RAS-dependent signaling is altered in more than half of human cancers. Targeting mutant RAS proteins and their downstream oncogenic signaling pathways has been elusive. However, recent results comprising detailed molecular studies, large scale omics studies and computational modeling have painted a new and more comprehensive portrait of RAS signaling that helps us to understand the intricacies of RAS, how its physiological and pathophysiological functions are regulated, and how we can target them. Here, we review these efforts particularly trying to relate the detailed mechanistic studies with global functional studies. We highlight the importance of computational modeling and data integration to derive an actionable understanding of RAS signaling that will allow us to design new mechanism-based therapies for RAS mutated cancers.
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Affiliation(s)
- Christina Kiel
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; (C.K.); (D.M.)
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - David Matallanas
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; (C.K.); (D.M.)
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Ireland; (C.K.); (D.M.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
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15
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Abankwa D, Gorfe AA. Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again. Biomolecules 2020; 10:E1522. [PMID: 33172116 PMCID: PMC7694788 DOI: 10.3390/biom10111522] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
Ras is the most frequently mutated oncogene and recent drug development efforts have spurred significant new research interest. Here we review progress toward understanding how Ras functions in nanoscale, proteo-lipid signaling complexes on the plasma membrane, called nanoclusters. We discuss how G-domain reorientation is plausibly linked to Ras-nanoclustering and -dimerization. We then look at how these mechanistic features could cooperate in the engagement and activation of RAF by Ras. Moreover, we show how this structural information can be integrated with microscopy data that provide nanoscale resolution in cell biological experiments. Synthesizing the available data, we propose to distinguish between two types of Ras nanoclusters, an active, immobile RAF-dependent type and an inactive/neutral membrane anchor-dependent. We conclude that it is possible that Ras reorientation enables dynamic Ras dimerization while the whole Ras/RAF complex transits into an active state. These transient di/oligomer interfaces of Ras may be amenable to pharmacological intervention. We close by highlighting a number of open questions including whether all effectors form active nanoclusters and whether there is an isoform specific composition of Ras nanocluster.
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Affiliation(s)
- Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA
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16
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Abstract
While the organization of inanimate systems such as gases or liquids is predominantly thermodynamically driven—a mixture of two gases will tend to mix until they reach equilibrium—biological systems frequently exhibit organization that is far from a well-mixed equilibrium. The anisotropies displayed by cells are evident in some of the dynamic processes that constitute life including cell development, movement, and division. These anisotropies operate at different length-scales, from the meso- to the nanoscale, and are proposed to reflect self-organization, a characteristic of living systems that is becoming accessible to reconstitution from purified components, and thus a more thorough understanding. Here, some examples of self-organization underlying cellular anisotropies at the cellular level are reviewed, with an emphasis on Rho-family GTPases operating at the plasma membrane. Given the technical challenges of studying these dynamic proteins, some of the successful approaches that are being employed to study their self-organization will also be considered.
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Affiliation(s)
- Derek McCusker
- Dynamics of Cell Growth and Division, European Institute of Chemistry and Biology, F-33607 Bordeaux, France; Institute of Biochemistry and Cellular Genetics, UMR 5095, University of Bordeaux and Centre National de la Recherche Scientifique, F-33000 Bordeaux, France
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17
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Kattan WE, Hancock JF. RAS Function in cancer cells: translating membrane biology and biochemistry into new therapeutics. Biochem J 2020; 477:2893-2919. [PMID: 32797215 PMCID: PMC7891675 DOI: 10.1042/bcj20190839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023]
Abstract
The three human RAS proteins are mutated and constitutively activated in ∼20% of cancers leading to cell growth and proliferation. For the past three decades, many attempts have been made to inhibit these proteins with little success. Recently; however, multiple methods have emerged to inhibit KRAS, the most prevalently mutated isoform. These methods and the underlying biology will be discussed in this review with a special focus on KRAS-plasma membrane interactions.
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Affiliation(s)
- Walaa E. Kattan
- Department of Integrative Biology and Pharmacology, McGovern Medical School University of Texas Health Science Center at Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, TX 77030, USA
| | - John F. Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School University of Texas Health Science Center at Houston, TX 77030, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, TX 77030, USA
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18
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Garrido CM, Henkels KM, Rehl KM, Liang H, Zhou Y, Gutterman JU, Cho KJ. Avicin G is a potent sphingomyelinase inhibitor and blocks oncogenic K- and H-Ras signaling. Sci Rep 2020; 10:9120. [PMID: 32499517 PMCID: PMC7272413 DOI: 10.1038/s41598-020-65882-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/05/2020] [Indexed: 12/23/2022] Open
Abstract
K-Ras must interact primarily with the plasma membrane (PM) for its biological activity. Therefore, disrupting K-Ras PM interaction is a tractable approach to block oncogenic K-Ras activity. Here, we found that avicin G, a family of natural plant-derived triterpenoid saponins from Acacia victoriae, mislocalizes K-Ras from the PM and disrupts PM spatial organization of oncogenic K-Ras and H-Ras by depleting phosphatidylserine (PtdSer) and cholesterol contents, respectively, at the inner PM leaflet. Avicin G also inhibits oncogenic K- and H-Ras signal output and the growth of K-Ras-addicted pancreatic and non-small cell lung cancer cells. We further identified that avicin G perturbs lysosomal activity, and disrupts cellular localization and activity of neutral and acid sphingomyelinases (SMases), resulting in elevated cellular sphingomyelin (SM) levels and altered SM distribution. Moreover, we show that neutral SMase inhibitors disrupt the PM localization of K-Ras and PtdSer and oncogenic K-Ras signaling. In sum, this study identifies avicin G as a new potent anti-Ras inhibitor, and suggests that neutral SMase can be a tractable target for developing anti-K-Ras therapeutics.
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Affiliation(s)
- Christian M Garrido
- Department of Biochemistry and Molecular Biology, School of Boonshoft Medical School, Wright State University, Dayton, OH, 45435, United States
| | - Karen M Henkels
- Department of Biochemistry and Molecular Biology, School of Boonshoft Medical School, Wright State University, Dayton, OH, 45435, United States
| | - Kristen M Rehl
- Department of Biochemistry and Molecular Biology, School of Boonshoft Medical School, Wright State University, Dayton, OH, 45435, United States
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, United States
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, United States
| | - Jordan U Gutterman
- Department of Systems Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, 77030, United States
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, School of Boonshoft Medical School, Wright State University, Dayton, OH, 45435, United States.
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19
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Jung J, Venkatachalam K. TRPML1 and RAS-driven cancers - exploring a link with great therapeutic potential. Channels (Austin) 2019; 13:374-381. [PMID: 31526156 PMCID: PMC6768051 DOI: 10.1080/19336950.2019.1666457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/04/2019] [Accepted: 09/08/2019] [Indexed: 12/05/2022] Open
Abstract
Activating mutations in the RAS family of proto-oncogenes represent some of the leading causes of cancer. Unmitigated proliferation of cells harboring oncogenic RAS mutations is accompanied by a massive increase in cellular bioenergetic demands, which offers unique opportunities for therapeutic intervention. To withstand the steep requirements for metabolic intermediates, RAS-driven cancer cells enhance endolysosome and autophagosome biogenesis. By degrading cellular macromolecules into metabolites that can be used by biosynthetic pathways, endolysosomes permit continued proliferation and survival in otherwise detrimental conditions. We recently showed that human cancers with activating mutations in HRAS elevate the expression of MCOLN1, which encodes an endolysosomal cation channel called TRPML1. Increased TRPML1 activity in HRAS-driven cancer cells is needed for the restoration of plasma membrane cholesterol that gets collaterally internalized during endocytosis. Inhibition of TRPML1 or knockdown of MCOLN1 leads to mislocalization of cholesterol from the plasma membrane to endolysosomes, loss of oncogenic HRAS from the cell surface, and attenuation of downstream signaling. Here, we discuss the implications of our findings and suggest strategies to leverage pathways that impinge upon TRPML1 as novel anti-cancer treatments.
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Affiliation(s)
- Jewon Jung
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Kartik Venkatachalam
- Department of Integrative Biology and Pharmacology, McGovern Medical School at the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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20
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Barklis E, Stephen AG, Staubus AO, Barklis RL, Alfadhli A. Organization of Farnesylated, Carboxymethylated KRAS4B on Membranes. J Mol Biol 2019; 431:3706-3717. [PMID: 31330153 PMCID: PMC6733658 DOI: 10.1016/j.jmb.2019.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 11/24/2022]
Abstract
Mutations of the Ras proteins HRAS, KRAS4A, KRAS4B, and NRAS are associated with a high percentage of all human cancers. The proteins are composed of highly homologous N-terminal catalytic or globular domains, plus C-terminal hypervariable regions (HVRs). Post-translational modifications of all RAS HVRs helps target RAS proteins to cellular membrane locations where they perform their signaling functions. For the predominant KRAS4 isoform, KRAS4B, post-translational farnesylation and carboxymethylation, along with a patch of HVR basic residues help foster membrane binding. Recent investigations implicate membrane-bound RAS dimers, oligomers, and nanoclusters as landing pads for effector proteins that relay RAS signals. The details of these RAS signaling platforms have not been elucidated completely, in part due to the difficulties in preparing modified proteins. We have employed properly farnesylated and carboxymethylated KRAS4B in lipid monolayer incubations to examine how the proteins assemble on membranes. Our results reveal novel insights into to how KRAS4B may organize on membranes.
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Affiliation(s)
- Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA.
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21072, USA
| | - August O Staubus
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, 97239, OR, USA
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21
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Man RJ, Zhang YL, Jiang AQ, Zhu HL. A patent review of RAF kinase inhibitors (2010–2018). Expert Opin Ther Pat 2019; 29:675-688. [DOI: 10.1080/13543776.2019.1651842] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ruo-Jun Man
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, People’s Republic of China
- College of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, People’s Republic of China
| | - Ya-Liang Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, People’s Republic of China
| | - Ai-Qin Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, People’s Republic of China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, People’s Republic of China
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22
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Jung J, Cho KJ, Naji AK, Clemons KN, Wong CO, Villanueva M, Gregory S, Karagas NE, Tan L, Liang H, Rousseau MA, Tomasevich KM, Sikora AG, Levental I, van der Hoeven D, Zhou Y, Hancock JF, Venkatachalam K. HRAS-driven cancer cells are vulnerable to TRPML1 inhibition. EMBO Rep 2019; 20:e46685. [PMID: 30787043 PMCID: PMC6446245 DOI: 10.15252/embr.201846685] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/28/2019] [Accepted: 02/01/2019] [Indexed: 12/28/2022] Open
Abstract
By serving as intermediaries between cellular metabolism and the bioenergetic demands of proliferation, endolysosomes allow cancer cells to thrive under normally detrimental conditions. Here, we show that an endolysosomal TRP channel, TRPML1, is necessary for the proliferation of cancer cells that bear activating mutations in HRAS Expression of MCOLN1, which encodes TRPML1, is significantly elevated in HRAS-positive tumors and inversely correlated with patient prognosis. Concordantly, MCOLN1 knockdown or TRPML1 inhibition selectively reduces the proliferation of cancer cells that express oncogenic, but not wild-type, HRAS Mechanistically, TRPML1 maintains oncogenic HRAS in signaling-competent nanoclusters at the plasma membrane by mediating cholesterol de-esterification and transport. TRPML1 inhibition disrupts the distribution and levels of cholesterol and thereby attenuates HRAS nanoclustering and plasma membrane abundance, ERK phosphorylation, and cell proliferation. These findings reveal a selective vulnerability of HRAS-driven cancers to TRPML1 inhibition, which may be leveraged as an actionable therapeutic strategy.
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Affiliation(s)
- Jewon Jung
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
| | - Ali K Naji
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center, Houston, TX, USA
| | - Kristen N Clemons
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Ching On Wong
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Mariana Villanueva
- Bobby R. Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA
- Patient Derived Xenografts and Advanced in vivo Models Core Facility, Baylor College of Medicine, Houston, TX, USA
| | - Steven Gregory
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Nicholas E Karagas
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Lingxiao Tan
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Morgan A Rousseau
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Kelly M Tomasevich
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
| | - Andrew G Sikora
- Bobby R. Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, TX, USA
- Patient Derived Xenografts and Advanced in vivo Models Core Facility, Baylor College of Medicine, Houston, TX, USA
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center, Houston, TX, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Kartik Venkatachalam
- Department of Integrative Biology and Pharmacology, McGovern Medical School, the University of Texas Health Sciences Center (UTHealth), Houston, TX, USA
- Graduate Program in Biochemistry and Cell Biology, MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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23
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Bugaj LJ, Sabnis AJ, Mitchell A, Garbarino JE, Toettcher JE, Bivona TG, Lim WA. Cancer mutations and targeted drugs can disrupt dynamic signal encoding by the Ras-Erk pathway. Science 2018; 361:361/6405/eaao3048. [PMID: 30166458 DOI: 10.1126/science.aao3048] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/16/2018] [Indexed: 12/16/2022]
Abstract
The Ras-Erk (extracellular signal-regulated kinase) pathway encodes information in its dynamics; the duration and frequency of Erk activity can specify distinct cell fates. To enable dynamic encoding, temporal information must be accurately transmitted from the plasma membrane to the nucleus. We used optogenetic profiling to show that both oncogenic B-Raf mutations and B-Raf inhibitors can cause corruption of this transmission, so that short pulses of input Ras activity are distorted into abnormally long Erk outputs. These changes can reshape downstream transcription and cell fates, resulting in improper decisions to proliferate. These findings illustrate how altered dynamic signal transmission properties, and not just constitutively increased signaling, can contribute to cell proliferation and perhaps cancer, and how optogenetic profiling can dissect mechanisms of signaling dysfunction in disease.
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Affiliation(s)
- L J Bugaj
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - A J Sabnis
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - A Mitchell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - J E Garbarino
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - J E Toettcher
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - T G Bivona
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - W A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA
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24
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Zhou Y, Prakash P, Gorfe AA, Hancock JF. Ras and the Plasma Membrane: A Complicated Relationship. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031831. [PMID: 29229665 DOI: 10.1101/cshperspect.a031831] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The primary site of Ras signal transduction is the plasma membrane (PM). On the PM, the ubiquitously expressed Ras isoforms, H-, N-, and K-Ras, spatially segregate to nonoverlapping nanometer-sized domains, called nanoclusters, with further lateral segregation into nonoverlapping guanosine triphosphate (GTP)-bound and guanosine diphosphate (GDP)-bound nanoclusters. Effector binding and activation is restricted to GTP nanoclusters, rendering the underlying assembly mechanism essential to Ras signaling. Ras nanoclusters have distinct lipid compositions as a result of lipid-sorting specificity encoded in each Ras carboxy-terminal membrane anchor. The role of the G-domain in regulating anchor-membrane interactions is becoming clearer. Ras G-domains undergo significant conformational orientation changes on guanine nucleotide switch, leading to differential direct contacts between the G-domain and reorganization of the membrane anchor. Ras G-domains also contain weak dimer interfaces, resulting in homodimerization, which is an obligate step of nanoclustering. Modulating the formation of Ras dimers, the lipid composition of the PM or lateral dynamics of key PM phospholipids represent novel mechanisms whereby the extent of Ras nanoclustering can be regulated to tune the gain in Ras signaling circuits.
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Affiliation(s)
- Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030
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25
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Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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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, Maryland. .,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, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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26
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Nussinov R, Tsai CJ, Jang H. Oncogenic Ras Isoforms Signaling Specificity at the Membrane. Cancer Res 2018; 78:593-602. [PMID: 29273632 PMCID: PMC5811325 DOI: 10.1158/0008-5472.can-17-2727] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 01/21/2023]
Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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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, Maryland.
- 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, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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27
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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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28
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Spencer-Smith R, O'Bryan JP. Direct inhibition of RAS: Quest for the Holy Grail? Semin Cancer Biol 2017; 54:138-148. [PMID: 29248537 DOI: 10.1016/j.semcancer.2017.12.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/13/2017] [Indexed: 12/25/2022]
Abstract
RAS GTPases (H-, K-, and N-RAS) are the most frequently mutated oncoprotein family in human cancer. However, the relatively smooth surface architecture of RAS and its picomolar affinity for nucleotide have given rise to the assumption that RAS is an "undruggable" target. Recent advancements in drug screening, molecular modeling, and a greater understanding of RAS function have led to a resurgence in efforts to pharmacologically target this challenging foe. This review focuses on the state of the art of RAS inhibition, the approaches taken to achieve this goal, and the challenges of translating these discoveries into viable therapeutics.
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Affiliation(s)
- Russell Spencer-Smith
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, USA; University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, USA; Jesse Brown VA Medical Center, Chicago, IL, USA
| | - John P O'Bryan
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, USA; University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, IL, USA; Jesse Brown VA Medical Center, Chicago, IL, USA.
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29
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Concepts and advances in cancer therapeutic vulnerabilities in RAS membrane targeting. Semin Cancer Biol 2017; 54:121-130. [PMID: 29203271 DOI: 10.1016/j.semcancer.2017.11.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/30/2017] [Indexed: 01/05/2023]
Abstract
For decades oncogenic RAS proteins were considered undruggable due to a lack of accessible binding pockets on the protein surfaces. Seminal early research in RAS biology uncovered the basic paradigm of post-translational isoprenylation of RAS polypeptides, typically with covalent attachment of a farnesyl group, leading to isoprenyl-mediated RAS anchorage at the plasma membrane and signal initiation at those sites. However, the failure of farnesyltransferase inhibitors to translate to the clinic stymied anti-RAS therapy development. Over the past ten years, a more complete picture has emerged of RAS protein maturation, intracellular trafficking, and location, positioning and retention in subdomains at the plasma membrane, with a corresponding expansion in our understanding of how these properties of RAS contribute to signal outputs. Each of these aspects of RAS regulation presents a potential vulnerability in RAS function that may be exploited for therapeutic targeting, and inhibitors have been identified or developed that interfere with RAS for nearly all of them. This review will summarize current understanding of RAS membrane targeting with a focus on highlighting development and outcomes of inhibitors at each step.
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30
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RAF inhibitors promote RAS-RAF interaction by allosterically disrupting RAF autoinhibition. Nat Commun 2017; 8:1211. [PMID: 29084939 PMCID: PMC5662619 DOI: 10.1038/s41467-017-01274-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 09/01/2017] [Indexed: 12/19/2022] Open
Abstract
First-generation RAF inhibitors paradoxically induce ERK signaling in normal and tumor cells exhibiting RAS activity. Compound-induced RAF dimerization through stabilization of the RAF ON/active state by inhibitors has emerged as a critical contributing factor. RAF inhibitors also enhance RAS−RAF association. Although this event is thought to play a key role in priming RAF activation, the underlying mechanism is not known. Here we report that RAF inhibitors induce the disruption of intramolecular interactions between the kinase domain and its N-terminal regulatory region independently of RAS activity. This provides a molecular basis to explain the induction of RAS−RAF association by RAF inhibitors, as well as the co-operativity observed between RAS activity and RAF kinase inhibitors in driving RAF activation. Profiling of second-generation RAF inhibitors confirmed their improved mode of action, but also revealed liabilities that allowed us to discern two properties of an ideal RAF inhibitor: high-binding affinity to all RAF paralogs and maintenance of the OFF/autoinhibited state of the enzyme. RAF family kinases transmit signals from activated RAS at the plasma membrane to downstream kinases to control cell proliferation, differentiation and survival. Here the authors shed light on the molecular mechanisms whereby small molecule RAF inhibitors induce RAS-RAF association and paradoxical RAF activation.
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31
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Posada IMD, Lectez B, Siddiqui FA, Oetken-Lindholm C, Sharma M, Abankwa D. Opposite feedback from mTORC1 to H-ras and K-ras4B downstream of SREBP1. Sci Rep 2017; 7:8944. [PMID: 28827765 PMCID: PMC5567141 DOI: 10.1038/s41598-017-09387-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/26/2017] [Indexed: 01/12/2023] Open
Abstract
As a major growth factor transducer, Ras is an upstream activator of mTORC1, which further integrates nutrient and energy inputs. To ensure a contextual coupling of cell division via Ras/MAPK-signalling and growth via mTORC1-signalling, feedback loops from one pathway back to the other are required. Here we describe a novel feedback from mTORC1, which oppositely affects oncogenic H-ras- and K-ras-signalling output, and as a consequence stemness properties of tumourigenic cells. Amino acid stimulation of mTORC1 increases the processed form of SREBP1, a major lipidome regulator. We show that modulation of the SREBP1 levels downstream of S6K1 has opposite effects on oncogenic H-ras and K-ras nanoscale membrane organisation, ensuing signalling output and promotion of mammospheres expressing these oncogenes. Our data suggest that modulation of phosphatidic acid, a major target of SREBP1 controlled lipid metabolism, is sufficient to affect H-ras and K-ras oppositely in the membrane. Thus mTORC1 activation increases H-ras-, but decreases K-ras-signalling output in cells transformed with the respective oncogene. Given the different impact of these two Ras isoforms on stemness, our results could have implications for stem cell biology and inhibition of cancer stem cells.
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Affiliation(s)
- Itziar M D Posada
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520, Turku, Finland
| | - Benoit Lectez
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520, Turku, Finland
| | - Farid A Siddiqui
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520, Turku, Finland
| | | | - Mukund Sharma
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520, Turku, Finland
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520, Turku, Finland.
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32
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SPRED1 Interferes with K-ras but Not H-ras Membrane Anchorage and Signaling. Mol Cell Biol 2016; 36:2612-25. [PMID: 27503857 DOI: 10.1128/mcb.00191-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/03/2016] [Indexed: 12/13/2022] Open
Abstract
The Ras/mitogen-activated protein kinase (MAPK) signaling pathway is tightly controlled by negative feedback regulators, such as the tumor suppressor SPRED1. The SPRED1 gene also carries loss-of-function mutations in the RASopathy Legius syndrome. Growth factor stimulation translocates SPRED1 to the plasma membrane, triggering its inhibitory activity. However, it remains unclear whether SPRED1 there acts at the level of Ras or Raf. We show that pharmacological or galectin-1 (Gal-1)-mediated induction of B- and C-Raf-containing dimers translocates SPRED1 to the plasma membrane. This is facilitated in particular by SPRED1 interaction with B-Raf and, via its N terminus, with Gal-1. The physiological significance of these novel interactions is supported by two Legius syndrome-associated mutations that show diminished binding to both Gal-1 and B-Raf. On the plasma membrane, SPRED1 becomes enriched in acidic membrane domains to specifically perturb membrane organization and extracellular signal-regulated kinase (ERK) signaling of active K-ras4B (here, K-ras) but not H-ras. However, SPRED1 also blocks on the nanoscale the positive effects of Gal-1 on H-ras. Therefore, a combinatorial expression of SPRED1 and Gal-1 potentially regulates specific patterns of K-ras- and H-ras-dependent signaling output. More broadly, our results open up the possibility that related SPRED and Sprouty proteins act in a similar Ras and Raf isoform-specific manner.
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33
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Zhuo C, Li Q, Wu Y, Li Y, Nie J, Li D, Peng J, Lian P, Li B, Cai G, Li X, Cai S. LINE-1 hypomethylation in normal colon mucosa is associated with poor survival in Chinese patients with sporadic colon cancer. Oncotarget 2016; 6:23820-36. [PMID: 26172297 PMCID: PMC4695154 DOI: 10.18632/oncotarget.4450] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/19/2015] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic pathways are not independent in colorectal cancer (CRC) carcinogenesis. We aimed to determine the influence of various molecular features on Chinese patients' colon cancer-specific survival (CCSS). Various genetic and epigenetic modifications were detected in paired tumor and normal mucosa tissue samples. The prognostic variables regarding patient CCSS were determined. Overall, 127 patients, including 83 males and 44 females, completed a median follow-up of 65 (3–85) months. A mean LINE-1 methylation rate of 64.62% (range, 9.45–86.93) was observed. Hypermethylation at the hMLH1 gene promoter was detected in 26 (20.47%) patients. KRAS was mutated in 52 (40.94%) patients. Sixteen (12.60%) patients were confirmed as microsatellite instability (MSI)-High, and 76 (59.84%) were found to have loss of heterozygosity at 18q. The LINE-1 methylation level, MSI status, perineural invasion and distant metastases were confirmed as independent prognostic factors for patient CCSS. A stratified survival analysis further revealed that certain subgroups of patients with LINE-1 hypomethylation had significantly worse survival (all p < 0.05). Our data revealed that both genetic and epigenetic abnormalities can concurrently exist during colonic tumorigenesis. As a global epigenetic change, LINE-1 hypomethylation in normal colon mucosa might be associated with a worse outcome in certain Chinese patients with colon cancer.
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Affiliation(s)
- Changhua Zhuo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China.,Department of Surgical Oncology, Fujian Provincial Cancer Hospital, Teaching Hospital of Fujian Medical University, Fuzhou 350014, People's Republic of China
| | - Qingguo Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Yuchen Wu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Yiwei Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Jia Nie
- Key Laboratory of Molecular Virology & Immunology, Unit of Molecular Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Dawei Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Junjie Peng
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Peng Lian
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Bin Li
- Key Laboratory of Molecular Virology & Immunology, Unit of Molecular Immunology, Institut Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Guoxiang Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Xinxiang Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
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34
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Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R. Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers. Biochem J 2016; 473:1719-32. [PMID: 27057007 PMCID: PMC7830773 DOI: 10.1042/bcj20160031] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/07/2016] [Indexed: 02/07/2023]
Abstract
Are the dimer structures of active Ras isoforms similar? This question is significant since Ras can activate its effectors as a monomer; however, as a dimer, it promotes Raf's activation and MAPK (mitogen-activated protein kinase) cell signalling. In the present study, we model possible catalytic domain dimer interfaces of membrane-anchored GTP-bound K-Ras4B and H-Ras, and compare their conformations. The active helical dimers formed by the allosteric lobe are isoform-specific: K-Ras4B-GTP favours the α3 and α4 interface; H-Ras-GTP favours α4 and α5. Both isoforms also populate a stable β-sheet dimer interface formed by the effector lobe; a less stable β-sandwich interface is sustained by salt bridges of the β-sheet side chains. Raf's high-affinity β-sheet interaction is promoted by the active helical interface. Collectively, Ras isoforms' dimer conformations are not uniform; instead, the isoform-specific dimers reflect the favoured interactions of the HVRs (hypervariable regions) with cell membrane microdomains, biasing the effector-binding site orientations, thus isoform binding selectivity.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, U.S.A
| | - Serena Muratcioglu
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, U.S.A. Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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35
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Blaževitš O, Mideksa YG, Šolman M, Ligabue A, Ariotti N, Nakhaeizadeh H, Fansa EK, Papageorgiou AC, Wittinghofer A, Ahmadian MR, Abankwa D. Galectin-1 dimers can scaffold Raf-effectors to increase H-ras nanoclustering. Sci Rep 2016; 6:24165. [PMID: 27087647 PMCID: PMC4834570 DOI: 10.1038/srep24165] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 03/22/2016] [Indexed: 12/12/2022] Open
Abstract
Galectin-1 (Gal-1) dimers crosslink carbohydrates on cell surface receptors. Carbohydrate-derived inhibitors have been developed for cancer treatment. Intracellularly, Gal-1 was suggested to interact with the farnesylated C-terminus of Ras thus specifically stabilizing GTP-H-ras nanoscale signalling hubs in the membrane, termed nanoclusters. The latter activity may present an alternative mechanism for how overexpressed Gal-1 stimulates tumourigenesis. Here we revise the current model for the interaction of Gal-1 with H-ras. We show that it indirectly forms a complex with GTP-H-ras via a high-affinity interaction with the Ras binding domain (RBD) of Ras effectors. A computationally generated model of the Gal-1/C-Raf-RBD complex is validated by mutational analysis. Both cellular FRET as well as proximity ligation assay experiments confirm interaction of Gal-1 with Raf proteins in mammalian cells. Consistently, interference with H-rasG12V-effector interactions basically abolishes H-ras nanoclustering. In addition, an intact dimer interface of Gal-1 is required for it to positively regulate H-rasG12V nanoclustering, but negatively K-rasG12V nanoclustering. Our findings suggest stacked dimers of H-ras, Raf and Gal-1 as building blocks of GTP-H-ras-nanocluster at high Gal-1 levels. Based on our results the Gal-1/effector interface represents a potential drug target site in diseases with aberrant Ras signalling.
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Affiliation(s)
- Olga Blaževitš
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Yonatan G. Mideksa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Maja Šolman
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Alessio Ligabue
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Nicholas Ariotti
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Hossein Nakhaeizadeh
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Eyad K. Fansa
- Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | | | | | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
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36
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Cho KJ, van der Hoeven D, Zhou Y, Maekawa M, Ma X, Chen W, Fairn GD, Hancock JF. Inhibition of Acid Sphingomyelinase Depletes Cellular Phosphatidylserine and Mislocalizes K-Ras from the Plasma Membrane. Mol Cell Biol 2016; 36:363-74. [PMID: 26572827 PMCID: PMC4719297 DOI: 10.1128/mcb.00719-15] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/07/2015] [Accepted: 10/28/2015] [Indexed: 11/20/2022] Open
Abstract
K-Ras must localize to the plasma membrane for biological activity; thus, preventing plasma membrane interaction blocks K-Ras signal output. Here we show that inhibition of acid sphingomyelinase (ASM) mislocalizes both the K-Ras isoforms K-Ras4A and K-Ras4B from the plasma membrane to the endomembrane and inhibits their nanoclustering. We found that fendiline, a potent ASM inhibitor, reduces the phosphatidylserine (PtdSer) and cholesterol content of the inner plasma membrane. These lipid changes are causative because supplementation of fendiline-treated cells with exogenous PtdSer rapidly restores K-Ras4A and K-Ras4B plasma membrane binding, nanoclustering, and signal output. Conversely, supplementation with exogenous cholesterol restores K-Ras4A but not K-Ras4B nanoclustering. These experiments reveal different operational pools of PtdSer on the plasma membrane. Inhibition of ASM elevates cellular sphingomyelin and reduces cellular ceramide levels. Concordantly, delivery of recombinant ASM or exogenous ceramide to fendiline-treated cells rapidly relocalizes K-Ras4B and PtdSer to the plasma membrane. K-Ras4B mislocalization is also recapitulated in ASM-deficient Neimann-Pick type A and B fibroblasts. This study identifies sphingomyelin metabolism as an indirect regulator of K-Ras4A and K-Ras4B signaling through the control of PtdSer plasma membrane content. It also demonstrates the critical and selective importance of PtdSer to K-Ras4A and K-Ras4B plasma membrane binding and nanoscale spatial organization.
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Affiliation(s)
- Kwang-Jin Cho
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Medical School, Houston, Texas, USA
| | - Dharini van der Hoeven
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry, Houston, Texas, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Medical School, Houston, Texas, USA
| | - Masashi Maekawa
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada Departments of Surgery and Biochemistry, University of Toronto, Toronto, Ontario, Canada Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Xiaoping Ma
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Medical School, Houston, Texas, USA
| | - Wei Chen
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Medical School, Houston, Texas, USA
| | - Gregory D Fairn
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada Departments of Surgery and Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Medical School, Houston, Texas, USA
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37
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Najumudeen AK, Posada IMD, Lectez B, Zhou Y, Landor SKJ, Fallarero A, Vuorela P, Hancock J, Abankwa D. Phenotypic Screening Identifies Protein Synthesis Inhibitors as H-Ras-Nanocluster-Increasing Tumor Growth Inducers. Biochemistry 2015; 54:7212-21. [PMID: 26568031 DOI: 10.1021/acs.biochem.5b00724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ras isoforms H-, N-, and K-ras are each mutated in specific cancer types at varying frequencies and have different activities in cell fate control. On the plasma membrane, Ras proteins are laterally segregated into isoform-specific nanoscale signaling hubs, termed nanoclusters. As Ras nanoclusters are required for Ras signaling, chemical modulators of nanoclusters represent ideal candidates for the specific modulation of Ras activity in cancer drug development. We therefore conducted a chemical screen with commercial and in-house natural product libraries using a cell-based H-ras-nanoclustering FRET assay. Next to established Ras inhibitors, such as a statin and farnesyl-transferase inhibitor, we surprisingly identified five protein synthesis inhibitors as positive regulators. Using commonly employed cycloheximide as a representative compound, we show that protein synthesis inhibition increased nanoclustering and effector recruitment specifically of active H-ras but not of K-ras. Consistent with these data, cycloheximide treatment activated both Erk and Akt kinases and specifically promoted H-rasG12V-induced, but not K-rasG12V-induced, PC12 cell differentiation. Intriguingly, cycloheximide increased the number of mammospheres, which are enriched for cancer stem cells. Depletion of H-ras in combination with cycloheximide significantly reduced mammosphere formation, suggesting an exquisite synthetic lethality. The potential of cycloheximide to promote tumor cell growth was also reflected in its ability to increase breast cancer cell tumors grown in ovo. These results illustrate the possibility of identifying Ras-isoform-specific modulators using nanocluster-directed screening. They also suggest an unexpected feedback from protein synthesis inhibition to Ras signaling, which might present a vulnerability in certain tumor cell types.
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Affiliation(s)
- Arafath K Najumudeen
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland
| | - Itziar M D Posada
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland
| | - Benoit Lectez
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland
| | - Yong Zhou
- University of Texas Health Science Center at Houston , Medical School, Houston, Texas 77030, United States
| | - Sebastian K-J Landor
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland.,Department of Cell and Molecular Biology (CMB), Karolinska Institutet , SE-171 77 Stockholm, Sweden
| | - Adyary Fallarero
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland
| | - Pia Vuorela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland
| | - John Hancock
- University of Texas Health Science Center at Houston , Medical School, Houston, Texas 77030, United States
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland
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38
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Wehrens M, ten Wolde PR, Mugler A. Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes. J Chem Phys 2015; 141:205102. [PMID: 25429963 DOI: 10.1063/1.4901888] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Clustering of molecules on biological membranes is a widely observed phenomenon. A key example is the clustering of the oncoprotein Ras, which is known to be important for signal transduction in mammalian cells. Yet, the mechanism by which Ras clusters form and are maintained remains unclear. Recently, it has been discovered that activated Ras promotes further Ras activation. Here we show using particle-based simulation that this positive feedback is sufficient to produce persistent clusters of active Ras molecules at the nanometer scale via a dynamic nucleation mechanism. Furthermore, we find that our cluster statistics are consistent with experimental observations of the Ras system. Interestingly, we show that our model does not support a Turing regime of macroscopic reaction-diffusion patterning, and therefore that the clustering we observe is a purely stochastic effect, arising from the coupling of positive feedback with the discrete nature of individual molecules. These results underscore the importance of stochastic and dynamic properties of reaction diffusion systems for biological behavior.
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Affiliation(s)
- Martijn Wehrens
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | | | - Andrew Mugler
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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39
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Chavan TS, Muratcioglu S, Marszalek R, Jang H, Keskin O, Gursoy A, Nussinov R, Gaponenko V. Plasma membrane regulates Ras signaling networks. CELLULAR LOGISTICS 2015; 5:e1136374. [PMID: 27054048 PMCID: PMC4820813 DOI: 10.1080/21592799.2015.1136374] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/31/2022]
Abstract
Ras GTPases activate more than 20 signaling pathways, regulating such essential cellular functions as proliferation, survival, and migration. How Ras proteins control their signaling diversity is still a mystery. Several pieces of evidence suggest that the plasma membrane plays a critical role. Among these are: (1) selective recruitment of Ras and its effectors to particular localities allowing access to Ras regulators and effectors; (2) specific membrane-induced conformational changes promoting Ras functional diversity; and (3) oligomerization of membrane-anchored Ras to recruit and activate Raf. Taken together, the membrane does not only attract and retain Ras but also is a key regulator of Ras signaling. This can already be gleaned from the large variability in the sequences of Ras membrane targeting domains, suggesting that localization, environment and orientation are important factors in optimizing the function of Ras isoforms.
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Affiliation(s)
- Tanmay Sanjeev Chavan
- Department of Medicinal Chemistry; University of Illinois at Chicago; Chicago, IL USA
| | - Serena Muratcioglu
- Center for Computational Biology and Bioinformatics; Koc University; Istanbul, Turkey
| | - Richard Marszalek
- Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago; Chicago, IL USA
| | - Hyunbum Jang
- Cancer and Inflammation Program; Basic Science Program; Leidos Biomedical Research, Inc.; Frederick National Laboratory for Cancer Research; National Cancer Institute at Frederick; Frederick, MD USA
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics; Koc University; Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics; Koc University; Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program; Basic Science Program; Leidos Biomedical Research, Inc.; Frederick National Laboratory for Cancer Research; National Cancer Institute at Frederick; Frederick, MD USA
- Sackler Institute of Molecular Medicine; Department of Human Genetics and Molecular Medicine; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago; Chicago, IL USA
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40
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Kolch W, Halasz M, Granovskaya M, Kholodenko BN. The dynamic control of signal transduction networks in cancer cells. Nat Rev Cancer 2015; 15:515-27. [PMID: 26289315 DOI: 10.1038/nrc3983] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cancer is often considered a genetic disease. However, much of the enormous plasticity of cancer cells to evolve different phenotypes, to adapt to challenging microenvironments and to withstand therapeutic assaults is encoded by the structure and spatiotemporal dynamics of signal transduction networks. In this Review, we discuss recent concepts concerning how the rich signalling dynamics afforded by these networks are regulated and how they impinge on cancer cell proliferation, survival, invasiveness and drug resistance. Understanding this dynamic circuitry by mathematical modelling could pave the way to new therapeutic approaches and personalized treatments.
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Affiliation(s)
- Walter Kolch
- Systems Biology Ireland, University College Dublin
- Conway Institute of Biomolecular &Biomedical Research, University College Dublin
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Marina Granovskaya
- Roche Moscow Limited, Business Center Neglinnaya Plaza, Building 2, Trubnaya Square, 107031 Moscow, Russia
| | - Boris N Kholodenko
- Systems Biology Ireland, University College Dublin
- Conway Institute of Biomolecular &Biomedical Research, University College Dublin
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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41
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Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O. The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas. Mol Cancer Res 2015; 13:1265-73. [PMID: 26085527 PMCID: PMC4572916 DOI: 10.1158/1541-7786.mcr-15-0165] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/09/2015] [Indexed: 12/14/2022]
Abstract
KRAS4B is a highly oncogenic splice variant of the KRAS isoform. It is the only isoform associated with initiation of adenocarcinomas. Insight into why and how KRAS4B can mediate ductal adenocarcinomas, particularly of the pancreas, is vastly important for its therapeutics. Here we point out the overlooked critical role of calmodulin (CaM). Calmodulin selectively binds to GTP-bound K-Ras4B; but not to other Ras isoforms. Cell proliferation and growth require the MAPK (Raf/MEK/ERK) and PI3K/Akt pathways. We propose that Ca(2+)/calmodulin promote PI3Kα/Akt signaling, and suggest how. The elevated calcium levels clinically observed in adenocarcinomas may explain calmodulin's involvement in recruiting and stimulating PI3Kα through interaction with its n/cSH2 domains as well as K-Ras4B; importantly, it also explains why K-Ras4B specifically is a key player in ductal carcinomas, such as pancreatic (PDAC), colorectal (CRC), and lung cancers. We hypothesize that calmodulin recruits and helps activate PI3Kα at the membrane, and that this is the likely reason for Ca(2+)/calmodulin dependence in adenocarcinomas. Calmodulin can contribute to initiation/progression of ductal cancers via both PI3Kα/Akt and Raf/MEK/ERK pathways. Blocking the K-Ras4B/MAPK pathway and calmodulin/PI3Kα binding in a K-Ras4B/calmodulin/PI3Kα trimer could be a promising adenocarcinoma-specific therapeutic strategy.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI at Frederick, Frederick, Maryland. Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Serena Muratcioglu
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI at Frederick, Frederick, Maryland
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
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42
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Šolman M, Ligabue A, Blaževitš O, Jaiswal A, Zhou Y, Liang H, Lectez B, Kopra K, Guzmán C, Härmä H, Hancock JF, Aittokallio T, Abankwa D. Specific cancer-associated mutations in the switch III region of Ras increase tumorigenicity by nanocluster augmentation. eLife 2015; 4:e08905. [PMID: 26274561 PMCID: PMC4563131 DOI: 10.7554/elife.08905] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/13/2015] [Indexed: 01/09/2023] Open
Abstract
Hotspot mutations of Ras drive cell transformation and tumorigenesis. Less frequent mutations in Ras are poorly characterized for their oncogenic potential. Yet insight into their mechanism of action may point to novel opportunities to target Ras. Here, we show that several cancer-associated mutations in the switch III region moderately increase Ras activity in all isoforms. Mutants are biochemically inconspicuous, while their clustering into nanoscale signaling complexes on the plasma membrane, termed nanocluster, is augmented. Nanoclustering dictates downstream effector recruitment, MAPK-activity, and tumorigenic cell proliferation. Our results describe an unprecedented mechanism of signaling protein activation in cancer. DOI:http://dx.doi.org/10.7554/eLife.08905.001 Cancer is a disease that develops when cells within the body acquire genetic mutations that allow them to grow and divide rapidly. Many human cancers have mutations in a gene that encodes a protein called Ras, which promotes cell growth and division by controlling the activities of other proteins. Ras congregates at the membrane that surrounds the cell and can assemble into clusters (called nanoclusters) that each contain six to eight Ras proteins. The tight packing of the proteins in these nanoclusters increases the amount of Ras in the membrane locally, which allows Ras to interact with other proteins more efficiently to promote growth and cell division. In normal cells, other proteins control when Ras is active. However, in many cancer cells, Ras is active all the time due to mutations that occur in three ‘hotspots’ within its gene. Other mutations in the gene that encodes Ras are also found in cancer cells, but these are less common and it is not clear how they alter the activity of the protein. Here, Solman et al. used microscopy and biochemical techniques to study the effects of some of the less common mutations on Ras activity in human cells. The experiments show that several mutations that alter a region of Ras called the ‘switch III region’ moderately increase the activity of Ras. The mutations probably alter the way that Ras sits in the membrane, which in turn changes the way it interacts with other proteins and the membrane so that more Ras nanoclusters form. Solman et al.'s findings reveal a new way that Ras can be activated in cancer cells. The next challenge is to develop drugs that block the formation of Ras nanoclusters and to find out if they have the potential to be used to treat cancer. DOI:http://dx.doi.org/10.7554/eLife.08905.002
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Affiliation(s)
- Maja Šolman
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Alessio Ligabue
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Olga Blaževitš
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Alok Jaiswal
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, United States
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, United States
| | - Benoit Lectez
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Kari Kopra
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Camilo Guzmán
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Harri Härmä
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, United States
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
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43
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Abstract
Electron microscopy allows direct visualization of the underlying organization of cell surface components on a nano-scale. Immuno-gold labelling of isolated plasma membranes generates point patterns that enable mapping of protein and lipid distributions. 2D spatial statistics reveals the extent to which these distributions are clustered or dispersed and allows the extent of co-localization between different cell surface components to be precisely determined. This approach has been successfully applied to the study of signalling network organization and the consequences of physiological changes in modulating cell surface function.
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Affiliation(s)
- Alison J Beckett
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown St., Liverpool, L69 3BX, UK
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44
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Muratcioglu S, Chavan TS, Freed BC, Jang H, Khavrutskii L, Freed RN, Dyba MA, Stefanisko K, Tarasov SG, Gursoy A, Keskin O, Tarasova NI, Gaponenko V, Nussinov R. GTP-Dependent K-Ras Dimerization. Structure 2015; 23:1325-35. [PMID: 26051715 PMCID: PMC4497850 DOI: 10.1016/j.str.2015.04.019] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 11/18/2022]
Abstract
Ras proteins recruit and activate effectors, including Raf, that transmit receptor-initiated signals. Monomeric Ras can bind Raf; however, activation of Raf requires its dimerization. It has been suspected that dimeric Ras may promote dimerization and activation of Raf. Here, we show that the GTP-bound catalytic domain of K-Ras4B, a highly oncogenic splice variant of the K-Ras isoform, forms stable homodimers. We observe two major dimer interfaces. The first, highly populated β-sheet dimer interface is at the Switch I and effector binding regions, overlapping the binding surfaces of Raf, PI3K, RalGDS, and additional effectors. This interface has to be inhibitory to such effectors. The second, helical interface also overlaps the binding sites of some effectors. This interface may promote activation of Raf. Our data reveal how Ras self-association can regulate effector binding and activity, and suggest that disruption of the helical dimer interface by drugs may abate Raf signaling in cancer.
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Affiliation(s)
- Serena Muratcioglu
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Tanmay S Chavan
- Department of Medicinal Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Benjamin C Freed
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lyuba Khavrutskii
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - R Natasha Freed
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Marzena A Dyba
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Structural Biophysics Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Karen Stefanisko
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Sergey G Tarasov
- Structural Biophysics Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Nadya I Tarasova
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Basic Science Program, Leidos Biomedical Research, Inc., 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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45
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Abstract
RAF family kinases were among the first oncoproteins to be described more than 30 years ago. They primarily act as signalling relays downstream of RAS, and their close ties to cancer have fuelled a large number of studies. However, we still lack a systems-level understanding of their regulation and mode of action. The recent discovery that the catalytic activity of RAF depends on an allosteric mechanism driven by kinase domain dimerization is providing a vital new piece of information towards a comprehensive model of RAF function. The fact that current RAF inhibitors unexpectedly induce ERK signalling by stimulating RAF dimerization also calls for a deeper structural characterization of this family of kinases.
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46
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Jang H, Abraham SJ, Chavan TS, Hitchinson B, Khavrutskii L, Tarasova NI, Nussinov R, Gaponenko V. Mechanisms of membrane binding of small GTPase K-Ras4B farnesylated hypervariable region. J Biol Chem 2015; 290:9465-77. [PMID: 25713064 PMCID: PMC4392252 DOI: 10.1074/jbc.m114.620724] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/19/2015] [Indexed: 01/08/2023] Open
Abstract
K-Ras4B belongs to a family of small GTPases that regulates cell growth, differentiation and survival. K-ras is frequently mutated in cancer. K-Ras4B association with the plasma membrane through its farnesylated and positively charged C-terminal hypervariable region (HVR) is critical to its oncogenic function. However, the structural mechanisms of membrane association are not fully understood. Here, using confocal microscopy, surface plasmon resonance, and molecular dynamics simulations, we observed that K-Ras4B can be distributed in rigid and loosely packed membrane domains. Its membrane binding domain interaction with phospholipids is driven by membrane fluidity. The farnesyl group spontaneously inserts into the disordered lipid microdomains, whereas the rigid microdomains restrict the farnesyl group penetration. We speculate that the resulting farnesyl protrusion toward the cell interior allows oligomerization of the K-Ras4B membrane binding domain in rigid microdomains. Unlike other Ras isoforms, K-Ras4B HVR contains a single farnesyl modification and positively charged polylysine sequence. The high positive charge not only modulates specific HVR binding to anionic phospholipids but farnesyl membrane orientation. Phosphorylation of Ser-181 prohibits spontaneous farnesyl membrane insertion. The mechanism illuminates the roles of HVR modifications in K-Ras4B targeting microdomains of the plasma membrane and suggests an additional function for HVR in regulation of Ras signaling.
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Affiliation(s)
- Hyunbum Jang
- From the Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research and Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Sherwin J Abraham
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, Departments of Biochemistry and Molecular Genetics and
| | - Tanmay S Chavan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305, Medicinal Chemistry, University of Illinois, Chicago, Illinois 60607, and
| | | | - Lyuba Khavrutskii
- From the Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research and Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Nadya I Tarasova
- Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702,
| | - Ruth Nussinov
- From the Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research and Cancer and Inflammation Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vadim Gaponenko
- Departments of Biochemistry and Molecular Genetics and Medicinal Chemistry, University of Illinois, Chicago, Illinois 60607, and
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47
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Najumudeen AK, Guzmán C, Posada IMD, Abankwa D. Rab-NANOPS: FRET biosensors for Rab membrane nanoclustering and prenylation detection in mammalian cells. Methods Mol Biol 2015; 1298:29-45. [PMID: 25800830 DOI: 10.1007/978-1-4939-2569-8_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Rab proteins constitute the largest subfamily of Ras-like small GTPases. They are central to vesicular transport and organelle definition in eukaryotic cells. Unlike their Ras counterparts, they are not a hallmark of cancer. However, a number of diseases, including cancer, show a misregulation of Rab protein activity. As for all membrane-anchored signaling proteins, correct membrane organization is critical for Rabs to operate. In this chapter, we provide a detailed protocol for the use of a flow cytometry-based Fluorescence Resonance Energy Transfer (FRET)-biosensors assay, which allows to detect changes in membrane anchorage, subcellular distribution, and of the nanoscale organization of Rab-GTPases in mammalian cell lines. This assay is high-throughput amenable and can therefore be utilized in chemical-genomic and drug discovery efforts.
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Affiliation(s)
- Arafath Kaja Najumudeen
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520, Turku, Finland
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Nussinov R, Jang H. Dynamic multiprotein assemblies shape the spatial structure of cell signaling. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:158-64. [PMID: 25046855 PMCID: PMC4250281 DOI: 10.1016/j.pbiomolbio.2014.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/07/2014] [Indexed: 11/25/2022]
Abstract
Cell signaling underlies critical cellular decisions. Coordination, efficiency as well as fail-safe mechanisms are key elements. How the cell ensures that these hallmarks are at play are important questions. Cell signaling is often viewed as taking place through discrete and cross-talking pathways; oftentimes these are modularized to emphasize distinct functions. While simple, convenient and clear, such models largely neglect the spatial structure of cell signaling; they also convey inter-modular (or inter-protein) spatial separation that may not exist. Here our thesis is that cell signaling is shaped by a network of multiprotein assemblies. While pre-organized, the assemblies and network are loose and dynamic. They contain transiently-associated multiprotein complexes which are often mediated by scaffolding proteins. They are also typically anchored in the membrane, and their continuum may span the cell. IQGAP1 scaffolding protein which binds proteins including Raf, calmodulin, Mek, Erk, actin, and tens more, with actin shaping B-cell (and likely other) membrane-anchored nanoclusters and allosterically polymerizing in dynamic cytoskeleton formation, and Raf anchoring in the membrane along with Ras, provides a striking example. The multivalent network of dynamic proteins and lipids, with specific interactions forming and breaking, can be viewed as endowing gel-like properties. Collectively, this reasons that efficient, productive and reliable cell signaling takes place primarily through transient, preorganized and cooperative protein-protein interactions spanning the cell rather than stochastic, diffusion-controlled processes.
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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, Frederick, MD 21702, USA; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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Guzmán C, Šolman M, Ligabue A, Blaževitš O, Andrade DM, Reymond L, Eggeling C, Abankwa D. The efficacy of Raf kinase recruitment to the GTPase H-ras depends on H-ras membrane conformer-specific nanoclustering. J Biol Chem 2014; 289:9519-33. [PMID: 24569991 DOI: 10.1074/jbc.m113.537001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Solution structures and biochemical data have provided a wealth of mechanistic insight into Ras GTPases. However, information on how much the membrane organization of these lipid-modified proteins impacts on their signaling is still scarce. Ras proteins are organized into membrane nanoclusters, which are necessary for Ras-MAPK signaling. Using quantitative conventional and super-resolution fluorescence methods, as well as mathematical modeling, we investigated nanoclustering of H-ras helix α4 and hypervariable region mutants that have different bona fide conformations on the membrane. By following the emergence of conformer-specific nanoclusters in the plasma membrane of mammalian cells, we found that conformers impart distinct nanoclustering responses depending on the cytoplasmic levels of the nanocluster scaffold galectin-1. Computational modeling revealed that complexes containing H-ras conformers and galectin-1 affect both the number and lifetime of nanoclusters and thus determine the specific Raf effector recruitment. Our results show that mutations in Ras can affect its nanoclustering response and thus allosterically effector recruitment and downstream signaling. We postulate that cancer- and developmental disease-linked mutations that are associated with the Ras membrane conformation may exhibit so far unrecognized Ras nanoclustering and therefore signaling alterations.
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Affiliation(s)
- Camilo Guzmán
- From the Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
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Nussinov R, Ma B, Tsai CJ. Multiple conformational selection and induced fit events take place in allosteric propagation. Biophys Chem 2014; 186:22-30. [PMID: 24239303 PMCID: PMC6361548 DOI: 10.1016/j.bpc.2013.10.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/07/2013] [Accepted: 10/09/2013] [Indexed: 12/16/2022]
Abstract
The fact that we observe a single conformational selection event during binding does not necessarily mean that only a single conformational selection event takes place, even though this is the common assumption. Here we suggest that conformational selection takes place not once in a given binding/allosteric event, but at every step along the allosteric pathway. This view generalizes conformational selection and makes it applicable also to other allosteric events, such as post-translational modifications (PTMs) and photon absorption. Similar to binding, at each step along a propagation pathway, conformational selection is coupled with induced fit which optimizes the interactions. Thus, as in binding, the allosteric effects induced by PTMs and light relate not only to population shift; but to conformational selection as well. Conformational selection and population shift take place conjointly.
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Affiliation(s)
- Ruth Nussinov
- Leidos Biomedical Research, Inc., Frederick National Laboratory, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Buyong Ma
- Leidos Biomedical Research, Inc., Frederick National Laboratory, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States
| | - Chung-Jung Tsai
- Leidos Biomedical Research, Inc., Frederick National Laboratory, Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States
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