1
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Damianou A, Liang Z, Lassen F, Vendrell I, Vere G, Hester S, Charles PD, Pinto-Fernandez A, Santos A, Fischer R, Kessler BM. Oncogenic mutations of KRAS modulate its turnover by the CUL3/LZTR1 E3 ligase complex. Life Sci Alliance 2024; 7:e202302245. [PMID: 38453365 PMCID: PMC10921066 DOI: 10.26508/lsa.202302245] [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: 06/30/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
KRAS is a proto-oncogene encoding a small GTPase. Mutations contribute to ∼30% of human solid tumours, including lung adenocarcinoma, pancreatic, and colorectal carcinomas. Most KRAS activating mutations interfere with GTP hydrolysis, essential for its role as a molecular switch, leading to alterations in their molecular environment and oncogenic signalling. However, the precise signalling cascades these mutations affect are poorly understood. Here, APEX2 proximity labelling was used to profile the molecular environment of WT, G12D, G13D, and Q61H-activating KRAS mutants under starvation and stimulation conditions. Through quantitative proteomics, we demonstrate the presence of known KRAS interactors, including ARAF and LZTR1, which are differentially captured by WT and KRAS mutants. Notably, the KRAS mutations G12D, G13D, and Q61H abrogate their association with LZTR1, thereby affecting turnover. Elucidating the implications of LZTR1-mediated regulation of KRAS protein levels in cancer may offer insights into therapeutic strategies targeting KRAS-driven malignancies.
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Affiliation(s)
- Andreas Damianou
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zhu Liang
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Frederik Lassen
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Iolanda Vendrell
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Svenja Hester
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip D Charles
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adan Pinto-Fernandez
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alberto Santos
- https://ror.org/052gg0110 Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Center for Health Data Science, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roman Fischer
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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2
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Faubert D, Thibault MP, Kmita M, Baskin JM, Gingras AC, Smith MJ, Côté JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. J Cell Sci 2024; 137:jcs262140. [PMID: 38606629 PMCID: PMC11166204 DOI: 10.1242/jcs.262140] [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: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARL) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we used proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ∼3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely, SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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Affiliation(s)
- Laura Quirion
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Amélie Robert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Jonathan Boulais
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Shiying Huang
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Gabriela Bernal Astrain
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Regina Strakhova
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Chang Hwa Jo
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Yacine Kherdjemil
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | - Denis Faubert
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
| | | | - Marie Kmita
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montréal, QC H3G 2M1, Canada
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew J. Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Jean-François Côté
- Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada
- Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
- Department of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada
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3
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Zhao Q, Shimada I, Nishida N. Real-Time Monitoring of RAS Activity Using In Vitro and In-Cell NMR Spectroscopy. Methods Mol Biol 2024; 2797:237-252. [PMID: 38570464 DOI: 10.1007/978-1-0716-3822-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The activation level of RAS can be determined by GTP hydrolysis rate (khy) and GDP-GTP exchange rates (kex). Either impaired GTP hydrolysis or enhanced GDP-GTP exchange causes the aberrant activation of RAS in oncogenic mutants. Therefore, it is important to quantify the khy and kex for understanding the mechanisms of RAS oncogenesis and drug development. Conventional methods have individually measured the kex and khy of RAS. However, within the intracellular environment, GTP hydrolysis and GDP-GTP exchange reactions occur simultaneously under conditions where GTP concentration is kept constant. In addition, the intracellular activity of RAS is influenced by endogenous regulatory proteins, such as RAS GTPase activating proteins (GAPs) and the guanine-nucleotide exchange factors (GEFs). Here, we describe the in vitro and in-cell NMR methods to estimate the khy and kex simultaneously by measuring the time-dependent changes of the fraction of GTP-bound ratio under the condition of constant GTP concentration.
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Affiliation(s)
- Qingci Zhao
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Ichio Shimada
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan.
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
| | - Noritaka Nishida
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan.
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4
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Strakhova R, Smith MJ. Profiling Complex RAS-Effector Interactions Using NMR Spectroscopy. Methods Mol Biol 2024; 2797:195-209. [PMID: 38570461 DOI: 10.1007/978-1-0716-3822-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Knowledge of how effectors interact with RAS GTPases is key to understanding how these switch-like proteins function in cells. Effectors bind specifically to GTP-loaded RAS using RAS association (RA) or RAS binding domains (RBDs) that show wide-ranging affinities and thermodynamic characteristics. Both normal development and RAS-induced tumorigenesis depend on multiple distinct effector proteins that are frequently co-expressed and co-localized, suggesting an antagonistic nature to signaling whereby multiple proteins compete for a limited pool of activated GTPase. NMR spectroscopy offers a powerful approach to multiplex effectors and/or regulatory enzymes and quantifies their interaction with RAS, expanding our biophysical and systems-level understanding of RAS signaling in a more integrated and physiologically relevant setting. Here we describe a method to directly quantitate GTPase binding to competing effectors, using wild-type KRAS complex with ARAF and PLCε1 as a model. Unlabeled RBD/RA domains are added simultaneously to isotopically labeled RAS, and peak intensities at chemical shifts characteristic of individually bound domains provide quantitation. Similar competition-based assays can be run with small molecule interactors, GEF/GAP domains, or regulatory enzymes that drive posttranslational modifications. Such efforts bring in vitro interaction experiments in line with more complex cellular environments.
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Affiliation(s)
- Regina Strakhova
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada.
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.
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5
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Johnson CW, Fetics SK, Davis KP, Rodrigues JA, Mattos C. Allosteric site variants affect GTP hydrolysis on Ras. Protein Sci 2023; 32:e4767. [PMID: 37615343 PMCID: PMC10510474 DOI: 10.1002/pro.4767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 08/25/2023]
Abstract
RAS GTPases are proto-oncoproteins that regulate cell growth, proliferation, and differentiation in response to extracellular signals. The signaling functions of RAS, and other small GTPases, are dependent on their ability to cycle between GDP-bound and GTP-bound states. Structural analyses suggest that GTP hydrolysis catalyzed by HRAS can be regulated by an allosteric site located between helices 3, 4, and loop 7. Here we explore the relationship between intrinsic GTP hydrolysis on HRAS and the position of helix 3 and loop 7 through manipulation of the allosteric site, showing that the two sites are functionally connected. We generated several hydrophobic mutations in the allosteric site of HRAS to promote shifts in helix 3 relative to helix 4. By combining crystallography and enzymology to study these mutants, we show that closure of the allosteric site correlates with increased hydrolysis of GTP on HRAS in solution. Interestingly, binding to the RAS binding domain of RAF kinase (RAF-RBD) inhibits GTP hydrolysis in the mutants. This behavior may be representative of a cluster of mutations found in human tumors, which potentially cooperate with RAF complex formation to stabilize the GTP-bound state of RAS.
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Affiliation(s)
- Christian W. Johnson
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Susan K. Fetics
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Kathleen P. Davis
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Jose A. Rodrigues
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
| | - Carla Mattos
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMassachusettsUSA
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
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6
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Affiliation(s)
- Ryan B Corcoran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
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7
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Gadanecz M, Fazekas Z, Pálfy G, Karancsiné Menyhárd D, Perczel A. NMR-Chemical-Shift-Driven Protocol Reveals the Cofactor-Bound, Complete Structure of Dynamic Intermediates of the Catalytic Cycle of Oncogenic KRAS G12C Protein and the Significance of the Mg 2+ Ion. Int J Mol Sci 2023; 24:12101. [PMID: 37569478 PMCID: PMC10418480 DOI: 10.3390/ijms241512101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
In this work, catalytically significant states of the oncogenic G12C variant of KRAS, those of Mg2+-free and Mg2+-bound GDP-loaded forms, have been determined using CS-Rosetta software and NMR-data-driven molecular dynamics simulations. There are several Mg2+-bound G12C KRAS/GDP structures deposited in the Protein Data Bank (PDB), so this system was used as a reference, while the structure of the Mg2+-free but GDP-bound state of the RAS cycle has not been determined previously. Due to the high flexibility of the Switch-I and Switch-II regions, which also happen to be the catalytically most significant segments, only chemical shift information could be collected for the most important regions of both systems. CS-Rosetta was used to derive an "NMR ensemble" based on the measured chemical shifts, which, however, did not contain the nonprotein components of the complex. We developed a torsional restraint set for backbone torsions based on the CS-Rosetta ensembles for MD simulations, overriding the force-field-based parametrization in the presence of the reinserted cofactors. This protocol (csdMD) resulted in complete models for both systems that also retained the structural features and heterogeneity defined by the measured chemical shifts and allowed a detailed comparison of the Mg2+-bound and Mg2+-free states of G12C KRAS/GDP.
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Affiliation(s)
- Márton Gadanecz
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary; (M.G.); (D.K.M.)
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary
| | - Zsolt Fazekas
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary; (M.G.); (D.K.M.)
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary; (M.G.); (D.K.M.)
- ELKH-ELTE Protein Modeling Research Group, Eötvös Loránd Research Network (ELKH), Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary
- Department of Biology, Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Dóra Karancsiné Menyhárd
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary; (M.G.); (D.K.M.)
- ELKH-ELTE Protein Modeling Research Group, Eötvös Loránd Research Network (ELKH), Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary; (M.G.); (D.K.M.)
- ELKH-ELTE Protein Modeling Research Group, Eötvös Loránd Research Network (ELKH), Pázmány Péter stny. 1/A, H-1117 Budapest, Hungary
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8
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Kim D, Herdeis L, Rudolph D, Zhao Y, Böttcher J, Vides A, Ayala-Santos CI, Pourfarjam Y, Cuevas-Navarro A, Xue JY, Mantoulidis A, Bröker J, Wunberg T, Schaaf O, Popow J, Wolkerstorfer B, Kropatsch KG, Qu R, de Stanchina E, Sang B, Li C, McConnell DB, Kraut N, Lito P. Pan-KRAS inhibitor disables oncogenic signalling and tumour growth. Nature 2023; 619:160-166. [PMID: 37258666 PMCID: PMC10322706 DOI: 10.1038/s41586-023-06123-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 04/24/2023] [Indexed: 06/02/2023]
Abstract
KRAS is one of the most commonly mutated proteins in cancer, and efforts to directly inhibit its function have been continuing for decades. The most successful of these has been the development of covalent allele-specific inhibitors that trap KRAS G12C in its inactive conformation and suppress tumour growth in patients1-7. Whether inactive-state selective inhibition can be used to therapeutically target non-G12C KRAS mutants remains under investigation. Here we report the discovery and characterization of a non-covalent inhibitor that binds preferentially and with high affinity to the inactive state of KRAS while sparing NRAS and HRAS. Although limited to only a few amino acids, the evolutionary divergence in the GTPase domain of RAS isoforms was sufficient to impart orthosteric and allosteric constraints for KRAS selectivity. The inhibitor blocked nucleotide exchange to prevent the activation of wild-type KRAS and a broad range of KRAS mutants, including G12A/C/D/F/V/S, G13C/D, V14I, L19F, Q22K, D33E, Q61H, K117N and A146V/T. Inhibition of downstream signalling and proliferation was restricted to cancer cells harbouring mutant KRAS, and drug treatment suppressed KRAS mutant tumour growth in mice, without having a detrimental effect on animal weight. Our study suggests that most KRAS oncoproteins cycle between an active state and an inactive state in cancer cells and are dependent on nucleotide exchange for activation. Pan-KRAS inhibitors, such as the one described here, have broad therapeutic implications and merit clinical investigation in patients with KRAS-driven cancers.
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Affiliation(s)
- Dongsung Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Yulei Zhao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Alberto Vides
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carlos I Ayala-Santos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasin Pourfarjam
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antonio Cuevas-Navarro
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Y Xue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | | | | | | | - Rui Qu
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ben Sang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chuanchuan Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Piro Lito
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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9
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Fleming IR, Hannan JP, Swisher GH, Tesdahl CD, Martyr JG, Cordaro NJ, Erbse AH, Falke JJ. Binding of active Ras and its mutants to the Ras binding domain of PI-3-kinase: A quantitative approach to K D measurements. Anal Biochem 2023; 663:115019. [PMID: 36526022 PMCID: PMC9884175 DOI: 10.1016/j.ab.2022.115019] [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: 10/15/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Ras family GTPases (H/K/N-Ras) modulate numerous effectors, including the lipid kinase PI3K (phosphatidylinositol-3-kinase) that generates growth signal lipid PIP3 (phosphatidylinositol-3,4,5-triphosphate). Active GTP-Ras binds PI3K with high affinity, thereby stimulating PIP3 production. We hypothesize the affinity of this binding interaction could be significantly increased or decreased by Ras mutations at PI3K contact positions, with clinical implications since some Ras mutations at PI3K contact positions are disease-linked. To enable tests of this hypothesis, we have developed an approach combining UV spectral deconvolution, HPLC, and microscale thermophoresis to quantify the KD for binding. The approach measures the total Ras concentration, the fraction of Ras in the active state, and the affinity of active Ras binding to its docking site on PI3K Ras binding domain (RBD) in solution. The approach is illustrated by KD measurements for the binding of active H-Ras and representative mutants, each loaded with GTP or GMPPNP, to PI3Kγ RBD. The findings demonstrate that quantitation of the Ras activation state increases the precision of KD measurements, while also revealing that Ras mutations can increase (Q25L), decrease (D38E, Y40C), or have no effect (G13R) on PI3K binding affinity. Significant Ras affinity changes are predicted to alter PI3K regulation and PIP3 growth signals.
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Affiliation(s)
- Ian R Fleming
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - George Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Corey D Tesdahl
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Justin G Martyr
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, USA.
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10
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Pálfy G, Menyhárd DK, Ákontz‐Kiss H, Vida I, Batta G, Tőke O, Perczel A. The Importance of Mg 2+ -Free State in Nucleotide Exchange of Oncogenic K-Ras Mutants. Chemistry 2022; 28:e202201449. [PMID: 35781716 PMCID: PMC9804424 DOI: 10.1002/chem.202201449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Indexed: 01/05/2023]
Abstract
For efficient targeting of oncogenic K-Ras interaction sites, a mechanistic picture of the Ras-cycle is necessary. Herein, we used NMR relaxation techniques and molecular dynamics simulations to decipher the role of slow dynamics in wild-type and three oncogenic P-loop mutants of K-Ras. Our measurements reveal a dominant two-state conformational exchange on the ms timescale in both GDP- and GTP-bound K-Ras. The identified low-populated higher energy state in GDP-loaded K-Ras has a conformation reminiscent of a nucleotide-bound/Mg2+ -free state characterized by shortened β2/β3-strands and a partially released switch-I region preparing K-Ras for the interaction with the incoming nucleotide exchange factor and subsequent reactivation. By providing insight into mutation-specific differences in K-Ras structural dynamics, our systematic analysis improves our understanding of prolonged K-Ras signaling and may aid the development of allosteric inhibitors targeting nucleotide exchange in K-Ras.
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Affiliation(s)
- Gyula Pálfy
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary,MTA-ELTE Protein Modeling Research GroupEötvös Loránd Research Network (ELKH)1/a Pázmány Péter stny.Budapest1117Hungary
| | - Dóra K. Menyhárd
- MTA-ELTE Protein Modeling Research GroupEötvös Loránd Research Network (ELKH)1/a Pázmány Péter stny.Budapest1117Hungary
| | - Hanna Ákontz‐Kiss
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary,Hevesy György PhD School of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary
| | - István Vida
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary,Hevesy György PhD School of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary
| | - Gyula Batta
- Structural Biology Research GroupDepartment of Organic ChemistryUniversity of Debrecen1 Egyetem térDebrecen4032Hungary
| | - Orsolya Tőke
- Laboratory for NMR SpectroscopyResearch Centre for Natural Sciences (RCNS)2 Magyar tudósok körútjaBudapest1117Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and BiologyInstitute of ChemistryEötvös Loránd University1/a Pázmány Péter stny.Budapest1117Hungary,MTA-ELTE Protein Modeling Research GroupEötvös Loránd Research Network (ELKH)1/a Pázmány Péter stny.Budapest1117Hungary
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11
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Thermal Shift Assay for Small GTPase Stability Screening: Evaluation and Suitability. Int J Mol Sci 2022; 23:ijms23137095. [PMID: 35806100 PMCID: PMC9266822 DOI: 10.3390/ijms23137095] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Thermal unfolding methods are commonly used as a predictive technique by tracking the protein's physical properties. Inherent protein thermal stability and unfolding profiles of biotherapeutics can help to screen or study potential drugs and to find stabilizing or destabilizing conditions. Differential scanning calorimetry (DSC) is a 'Gold Standard' for thermal stability assays (TSA), but there are also a multitude of other methodologies, such as differential scanning fluorimetry (DSF). The use of an external probe increases the assay throughput, making it more suitable for screening studies, but the current methodologies suffer from relatively low sensitivity. While DSF is an effective tool for screening, interpretation and comparison of the results is often complicated. To overcome these challenges, we compared three thermal stability probes in small GTPase stability studies: SYPRO Orange, 8-anilino-1-naphthalenesulfonic acid (ANS), and the Protein-Probe. We studied mainly KRAS, as a proof of principle to obtain biochemical knowledge through TSA profiles. We showed that the Protein-Probe can work at lower concentration than the other dyes, and its sensitivity enables effective studies with non-covalent and covalent drugs at the nanomolar level. Using examples, we describe the parameters, which must be taken into account when characterizing the effect of drug candidates, of both small molecules and Designed Ankyrin Repeat Proteins.
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12
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Rac1 as a Target to Treat Dysfunctions and Cancer of the Bladder. Biomedicines 2022; 10:biomedicines10061357. [PMID: 35740379 PMCID: PMC9219850 DOI: 10.3390/biomedicines10061357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/28/2022] Open
Abstract
Bladder pathologies, very common in the aged population, have a considerable negative impact on quality of life. Novel targets are needed to design drugs and combinations to treat diseases such as overactive bladder and bladder cancers. A promising new target is the ubiquitous Rho GTPase Rac1, frequently dysregulated and overexpressed in bladder pathologies. We have analyzed the roles of Rac1 in different bladder pathologies, including bacterial infections, diabetes-induced bladder dysfunctions and bladder cancers. The contribution of the Rac1 protein to tumorigenesis, tumor progression, epithelial-mesenchymal transition of bladder cancer cells and their metastasis has been analyzed. Small molecules selectively targeting Rac1 have been discovered or designed, and two of them—NSC23766 and EHT 1864—have revealed activities against bladder cancer. Their mode of interaction with Rac1, at the GTP binding site or the guanine nucleotide exchange factors (GEF) interaction site, is discussed. Our analysis underlines the possibility of targeting Rac1 with small molecules with the objective to combat bladder dysfunctions and to reduce lower urinary tract symptoms. Finally, the interest of a Rac1 inhibitor to treat advanced chemoresistance prostate cancer, while reducing the risk of associated bladder dysfunction, is discussed. There is hope for a better management of bladder pathologies via Rac1-targeted approaches.
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13
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Functional diversity in the RAS subfamily of small GTPases. Biochem Soc Trans 2022; 50:921-933. [PMID: 35356965 DOI: 10.1042/bst20211166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022]
Abstract
RAS small GTPases regulate important signalling pathways and are notorious drivers of cancer development and progression. While most research to date has focused on understanding and addressing the oncogenic potential of three RAS oncogenes: HRAS, KRAS, and NRAS; the full RAS subfamily is composed of 35 related GTPases with diverse cellular functions. Most remain deeply understudied despite strong evolutionary conservation. Here, we highlight a group of 17 poorly characterized RAS GTPases that are frequently down-regulated in cancer and evidence suggests may function not as oncogenes, but as tumour suppressors. These GTPases remain largely enigmatic in terms of their cellular function, regulation, and interaction with effector proteins. They cluster within two families we designate as 'distal-RAS' (D-RAS; comprised of DIRAS, RASD, and RASL10) and 'CaaX-Less RAS' (CL-RAS; comprised of RGK, NKIRAS, RERG, and RASL11/12 GTPases). Evidence of a tumour suppressive role for many of these GTPases supports the premise that RAS subfamily proteins may collectively regulate cellular proliferation.
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14
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Khan I, Koide A, Zuberi M, Ketavarapu G, Denbaum E, Teng KW, Rhett JM, Spencer-Smith R, Hobbs GA, Camp ER, Koide S, O'Bryan JP. Identification of the nucleotide-free state as a therapeutic vulnerability for inhibition of selected oncogenic RAS mutants. Cell Rep 2022; 38:110322. [PMID: 35139380 PMCID: PMC8936000 DOI: 10.1016/j.celrep.2022.110322] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/12/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
RAS guanosine triphosphatases (GTPases) are mutated in nearly 20% of human tumors, making them an attractive therapeutic target. Following our discovery that nucleotide-free RAS (apo RAS) regulates cell signaling, we selectively target this state as an approach to inhibit RAS function. Here, we describe the R15 monobody that exclusively binds the apo state of all three RAS isoforms in vitro, regardless of the mutation status, and captures RAS in the apo state in cells. R15 inhibits the signaling and transforming activity of a subset of RAS mutants with elevated intrinsic nucleotide exchange rates (i.e., fast exchange mutants). Intracellular expression of R15 reduces the tumor-forming capacity of cancer cell lines driven by select RAS mutants and KRAS(G12D)-mutant patient-derived xenografts (PDXs). Thus, our approach establishes an opportunity to selectively inhibit a subset of RAS mutants by targeting the apo state with drug-like molecules. Khan et al. develop a high-affinity monobody to nucleotide-free RAS that, when expressed intracellularly, inhibits oncogenic RAS-mediated signaling and tumorigenesis. This study reveals the feasibility of targeting the nucleotide-free state to inhibit tumors driven by oncogenic RAS mutants that possess elevated nucleotide exchange activity.
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Affiliation(s)
- Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, USA; Department of Pharmacology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Mariyam Zuberi
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Gayatri Ketavarapu
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Eric Denbaum
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - J Matthew Rhett
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Russell Spencer-Smith
- Department of Pharmacology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - G Aaron Hobbs
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ernest Ramsay Camp
- Department of Surgery, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA; Ralph H. Johnson VA Medical Center, Charleston, SC 29401, USA; Department of Pharmacology, University of Illinois at Chicago, Chicago, IL 60612, USA.
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15
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Tripathi S, Dsouza NR, Mathison AJ, Leverence E, Urrutia R, Zimmermann MT. Enhanced interpretation of 935 hotspot and non-hotspot RAS variants using evidence-based structural bioinformatics. Comput Struct Biotechnol J 2022; 20:117-127. [PMID: 34976316 PMCID: PMC8688876 DOI: 10.1016/j.csbj.2021.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/05/2021] [Accepted: 12/05/2021] [Indexed: 12/30/2022] Open
Abstract
In the current study, we report computational scores for advancing genomic interpretation of disease-associated genomic variation in members of the RAS family of genes. For this purpose, we applied 31 sequence- and 3D structure-based computational scores, chosen by their breadth of biophysical properties. We parametrized our data by assembling a numerically homogenized experimentally-derived dataset, which when use in our calculations reveal that computational scores using 3D structure highly correlate with experimental measures (e.g., GAP-mediated hydrolysis RSpearman = 0.80 and RAF affinity Rspearman = 0.82), while sequence-based scores are discordant with this data. Performing all-against-all comparisons, we applied this parametrized modeling approach to the study of 935 RAS variants from 7 RAS genes, which led us to identify 4 groups of mutations according to distinct biochemical scores within each group. Each group was comprised of hotspot and non-hotspot KRAS variants, indicating that poorly characterized variants could functionally behave like pathogenic mutations. Combining computational scores using dimensionality reduction indicated that changes to local unfolding propensity associate with changes in enzyme activity by genomic variants. Hence, our systematic approach, combining methodologies from both clinical genomics and 3D structural bioinformatics, represents an expansion for interpreting genomic data, provides information of mechanistic value, and that is transferable to other proteins.
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Affiliation(s)
- Swarnendu Tripathi
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Angela J Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Elise Leverence
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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16
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Hannan JP, Swisher GH, Martyr JG, Cordaro NJ, Erbse AH, Falke JJ. HPLC method to resolve, identify and quantify guanine nucleotides bound to recombinant ras GTPase. Anal Biochem 2021; 631:114338. [PMID: 34433016 PMCID: PMC8511091 DOI: 10.1016/j.ab.2021.114338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/31/2022]
Abstract
The Ras superfamily of small G proteins play central roles in diverse signaling pathways. Superfamily members act as molecular on-off switches defined by their occupancy with GTP or GDP, respectively. In vitro functional studies require loading with a hydrolysis-resistant GTP analogue to increase the on-state lifetime, as well as knowledge of fractional loading with activating and inactivating nucleotides. The present study describes a method combining elements of previous approaches with new, optimized features to analyze the bound nucleotide composition of a G protein loaded with activating (GMPPNP) or inactivating (GDP) nucleotide. After nucleotide loading, the complex is washed to remove unbound nucleotides then bound nucleotides are heat-extracted and subjected to ion-paired, reverse-phase HPLC-UV to resolve, identify and quantify the individual nucleotide components. These data enable back-calculation to the nucleotide composition and fractional activation of the original, washed G protein population prior to heat extraction. The method is highly reproducible. Application to multiple HRas preparations and mutants confirms its ability to fully extract and analyze bound nucleotides, and to resolve the fractional on- and off-state populations. Furthermore, the findings yield a novel hypothesis for the molecular disease mechanism of Ras mutations at the E63 and Y64 positions.
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Affiliation(s)
- Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - G Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Justin G Martyr
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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17
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Killoran RC, Smith MJ. NMR Detection Methods for Profiling RAS Nucleotide Cycling. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:169-182. [PMID: 33977476 DOI: 10.1007/978-1-0716-1190-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RAS oncoproteins exhibit a switch-like behavior to drive diverse signaling cascades. In the active GTP-bound state, a conformational change occurs in these enzymes that enables interaction with downstream effectors. Nucleotide-dependent conformational exchange is easily detected with real-time NMR (RT-NMR) spectroscopy. RT-NMR has been firmly established as an effective assay to measure RAS oncoprotein nucleotide exchange and GTP hydrolysis kinetics and can further determine the regulatory activity of guanine exchange factors (GEFs) and GTPase activating proteins (GAPs). It is now possible to multiplex these assays, allowing for the precise monitoring of activation states for mixtures of RAS oncoproteins or other RAS superfamily GTPases. Here, we describe the protocols necessary to express and purify isotopically labeled RAS and detail how to carry out an RT-NMR assay on a singular RAS protein or on a mixture of small GTPases.
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Affiliation(s)
- Ryan C Killoran
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada. .,Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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18
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Addeo A, Banna GL, Friedlaender A. KRAS G12C Mutations in NSCLC: From Target to Resistance. Cancers (Basel) 2021; 13:cancers13112541. [PMID: 34064232 PMCID: PMC8196854 DOI: 10.3390/cancers13112541] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/11/2022] Open
Abstract
Lung cancer represents the most common form of cancer, accounting for 1.8 million deaths globally in 2020. Over the last decade the treatment for advanced and metastatic non-small cell lung cancer have dramatically improved largely thanks to the emergence of two therapeutic breakthroughs: the discovery of immune checkpoint inhibitors and targeting of oncogenic driver alterations. While these therapies hold great promise, they face the same limitation as other inhibitors: the emergence of resistant mechanisms. One such alteration in non-small cell lung cancer is the Kirsten Rat Sarcoma (KRAS) oncogene. KRAS mutations are the most common oncogenic driver in NSCLC, representing roughly 20-25% of cases. The mutation is almost exclusively detected in adenocarcinoma and is found among smokers 90% of the time. Along with the development of new drugs that have been showing promising activity, resistance mechanisms have begun to be clarified. The aim of this review is to unwrap the biology of KRAS in NSCLC with a specific focus on primary and secondary resistance mechanisms and their possible clinical implications.
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Affiliation(s)
- Alfredo Addeo
- Swiss Cancer Center Leman, Oncology Department, Switzerland University of Geneva, University Hospital Geneva, 1205 Geneva, Switzerland;
- Correspondence:
| | | | - Alex Friedlaender
- Swiss Cancer Center Leman, Oncology Department, Switzerland University of Geneva, University Hospital Geneva, 1205 Geneva, Switzerland;
- Oncology Service, Clinique Générale Beaulieu, 1206 Geneva, Switzerland
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19
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Abstract
What level of Ras genes activity leads to the development of cancer?
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Affiliation(s)
- Zohra Butt
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Ian Prior
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
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20
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Engineering subtilisin proteases that specifically degrade active RAS. Commun Biol 2021; 4:299. [PMID: 33674772 PMCID: PMC7935941 DOI: 10.1038/s42003-021-01818-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
We describe the design, kinetic properties, and structures of engineered subtilisin proteases that degrade the active form of RAS by cleaving a conserved sequence in switch 2. RAS is a signaling protein that, when mutated, drives a third of human cancers. To generate high specificity for the RAS target sequence, the active site was modified to be dependent on a cofactor (imidazole or nitrite) and protease sub-sites were engineered to create a linkage between substrate and cofactor binding. Selective proteolysis of active RAS arises from a 2-step process wherein sub-site interactions promote productive binding of the cofactor, enabling cleavage. Proteases engineered in this way specifically cleave active RAS in vitro, deplete the level of RAS in a bacterial reporter system, and also degrade RAS in human cell culture. Although these proteases target active RAS, the underlying design principles are fundamental and will be adaptable to many target proteins.
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21
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Swisher GH, Hannan JP, Cordaro NJ, Erbse AH, Falke JJ. Ras-guanine nucleotide complexes: A UV spectral deconvolution method to analyze protein concentration, nucleotide stoichiometry, and purity. Anal Biochem 2021; 618:114066. [PMID: 33485819 DOI: 10.1016/j.ab.2020.114066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/31/2022]
Abstract
The many members of the Ras superfamily are small GTPases that serve as molecular switches. These proteins bind the guanine nucleotides GTP and GDP with picomolar affinities, thereby stabilizing on- and off-signaling states, respectively. Quantitative in vitro Ras studies require accurate determination of total protein, its fractional occupancy with guanine nucleotide, and spectroscopic purity. Yet the high nucleotide affinity of Ras and the overlapping UV spectra of the protein and bound nucleotide make such determinations challenging. Here we describe a generalizable UV spectral deconvolution method to analyze the total protein concentration, total nucleotide stoichiometry, and purity of Ras complexes.
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Affiliation(s)
- G Hayden Swisher
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Jonathan P Hannan
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Nicholas J Cordaro
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Annette H Erbse
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States
| | - Joseph J Falke
- Molecular Biophysics Program and Department of Biochemistry, University of Colorado, Boulder, CO, 80309-0596, United States.
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22
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Dhanaraman T, Singh S, Killoran RC, Singh A, Xu X, Shifman JM, Smith MJ. RASSF effectors couple diverse RAS subfamily GTPases to the Hippo pathway. Sci Signal 2020; 13:13/653/eabb4778. [PMID: 33051258 DOI: 10.1126/scisignal.abb4778] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Small guanosine triphosphatases (GTPases) of the RAS superfamily signal by directly binding to multiple downstream effector proteins. Effectors are defined by a folded RAS-association (RA) domain that binds exclusively to GTP-loaded (activated) RAS, but the binding specificities of most RA domains toward more than 160 RAS superfamily GTPases have not been characterized. Ten RA domain family (RASSF) proteins comprise the largest group of related effectors and are proposed to couple RAS to the proapoptotic Hippo pathway. Here, we showed that RASSF1-6 formed complexes with the Hippo kinase ortholog MST1, whereas RASSF7-10 formed oligomers with the p53-regulating effectors ASPP1 and ASPP2. Moreover, only RASSF5 bound directly to activated HRAS and KRAS, and RASSFs did not augment apoptotic induction downstream of RAS oncoproteins. Structural modeling revealed that expansion of the RASSF effector family in vertebrates included amino acid substitutions to key residues that direct GTPase-binding specificity. We demonstrated that the tumor suppressor RASSF1A formed complexes with the RAS-related GTPases GEM, REM1, REM2, and the enigmatic RASL12. Furthermore, interactions between RASSFs and RAS GTPases blocked YAP1 nuclear localization. Thus, these simple scaffolds link the activation of diverse RAS family small G proteins to Hippo or p53 regulation.
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Affiliation(s)
- Thillaivillalan Dhanaraman
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Swati Singh
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Ryan C Killoran
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Anamika Singh
- Hebrew University of Jerusalem, Department of Biological Chemistry, Jerusalem 9190401, Israel
| | - Xingjian Xu
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Julia M Shifman
- Hebrew University of Jerusalem, Department of Biological Chemistry, Jerusalem 9190401, Israel
| | - Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3T 1J4, Canada. .,Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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23
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Génier S, Létourneau D, Gauthier E, Picard S, Boisvert M, Parent JL, Lavigne P. In-depth NMR characterization of Rab4a structure, nucleotide exchange and hydrolysis kinetics reveals an atypical GTPase profile. J Struct Biol 2020; 212:107582. [PMID: 32707235 DOI: 10.1016/j.jsb.2020.107582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
Rab4a is a small GTPase associated with endocytic compartments and a key regulator of early endosomes recycling. Gathering evidence indicates that its expression and activation are required for the development of metastases. Rab4a-intrinsic GTPase properties that control its activity, i.e. nucleotide exchange and hydrolysis rates, have not yet been thoroughly studied. The determination of these properties is of the utmost importance to understand its functions and contributions to tumorigenesis. Here, we used the constitutively active (Rab4aQ67L) and dominant negative (Rab4aS22N) mutants to characterize the thermodynamical and structural determinants of the interaction between Rab4a and GTP (GTPγS) as well as GDP. We report the first 1H, 13C, 15N backbone NMR assignments of a Rab GTPase family member with Rab4a in complex with GDP and GTPγS. We also provide a qualitative description of the extent of structural and dynamical changes caused by the Q67L and S22N mutations. Using a real-time NMR approach and the two aforementioned mutants as controls, we evaluated Rab4a intrinsic nucleotide exchange and hydrolysis rates. Compared to most small GTPases such as Ras, a rapid GTP exchange rate along with slow hydrolysis rate were observed. This suggests that, in a cellular context, Rab4a can self-activate and persist in an activated state in absence of regulatory mechanisms. This peculiar profile is uncommon among the Ras superfamily members, making Rab4a an atypical fast-cycling GTPase and may explain, at least in part, how it contributes to metastases.
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Affiliation(s)
- Samuel Génier
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Danny Létourneau
- Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Esther Gauthier
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Samuel Picard
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marilou Boisvert
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Luc Parent
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada.
| | - Pierre Lavigne
- Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada.
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24
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Prior IA, Hood FE, Hartley JL. The Frequency of Ras Mutations in Cancer. Cancer Res 2020; 80:2969-2974. [PMID: 32209560 PMCID: PMC7367715 DOI: 10.1158/0008-5472.can-19-3682] [Citation(s) in RCA: 491] [Impact Index Per Article: 122.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/13/2020] [Accepted: 03/19/2020] [Indexed: 02/06/2023]
Abstract
Ras is frequently mutated in cancer, however, there is a lack of consensus in the literature regarding the cancer mutation frequency of Ras, with quoted values varying from 10%-30%. This variability is at least in part due to the selective aggregation of data from different databases and the dominant influence of particular cancer types and particular Ras isoforms within these datasets. To provide a more definitive figure for Ras mutation frequency in cancer, we cross-referenced the data in all major publicly accessible cancer mutation databases to determine reliable mutation frequency values for each Ras isoform in all major cancer types. These percentages were then applied to current U.S. cancer incidence statistics to estimate the number of new patients each year that have Ras-mutant cancers. We find that approximately 19% of patients with cancer harbor Ras mutations, equivalent to approximately 3.4 million new cases per year worldwide. We discuss the Ras isoform and mutation-specific trends evident within the datasets that are relevant to current Ras-targeted therapies.
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Affiliation(s)
- Ian A Prior
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.
| | - Fiona E Hood
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - James L Hartley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
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Cooley R, Kara N, Hui NS, Tart J, Roustan C, George R, Hancock DC, Binkowski BF, Wood KV, Ismail M, Downward J. Development of a cell-free split-luciferase biochemical assay as a tool for screening for inhibitors of challenging protein-protein interaction targets. Wellcome Open Res 2020. [DOI: 10.12688/wellcomeopenres.15675.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Targeting the interaction of proteins with weak binding affinities or low solubility represents a particular challenge for drug screening. The NanoLuc ® Binary Technology (NanoBiT ®) was originally developed to detect protein-protein interactions in live mammalian cells. Here we report the successful translation of the NanoBit cellular assay into a biochemical, cell-free format using mammalian cell lysates. We show that the assay is suitable for the detection of both strong and weak protein interactions such as those involving the binding of RAS oncoproteins to either RAF or phosphoinositide 3-kinase (PI3K) effectors respectively, and that it is also effective for the study of poorly soluble protein domains such as the RAS binding domain of PI3K. Furthermore, the RAS interaction assay is sensitive and responds to both strong and weak RAS inhibitors. Our data show that the assay is robust, reproducible, cost-effective, and can be adapted for small and large-scale screening approaches. The NanoBit Biochemical Assay offers an attractive tool for drug screening against challenging protein-protein interaction targets, including the interaction of RAS with PI3K.
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26
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RAC1 as a Therapeutic Target in Malignant Melanoma. Trends Cancer 2020; 6:478-488. [PMID: 32460002 DOI: 10.1016/j.trecan.2020.02.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 12/22/2022]
Abstract
Small GTPases of the RAS and RHO families are related signaling proteins that, when activated by growth factors or by mutation, drive oncogenic processes. While activating mutations in KRAS, NRAS, and HRAS genes have long been recognized and occur in many types of cancer, similar mutations in RHO family genes, such as RAC1 and RHOA, have only recently been detected as the result of extensive cancer genome-sequencing efforts and are linked to a restricted set of malignancies. In this review, we focus on the role of RAC1 signaling in malignant melanoma, emphasizing recent advances that describe how this oncoprotein alters melanocyte proliferation and motility and how these findings might lead to new therapeutics in RAC1-mutant tumors.
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27
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Cooley R, Kara N, Hui NS, Tart J, Roustan C, George R, Hancock DC, Binkowski BF, Wood KV, Ismail M, Downward J. Development of a cell-free split-luciferase biochemical assay as a tool for screening for inhibitors of challenging protein-protein interaction targets. Wellcome Open Res 2020; 5:20. [PMID: 32587898 PMCID: PMC7308888 DOI: 10.12688/wellcomeopenres.15675.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2020] [Indexed: 12/14/2022] Open
Abstract
Targeting the interaction of proteins with weak binding affinities or low solubility represents a particular challenge for drug screening. The NanoLuc â ® Binary Technology (NanoBiT â ®) was originally developed to detect protein-protein interactions in live mammalian cells. Here we report the successful translation of the NanoBit cellular assay into a biochemical, cell-free format using mammalian cell lysates. We show that the assay is suitable for the detection of both strong and weak protein interactions such as those involving the binding of RAS oncoproteins to either RAF or phosphoinositide 3-kinase (PI3K) effectors respectively, and that it is also effective for the study of poorly soluble protein domains such as the RAS binding domain of PI3K. Furthermore, the RAS interaction assay is sensitive and responds to both strong and weak RAS inhibitors. Our data show that the assay is robust, reproducible, cost-effective, and can be adapted for small and large-scale screening approaches. The NanoBit Biochemical Assay offers an attractive tool for drug screening against challenging protein-protein interaction targets, including the interaction of RAS with PI3K.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Julian Downward
- Francis Crick Institute, London, UK
- Institute of Cancer Research, UK, London, UK
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28
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Nussinov R, Tsai CJ, Jang H. Why Are Some Driver Mutations Rare? Trends Pharmacol Sci 2019; 40:919-929. [PMID: 31699406 DOI: 10.1016/j.tips.2019.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Abstract
Understanding why driver mutations that promote cancer are sometimes rare is important for precision medicine since it would help in their identification. Driver mutations are largely discovered through their frequencies. Thus, rare mutations often escape detection. Unlike high-frequency drivers, low-frequency drivers can be tissue specific; rare drivers have extremely low frequencies. Here, we discuss rare drivers and strategies to discover them. We suggest that allosteric driver mutations shift the protein ensemble from the inactive to the active state. Rare allosteric drivers are statistically rare since, to switch the protein functional state, they cooperate with additional mutations, and these are not considered in the patient cancer-specific protein sequence analysis. A complete landscape of mutations that drive cancer will reveal tumor-specific therapeutic vulnerabilities.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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